1
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Swaminath S, Russell AB. The use of single-cell RNA-seq to study heterogeneity at varying levels of virus-host interactions. PLoS Pathog 2024; 20:e1011898. [PMID: 38236826 PMCID: PMC10796064 DOI: 10.1371/journal.ppat.1011898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
The outcome of viral infection depends on the diversity of the infecting viral population and the heterogeneity of the cell population that is infected. Until almost a decade ago, the study of these dynamic processes during viral infection was challenging and limited to certain targeted measurements. Presently, with the use of single-cell sequencing technology, the complex interface defined by the interactions of cells with infecting virus can now be studied across the breadth of the transcriptome in thousands of individual cells simultaneously. In this review, we will describe the use of single-cell RNA sequencing (scRNA-seq) to study the heterogeneity of viral infections, ranging from individual virions to the immune response between infected individuals. In addition, we highlight certain key experimental limitations and methodological decisions that are critical to analyzing scRNA-seq data at each scale.
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Affiliation(s)
- Sharmada Swaminath
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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2
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Sherwood AV, Rivera-Rangel LR, Ryberg LA, Larsen HS, Anker KM, Costa R, Vågbø CB, Jakljevič E, Pham LV, Fernandez-Antunez C, Indrisiunaite G, Podolska-Charlery A, Grothen JER, Langvad NW, Fossat N, Offersgaard A, Al-Chaer A, Nielsen L, Kuśnierczyk A, Sølund C, Weis N, Gottwein JM, Holmbeck K, Bottaro S, Ramirez S, Bukh J, Scheel TKH, Vinther J. Hepatitis C virus RNA is 5'-capped with flavin adenine dinucleotide. Nature 2023:10.1038/s41586-023-06301-3. [PMID: 37407817 DOI: 10.1038/s41586-023-06301-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/08/2023] [Indexed: 07/07/2023]
Abstract
RNA viruses have evolved elaborate strategies to protect their genomes, including 5' capping. However, until now no RNA 5' cap has been identified for hepatitis C virus1,2 (HCV), which causes chronic infection, liver cirrhosis and cancer3. Here we demonstrate that the cellular metabolite flavin adenine dinucleotide (FAD) is used as a non-canonical initiating nucleotide by the viral RNA-dependent RNA polymerase, resulting in a 5'-FAD cap on the HCV RNA. The HCV FAD-capping frequency is around 75%, which is the highest observed for any RNA metabolite cap across all kingdoms of life4-8. FAD capping is conserved among HCV isolates for the replication-intermediate negative strand and partially for the positive strand. It is also observed in vivo on HCV RNA isolated from patient samples and from the liver and serum of a human liver chimeric mouse model. Furthermore, we show that 5'-FAD capping protects RNA from RIG-I mediated innate immune recognition but does not stabilize the HCV RNA. These results establish capping with cellular metabolites as a novel viral RNA-capping strategy, which could be used by other viruses and affect anti-viral treatment outcomes and persistence of infection.
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Affiliation(s)
- Anna V Sherwood
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Lizandro R Rivera-Rangel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Line A Ryberg
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Helena S Larsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Klara M Anker
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rui Costa
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Cathrine B Vågbø
- Proteomics and Modomics Experimental Core (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, Trondheim, Norway
| | - Eva Jakljevič
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Long V Pham
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Gabriele Indrisiunaite
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Agnieszka Podolska-Charlery
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Julius E R Grothen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Nicklas W Langvad
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Nicolas Fossat
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Anna Offersgaard
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Amal Al-Chaer
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Louise Nielsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Anna Kuśnierczyk
- Proteomics and Modomics Experimental Core (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, Trondheim, Norway
| | - Christina Sølund
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
| | - Judith M Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Kenn Holmbeck
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Sandro Bottaro
- Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark.
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark.
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark.
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark.
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Jeppe Vinther
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
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3
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Vicary AC, Mendes M, Swaminath S, Lekbua A, Reddan J, Rodriguez ZK, Russell AB. Maximal interferon induction by influenza lacking NS1 is infrequent owing to requirements for replication and export. PLoS Pathog 2023; 19:e1010943. [PMID: 37068114 PMCID: PMC10138204 DOI: 10.1371/journal.ppat.1010943] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/27/2023] [Accepted: 03/31/2023] [Indexed: 04/18/2023] Open
Abstract
Influenza A virus exhibits high rates of replicative failure due to a variety of genetic defects. Most influenza virions cannot, when acting as individual particles, complete the entire viral life cycle. Nevertheless influenza is incredibly successful in the suppression of innate immune detection and the production of interferons, remaining undetected in >99% of cells in tissue-culture models of infection. Notably, the same variation that leads to replication failure can, by chance, inactivate the major innate immune antagonist in influenza A virus, NS1. What explains the observed rarity of interferon production in spite of the frequent loss of this, critical, antagonist? By studying how genetic and phenotypic variation in a viral population lacking NS1 correlates with interferon production, we have built a model of the "worst-case" failure from an improved understanding of the steps at which NS1 acts in the viral life cycle to prevent the triggering of an innate immune response. In doing so, we find that NS1 prevents the detection of de novo innate immune ligands, defective viral genomes, and viral export from the nucleus, although only generation of de novo ligands appears absolutely required for enhanced detection of virus in the absence of NS1. Due to this, the highest frequency of interferon production we observe (97% of infected cells) requires a high level of replication in the presence of defective viral genomes with NS1 bearing an inactivating mutation that does not impact its partner encoded on the same segment, NEP. This is incredibly unlikely to occur given the standard variation found within a viral population, and would generally require direct, artificial, intervention to achieve at an appreciable rate. Thus from our study, we procure at least a partial explanation for the seeming contradiction between high rates of replicative failure and the rarity of the interferon response to influenza infection.
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Affiliation(s)
- Alison C. Vicary
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Marisa Mendes
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharmada Swaminath
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Asama Lekbua
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jack Reddan
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Zaida K. Rodriguez
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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4
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Slonchak A, Wang X, Aguado J, Sng JDJ, Chaggar H, Freney ME, Yan K, Torres FJ, Amarilla AA, Balea R, Setoh YX, Peng N, Watterson D, Wolvetang E, Suhrbier A, Khromykh AA. Zika virus noncoding RNA cooperates with the viral protein NS5 to inhibit STAT1 phosphorylation and facilitate viral pathogenesis. SCIENCE ADVANCES 2022; 8:eadd8095. [PMID: 36449607 PMCID: PMC9710884 DOI: 10.1126/sciadv.add8095] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/13/2022] [Indexed: 05/25/2023]
Abstract
All flaviviruses, including Zika virus, produce noncoding subgenomic flaviviral RNA (sfRNA), which plays an important role in viral pathogenesis. However, the exact mechanism of how sfRNA enables viral evasion of antiviral response is not well defined. Here, we show that sfRNA is required for transplacental virus dissemination in pregnant mice and subsequent fetal brain infection. We also show that sfRNA promotes apoptosis of neural progenitor cells in human brain organoids, leading to their disintegration. In infected human placental cells, sfRNA inhibits multiple antiviral pathways and promotes apoptosis, with signal transducer and activator of transcription 1 (STAT1) identified as a key shared factor. We further show that the production of sfRNA leads to reduced phosphorylation and nuclear translocation of STAT1 via a mechanism that involves sfRNA binding to and stabilizing viral protein NS5. Our results suggest the cooperation between viral noncoding RNA and a viral protein as a novel strategy for counteracting antiviral responses.
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Affiliation(s)
- Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Xiaohui Wang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Julio Aguado
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Julian D. J. Sng
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Harman Chaggar
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Morgan E. Freney
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kexin Yan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Francisco J. Torres
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Rickyle Balea
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yin Xiang Setoh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Nias Peng
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Center of Excellence, Brisbane, QLD, Australia
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Center of Excellence, Brisbane, QLD, Australia
| | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Center of Excellence, Brisbane, QLD, Australia
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5
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An Unexpected Encounter: Respiratory Syncytial Virus Nonstructural Protein 1 Interacts with Mediator Subunit MED25. J Virol 2022; 96:e0129722. [PMID: 36102648 PMCID: PMC9555202 DOI: 10.1128/jvi.01297-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Innate immune responses, including the production of type I and III interferons, play a crucial role in the first line of defense against RSV infection. However, only a poor induction of type I IFNs is observed during RSV infection, suggesting that RSV has evolved mechanisms to prevent type I IFN expression by the infected host cell.
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6
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Daza-Cajigal V, Albuquerque AS, Young DF, Ciancanelli MJ, Moulding D, Angulo I, Jeanne-Julien V, Rosain J, Minskaia E, Casanova JL, Boisson-Dupuis S, Bustamante J, Randall RE, McHugh TD, Thrasher AJ, Burns SO. Partial human Janus kinase 1 deficiency predominantly impairs responses to interferon gamma and intracellular control of mycobacteria. Front Immunol 2022; 13:888427. [PMID: 36159783 PMCID: PMC9501714 DOI: 10.3389/fimmu.2022.888427] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose Janus kinase-1 (JAK1) tyrosine kinase mediates signaling from multiple cytokine receptors, including interferon alpha/beta and gamma (IFN-α/β and IFN-γ), which are important for viral and mycobacterial protection respectively. We previously reported autosomal recessive (AR) hypomorphic JAK1 mutations in a patient with recurrent atypical mycobacterial infections and relatively minor viral infections. This study tests the impact of partial JAK1 deficiency on cellular responses to IFNs and pathogen control. Methods We investigated the role of partial JAK1 deficiency using patient cells and cell models generated with lentiviral vectors expressing shRNA. Results Partial JAK1 deficiency impairs IFN-γ-dependent responses in multiple cell types including THP-1 macrophages, Epstein-Barr Virus (EBV)-transformed B cells and primary dermal fibroblasts. In THP-1 myeloid cells, partial JAK1 deficiency reduced phagosome acidification and apoptosis and resulted in defective control of mycobacterial infection with enhanced intracellular survival. Although both EBV-B cells and primary dermal fibroblasts with partial JAK1 deficiency demonstrate reduced IFN-α responses, control of viral infection was impaired only in patient EBV-B cells and surprisingly intact in patient primary dermal fibroblasts. Conclusion Our data suggests that partial JAK1 deficiency predominantly affects susceptibility to mycobacterial infection through impact on the IFN-γ responsive pathway in myeloid cells. Susceptibility to viral infections as a result of reduced IFN-α responses is variable depending on cell type. Description of additional patients with inherited JAK1 deficiency will further clarify the spectrum of bacterial and viral susceptibility in this condition. Our results have broader relevance for anticipating infectious complications from the increasing use of selective JAK1 inhibitors.
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Affiliation(s)
- Vanessa Daza-Cajigal
- Institute of Immunity and Transplantation, University College London, London, United Kingdom.,Department of Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom.,School of Medicine, Universidad Complutense, Madrid, Spain.,Department of Immunology, Hospital Universitario Son Espases, Palma, Spain.,Research Unit, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Palma, Spain
| | - Adriana S Albuquerque
- Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Dan F Young
- School of Biology, University of St. Andrews, St. Andrews, United Kingdom
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, United States
| | - Dale Moulding
- Molecular and Cellular Immunology Section, University College London Institute of Child Health, London, United Kingdom
| | - Ivan Angulo
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Valentine Jeanne-Julien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, National Institute of Health and Medical Research (INSERM) U1163, Paris, France.,Paris Cité University, Imagine Institute, Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, National Institute of Health and Medical Research (INSERM) U1163, Paris, France.,Paris Cité University, Imagine Institute, Paris, France
| | - Ekaterina Minskaia
- Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, National Institute of Health and Medical Research (INSERM) U1163, Paris, France.,Paris Cité University, Imagine Institute, Paris, France.,Howard Hughes Medical Institute, New York, NY, United States
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, National Institute of Health and Medical Research (INSERM) U1163, Paris, France.,Paris Cité University, Imagine Institute, Paris, France
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, National Institute of Health and Medical Research (INSERM) U1163, Paris, France.,Paris Cité University, Imagine Institute, Paris, France.,Study Center of Immunodeficiencies, Necker Hospital for Sick Children, Paris, France
| | - Richard E Randall
- School of Biology, University of St. Andrews, St. Andrews, United Kingdom
| | - Timothy D McHugh
- Research Department of Infection, University College London Centre for Clinical Microbiology, London, United Kingdom
| | - Adrian J Thrasher
- Molecular and Cellular Immunology Section, University College London Institute of Child Health, London, United Kingdom.,Immunology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Siobhan O Burns
- Institute of Immunity and Transplantation, University College London, London, United Kingdom.,Department of Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
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7
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Mendes M, Russell AB. Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes. PLoS Pathog 2021; 17:e1010125. [PMID: 34882752 PMCID: PMC8691639 DOI: 10.1371/journal.ppat.1010125] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/21/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Found in a diverse set of viral populations, defective interfering particles are parasitic variants that are unable to replicate on their own yet rise to relatively high frequencies. Their presence is associated with a loss of population fitness, both through the depletion of key cellular resources and the stimulation of innate immunity. For influenza A virus, these particles contain large internal deletions in the genomic segments which encode components of the heterotrimeric polymerase. Using a library-based approach, we comprehensively profile the growth and replication of defective influenza species, demonstrating that they possess an advantage during genome replication, and that exclusion during population expansion reshapes population composition in a manner consistent with their final, observed, distribution in natural populations. We find that an innate immune response is not linked to the size of a deletion; however, replication of defective segments can enhance their immunostimulatory properties. Overall, our results address several key questions in defective influenza A virus biology, and the methods we have developed to answer those questions may be broadly applied to other defective viruses.
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Affiliation(s)
- Marisa Mendes
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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8
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Suomalainen M, Greber UF. Virus Infection Variability by Single-Cell Profiling. Viruses 2021; 13:1568. [PMID: 34452433 PMCID: PMC8402812 DOI: 10.3390/v13081568] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/05/2021] [Indexed: 12/15/2022] Open
Abstract
Cell-to-cell variability of infection has long been known, yet it has remained one of the least understood phenomena in infection research. It impacts on disease onset and development, yet only recently underlying mechanisms have been studied in clonal cell cultures by single-virion immunofluorescence microscopy and flow cytometry. In this review, we showcase how single-cell RNA sequencing (scRNA-seq), single-molecule RNA-fluorescence in situ hybridization (FISH), and copper(I)-catalyzed azide-alkyne cycloaddition (click) with alkynyl-tagged viral genomes dissect infection variability in human and mouse cells. We show how the combined use of scRNA-FISH and click-chemistry reveals highly variable onsets of adenoviral gene expression, and how single live cell plaques reveal lytic and nonlytic adenovirus transmissions. The review highlights how scRNA-seq profiling and scRNA-FISH of coxsackie, influenza, dengue, zika, and herpes simplex virus infections uncover transcriptional variability, and how the host interferon response tunes influenza and sendai virus infections. We introduce the concept of "cell state" in infection variability, and conclude with advances by single-cell simultaneous measurements of chromatin accessibility and mRNA counts at high-throughput. Such technology will further dissect the sequence of events in virus infection and pathology, and better characterize the genetic and genomic stability of viruses, cell autonomous innate immune responses, and mechanisms of tissue injury.
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Affiliation(s)
- Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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9
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Hare DN, Subapanditha MK, Mossman KL. Detecting single cell interferon-beta production using a fluorescent reporter telomerase-immortalized human fibroblast cell line. STAR Protoc 2021; 2:100436. [PMID: 33912845 PMCID: PMC8063907 DOI: 10.1016/j.xpro.2021.100436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recent data suggest that cells respond to infection by upregulating the antiviral cytokine interferon-beta (IFN-ß) in a fraction of infected cells. Approaches are thus needed to study these responses on a single-cell level rather than bulk population. Here, we describe a protocol to analyze the IFN-ß response of individual cells using flow cytometry and immunofluorescence microscopy. We show the heterogeneous IFN-ß response to inactivated Sendai virus and human cytomegalovirus, but this protocol can be adapted to other viruses. For complete details on the use and execution of this protocol, please refer to Hare et al. (2020). Single-cell assays are needed to measure IFN production in virus-infected cells Immortalized THF cells with IFN-b reporter are used to measure IFN production Individual cells are analyzed via flow cytometry and fluorescence microscopy Simple single-cell assays can uncover data obscured in bulk population measurements
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Affiliation(s)
- David N Hare
- Health Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Minomi K Subapanditha
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Karen L Mossman
- Health Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.,Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
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10
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Hare DN, Baid K, Dvorkin-Gheva A, Mossman KL. Virus-Intrinsic Differences and Heterogeneous IRF3 Activation Influence IFN-Independent Antiviral Protection. iScience 2020; 23:101864. [PMID: 33319181 PMCID: PMC7726339 DOI: 10.1016/j.isci.2020.101864] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/04/2020] [Accepted: 11/20/2020] [Indexed: 02/09/2023] Open
Abstract
Type 1 interferon (IFN) plays a critical role in early antiviral defense and priming of adaptive immunity by signaling upregulation of host antiviral IFN-stimulated genes (ISGs). Certain stimuli trigger strong activation of IFN regulatory factor 3 (IRF3) and direct upregulation of ISGs in addition to IFN. It remains unclear why some stimuli are stronger activators of IRF3 and how this leads to IFN-independent antiviral protection. We found that UV-inactivated human cytomegalovirus (HCMV) particles triggered an IFN-independent ISG signature that was absent in cells infected with UV-inactivated Sendai virus particles. HCMV particles triggered mostly uniform activation of IRF3 and low-level IFN-β production within the population while SeV particles triggered a small fraction of cells producing abundant IFN-β. These findings suggest that population-level activation of IRF3 and antiviral protection emerges from a diversity of responses occurring simultaneously in single cells. Moreover, this occurs in the absence of virus replication. The antiviral response to virus particles requires low levels of interferon Cells respond differently to HCMV or SeV particles Heterogeneous IRF3 activation influences the response to virus
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Affiliation(s)
- David N Hare
- Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Kaushal Baid
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Anna Dvorkin-Gheva
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Karen L Mossman
- Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S4L8, Canada.,Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S4L8, Canada
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11
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Mendonca P, Soliman KFA. Flavonoids Activation of the Transcription Factor Nrf2 as a Hypothesis Approach for the Prevention and Modulation of SARS-CoV-2 Infection Severity. Antioxidants (Basel) 2020; 9:E659. [PMID: 32722164 PMCID: PMC7463602 DOI: 10.3390/antiox9080659] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022] Open
Abstract
The Nrf2-Keap1-ARE pathway is the principal regulator of antioxidant and phase II detoxification genes. Its activation increases the expression of antioxidant and cytoprotective proteins, protecting cells against infections. Nrf2 modulates virus-induced oxidative stress, ROS generation, and disease pathogenesis, which are vital in the viral life cycle. During respiratory viral infections, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an inflammatory process, and oxidative stress of the epithelium lining cells activate the transcription factor Nrf2, which protects cells from oxidative stress and inflammation. Nrf2 reduces angiotensin-converting enzyme 2 (ACE2) receptors expression in respiratory epithelial cells. SARS-CoV2 has a high affinity for ACE2 that works as receptors for coronavirus surface spike glycoprotein, facilitating viral entry. Disease severity may also be modulated by pre-existing conditions, such as impaired immune response, obesity, and age, where decreased level of Nrf2 is a common feature. Consequently, Nrf2 activators may increase Nrf2 levels and enhance antiviral mediators' expression, which could initiate an "antiviral state", priming cells against viral infection. Therefore, this hypothesis paper describes the use of flavonoid supplements combined with vitamin D3 to activate Nrf2, which may be a potential target to prevent and/or decrease SARS-CoV-2 infection severity, reducing oxidative stress and inflammation, enhancing innate immunity, and downregulating ACE2 receptors.
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Affiliation(s)
| | - Karam F. A. Soliman
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA;
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12
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Wignall-Fleming EB, Vasou A, Young D, Short JAL, Hughes DJ, Goodbourn S, Randall RE. Innate Intracellular Antiviral Responses Restrict the Amplification of Defective Virus Genomes of Parainfluenza Virus 5. J Virol 2020; 94:e00246-20. [PMID: 32295916 PMCID: PMC7307174 DOI: 10.1128/jvi.00246-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/08/2020] [Indexed: 12/24/2022] Open
Abstract
During the replication of parainfluenza virus 5 (PIV5), copyback defective virus genomes (DVGs) are erroneously produced and are packaged into "infectious" virus particles. Copyback DVGs are the primary inducers of innate intracellular responses, including the interferon (IFN) response. While DVGs can interfere with the replication of nondefective (ND) virus genomes and activate the IFN-induction cascade before ND PIV5 can block the production of IFN, we demonstrate that the converse is also true, i.e., high levels of ND virus can block the ability of DVGs to activate the IFN-induction cascade. By following the replication and amplification of DVGs in A549 cells that are deficient in a variety of innate intracellular antiviral responses, we show that DVGs induce an uncharacterized IFN-independent innate response(s) that limits their replication. High-throughput sequencing was used to characterize the molecular structure of copyback DVGs. While there appears to be no sequence-specific break or rejoining points for the generation of copyback DVGs, our findings suggest there are region, size, and/or structural preferences selected for during for their amplification.IMPORTANCE Copyback defective virus genomes (DVGs) are powerful inducers of innate immune responses both in vitro and in vivo They impact the outcome of natural infections, may help drive virus-host coevolution, and promote virus persistence. Due to their potent interfering and immunostimulatory properties, DVGs may also be used therapeutically as antivirals and vaccine adjuvants. However, little is known of the host cell restrictions which limit their amplification. We show here that the generation of copyback DVGs readily occurs during parainfluenza virus 5 (PIV5) replication, but that their subsequent amplification is restricted by the induction of innate intracellular responses. Molecular characterization of PIV5 copyback DVGs suggests that while there are no genome sequence-specific breaks or rejoin points for the generation of copyback DVGs, genome region, size, and structural preferences are selected for during their evolution and amplification.
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Affiliation(s)
| | - Andri Vasou
- School of Biology, Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, United Kingdom
| | - Dan Young
- School of Biology, Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, United Kingdom
| | - John A L Short
- School of Biology, Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, United Kingdom
| | - David J Hughes
- School of Biology, Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, United Kingdom
| | - Steve Goodbourn
- Institute for Infection and Immunity, St. George's, University of London, London, United Kingdom
| | - Richard E Randall
- School of Biology, Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, United Kingdom
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13
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Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection. mBio 2020; 11:mBio.02880-19. [PMID: 31937643 PMCID: PMC6960286 DOI: 10.1128/mbio.02880-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Defective influenza virus particles generated during viral replication carry incomplete viral genomes and can interfere with the replication of competent viruses. These defective genomes are thought to modulate the disease severity and pathogenicity of an influenza virus infection. Different defective viral genomes also introduce another source of variation across a heterogeneous cell population. Evaluating the impact of defective virus genomes on host cell responses cannot be fully resolved at the population level, requiring single-cell transcriptional profiling. Here, we characterized virus and host transcriptomes in individual influenza virus-infected cells, including those of defective viruses that arise during influenza A virus infection. We established an association between defective virus transcription and host responses and validated interfering and immunostimulatory functions of identified dominant defective viral genome species in vitro. This study demonstrates the intricate effects of defective viral genomes on host transcriptional responses and highlights the importance of capturing host-virus interactions at the single-cell level. Virus and host factors contribute to cell-to-cell variation in viral infections and determine the outcome of the overall infection. However, the extent of the variability at the single-cell level and how it impacts virus-host interactions at a system level are not well understood. To characterize the dynamics of viral transcription and host responses, we used single-cell RNA sequencing to quantify at multiple time points the host and viral transcriptomes of human A549 cells and primary bronchial epithelial cells infected with influenza A virus. We observed substantial variability in viral transcription between cells, including the accumulation of defective viral genomes (DVGs) that impact viral replication. We show (i) a correlation between DVGs and virus-induced variation of the host transcriptional program and (ii) an association between differential inductions of innate immune response genes and attenuated viral transcription in subpopulations of cells. These observations at the single-cell level improve our understanding of the complex virus-host interplay during influenza virus infection.
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14
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Leviyang S, Griva I. Investigating Functional Roles for Positive Feedback and Cellular Heterogeneity in the Type I Interferon Response to Viral Infection. Viruses 2018; 10:v10100517. [PMID: 30241427 PMCID: PMC6213501 DOI: 10.3390/v10100517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/16/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
Secretion of type I interferons (IFN) by infected cells mediates protection against many viruses, but prolonged or excessive type I IFN secretion can lead to immune pathology. A proper type I IFN response must therefore maintain a balance between protection and excessive IFN secretion. It has been widely noted that the type I IFN response is driven by positive feedback and is heterogeneous, with only a fraction of infected cells upregulating IFN expression even in clonal cell lines, but the functional roles of feedback and heterogeneity in balancing protection and excessive IFN secretion are not clear. To investigate the functional roles for feedback and heterogeneity, we constructed a mathematical model coupling IFN and viral dynamics that extends existing mathematical models by accounting for feedback and heterogeneity. We fit our model to five existing datasets, reflecting different experimental systems. Fitting across datasets allowed us to compare the IFN response across the systems and suggested different signatures of feedback and heterogeneity in the different systems. Further, through numerical experiments, we generated hypotheses of functional roles for IFN feedback and heterogeneity consistent with our mathematical model. We hypothesize an inherent tradeoff in the IFN response: a positive feedback loop prevents excessive IFN secretion, but also makes the IFN response vulnerable to viral antagonism. We hypothesize that cellular heterogeneity of the IFN response functions to protect the feedback loop from viral antagonism. Verification of our hypotheses will require further experimental studies. Our work provides a basis for analyzing the type I IFN response across systems.
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Affiliation(s)
- Sivan Leviyang
- Department of Mathematics and Statistics, Georgetown University, Washington, DC 20057, USA.
| | - Igor Griva
- Department of Mathematical Sciences, George Mason University, Fairfax, VA 22030, USA.
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15
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Russell AB, Trapnell C, Bloom JD. Extreme heterogeneity of influenza virus infection in single cells. eLife 2018; 7:e32303. [PMID: 29451492 PMCID: PMC5826275 DOI: 10.7554/elife.32303] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
Viral infection can dramatically alter a cell's transcriptome. However, these changes have mostly been studied by bulk measurements on many cells. Here we use single-cell mRNA sequencing to examine the transcriptional consequences of influenza virus infection. We find extremely wide cell-to-cell variation in the productivity of viral transcription - viral transcripts comprise less than a percent of total mRNA in many infected cells, but a few cells derive over half their mRNA from virus. Some infected cells fail to express at least one viral gene, but this gene absence only partially explains variation in viral transcriptional load. Despite variation in viral load, the relative abundances of viral mRNAs are fairly consistent across infected cells. Activation of innate immune pathways is rare, but some cellular genes co-vary in abundance with the amount of viral mRNA. Overall, our results highlight the complexity of viral infection at the level of single cells.
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Affiliation(s)
- Alistair B Russell
- Basic Sciences Division and Computational Biology ProgramFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Cole Trapnell
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology ProgramFred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
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16
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Doğanay S, Lee MY, Baum A, Peh J, Hwang SY, Yoo JY, Hergenrother PJ, García-Sastre A, Myong S, Ha T. Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression. Integr Biol (Camb) 2017; 9:857-867. [PMID: 29098213 PMCID: PMC6201300 DOI: 10.1039/c7ib00146k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RIG-I-like receptors (RLRs) are cytoplasmic sensors of viral RNA that trigger the signaling cascade that leads to type I interferon (IFN) production. Transcriptional induction of RLRs by IFN is believed to play the role of positive feedback to further amplify viral sensing. We found that RLRs and several other IFN-stimulated genes (ISGs) are induced early in viral infection independent of IFN. Expression of these early ISGs requires IRF3/IRF7 and is highly correlated amongst them. Simultaneous detection of mRNA of IFNB1, viral replicase, and ISGs revealed distinct populations of IFNB1 expressing and non-expressing cells which are highly correlated with the levels of early ISGs but are uncorrelated with IFN-dependent ISGs and viral gene expression. Individual expression of RLRs made IFNB1 expression more robust and earlier, suggesting a causal relation between levels of RLR and induction of IFN.
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Affiliation(s)
- Sultan Doğanay
- Center for Computational Biology and Biophysics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Physics, and Center for Physics of Living Cells, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Maurice Youzong Lee
- Department of Physics, and Center for Physics of Living Cells, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Biophysics Program, Stanford University, CA 94305, USA
| | - Alina Baum
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, New York, NY 10029, USA
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Jessie Peh
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Sun-Young Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, KOREA
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, KOREA
| | - Paul J. Hergenrother
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sua Myong
- Bioengineering Department, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Taekjip Ha
- Center for Computational Biology and Biophysics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Physics, and Center for Physics of Living Cells, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland
- Howard Hughes Medical Institute
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17
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Vasou A, Paulus C, Narloch J, Gage ZO, Rameix-Welti MA, Eléouët JF, Nevels M, Randall RE, Adamson CS. Modular cell-based platform for high throughput identification of compounds that inhibit a viral interferon antagonist of choice. Antiviral Res 2017; 150:79-92. [PMID: 29037975 PMCID: PMC5800491 DOI: 10.1016/j.antiviral.2017.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 02/07/2023]
Abstract
Viral interferon (IFN) antagonists are a diverse class of viral proteins that counteract the host IFN response, which is important for controlling viral infections. Viral IFN antagonists are often multifunctional proteins that perform vital roles in virus replication beyond IFN antagonism. The critical importance of viral IFN antagonists is highlighted by the fact that almost all viruses encode one of these proteins. Inhibition of viral IFN antagonists has the potential to exert pleiotropic antiviral effects and thus this important protein class represents a diverse plethora of novel therapeutic targets. To exploit this, we have successfully developed and executed a novel modular cell-based platform that facilitates the safe and rapid screening for inhibitors of a viral IFN antagonist of choice. The platform is based on two reporter cell-lines that provide a simple method to detect activation of IFN induction or signaling via an eGFP gene placed under the control of the IFNβ or an ISRE-containing promoter, respectively. Expression of a target IFN antagonist in the appropriate reporter cell-line will block the IFN response and hence eGFP expression. We hypothesized that addition of a compound that inhibits IFN antagonist function will release the block imposed on the IFN response and hence restore eGFP expression, providing a measurable parameter for high throughput screening (HTS). We demonstrate assay proof-of-concept by (i) exploiting hepatitis C virus (HCV) protease inhibitors to inhibit NS3-4A's capacity to block IFN induction and (ii) successfully executing two HTS targeting viral IFN antagonists that block IFN signaling; NS2 and IE1 from human respiratory syncytial virus (RSV) and cytomegalovirus (CMV) respectively, two clinically important viruses for which vaccine development has thus far been unsuccessful and new antivirals are required. Both screens performed robustly and Z′ Factor scores of >0.6 were achieved. We identified (i) four hit compounds that specifically inhibit RSV NS2's ability to block IFN signaling by mediating STAT2 degradation and exhibit modest antiviral activity and (ii) two hit compounds that interfere with IE1 transcription and significantly impair CMV replication. Overall, we demonstrate assay proof-of-concept as we target viral IFN antagonists from unrelated viruses and demonstrate its suitability for HTS. Viral IFN antagonists represent a plethora of novel therapeutic targets not specifically targeted by current antivirals. We developed a novel modular cell-based screening platform that potentially targets any viral IFN antagonist of choice. The assay is based on eGFP reporter gene expression at the end-point of activated IFN induction and signaling pathways. We demonstrate assay proof-of-concept via HCV protease inhibitors, which block NS3-4A's capacity to block IFN induction. We successfully execute two high-throughput screens targeting IFN antagonists NS2 and IE1 from RSV and CMV, respectively.
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Affiliation(s)
- Andri Vasou
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Christina Paulus
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Janina Narloch
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Zoe O Gage
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Marie-Anne Rameix-Welti
- UMR INSERM U1173 2I, UFR des Sciences de la Santé Simone Veil-UVSQ, 78180, Montigny-Le-Bretonneux, France; AP-HP, Laboratoire de Microbiologie, Hôpital Ambroise Paré, 92104, Boulogne-Billancourt, France
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires (UR892), INRA, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Michael Nevels
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Richard E Randall
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Catherine S Adamson
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom.
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18
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Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. PLoS Pathog 2017; 13:e1006650. [PMID: 29023600 PMCID: PMC5638565 DOI: 10.1371/journal.ppat.1006650] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/15/2017] [Indexed: 12/13/2022] Open
Abstract
Influenza A virus (IAV) infection can be severe or even lethal in toddlers, the elderly and patients with certain medical conditions. Infection of apparently healthy individuals nonetheless accounts for many severe disease cases and deaths, suggesting that viruses with increased pathogenicity co-circulate with pandemic or epidemic viruses. Looking for potential virulence factors, we have identified a polymerase PA D529N mutation detected in a fatal IAV case, whose introduction into two different recombinant virus backbones, led to reduced defective viral genomes (DVGs) production. This mutation conferred low induction of antiviral response in infected cells and increased pathogenesis in mice. To analyze the association between low DVGs production and pathogenesis in humans, we performed a genomic analysis of viruses isolated from a cohort of previously healthy individuals who suffered highly severe IAV infection requiring admission to Intensive Care Unit and patients with fatal outcome who additionally showed underlying medical conditions. These viruses were compared with those isolated from a cohort of mild IAV patients. Viruses with fewer DVGs accumulation were observed in patients with highly severe/fatal outcome than in those with mild disease, suggesting that low DVGs abundance constitutes a new virulence pathogenic marker in humans. Influenza A viruses are the causative agents of annual epidemics, sporadic zoonotic outbreaks and occasionally pandemics. Worldwide, acute respiratory infections caused by influenza A viruses continue to be one of the main causes of acute illness and death. The appearance in 2009 of a new H1N1 pandemic influenza strain reinforced the search to identify viral pathogenicity determinants for evaluation of the consequences of virus epidemics and potential pandemics for human health. Here we identify a new general virulence determinant found in a cohort of severe/fatal influenza virus-infected patients, a reduced accumulation of viral defective genomes. These molecules are incomplete viral genome segments that activate the innate immune response. This data will contribute to the prediction of influenza disease severity, to improved guidance of patient treatment and will enable the development of risk-based prevention strategies and policies.
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19
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Cai C, Zhou J, Sun X, Sun T, Xie W, Cui J. Integrated modeling and analysis of intracellular and intercellular mechanisms in shaping the interferon response to viral infection. PLoS One 2017; 12:e0186105. [PMID: 29020068 PMCID: PMC5636135 DOI: 10.1371/journal.pone.0186105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022] Open
Abstract
The interferons (IFNs) responses to viral infection are heterogeneous, while the underlying mechanisms for variability among cells are still not clear. In this study, we developed a hybrid model to systematically identify the sources of IFN induction heterogeneity. The experiment-integrated simulation demonstrated that the viral dose/type, the diversity in transcriptional factors activation and the intercellular paracrine signaling could strikingly shape the heterogeneity of IFN expression. We further determined that the IFNβ and IFNλ1 induced diverse dynamics of IFN-stimulated genes (ISGs) production. Collectively, our findings revealed the intracellular and intercellular mechanisms contributing to cell-to-cell variation in IFN induction, and further demonstrated the significant effects of IFN heterogeneity on antagonizing viruses.
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Affiliation(s)
- Chunmei Cai
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jie Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Xiaoqiang Sun
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | | | - Weihong Xie
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University, Guangzhou, P. R. China
- * E-mail:
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20
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Patzina C, Botting CH, García-Sastre A, Randall RE, Hale BG. Human interactome of the influenza B virus NS1 protein. J Gen Virol 2017; 98:2267-2273. [PMID: 28869005 PMCID: PMC5656757 DOI: 10.1099/jgv.0.000909] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
NS1 proteins of influenza A and B viruses share limited sequence homology, yet both are potent manipulators of host cell processes, particularly interferon (IFN) induction. Although many cellular partners are reported for A/NS1, only a few (e.g. PKR and ISG15) have been identified for B/NS1. Here, affinity-purification and mass spectrometry were used to expand the known host interactome of B/NS1. We identified 22 human proteins as new putative targets for B/NS1, validating several, including DHX9, ILF3, YBX1 and HNRNPC. Consistent with two RNA-binding domains in B/NS1, many of the identified factors bind RNA and some interact with B/NS1 in an RNA-dependent manner. Functional characterization of several B/NS1 interactors identified SNRNP200 as a potential positive regulator of host IFN responses, while ILF3 exhibited dual roles in both IFN induction and influenza B virus replication. These data provide a resource for future investigations into the mechanisms underpinning host cell modulation by influenza B virus NS1.
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Affiliation(s)
- Corinna Patzina
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Catherine H. Botting
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, KY16 9ST, UK
| | - Adolfo García-Sastre
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Richard E. Randall
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, KY16 9ST, UK
| | - Benjamin G. Hale
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- *Correspondence: Benjamin G. Hale,
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21
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Vasou A, Sultanoglu N, Goodbourn S, Randall RE, Kostrikis LG. Targeting Pattern Recognition Receptors (PRR) for Vaccine Adjuvantation: From Synthetic PRR Agonists to the Potential of Defective Interfering Particles of Viruses. Viruses 2017; 9:v9070186. [PMID: 28703784 PMCID: PMC5537678 DOI: 10.3390/v9070186] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/11/2017] [Accepted: 07/11/2017] [Indexed: 12/13/2022] Open
Abstract
Modern vaccinology has increasingly focused on non-living vaccines, which are more stable than live-attenuated vaccines but often show limited immunogenicity. Immunostimulatory substances, known as adjuvants, are traditionally used to increase the magnitude of protective adaptive immunity in response to a pathogen-associated antigen. Recently developed adjuvants often include substances that stimulate pattern recognition receptors (PRRs), essential components of innate immunity required for the activation of antigen-presenting cells (APCs), which serve as a bridge between innate and adaptive immunity. Nearly all PRRs are potential targets for adjuvants. Given the recent success of toll-like receptor (TLR) agonists in vaccine development, molecules with similar, but additional, immunostimulatory activity, such as defective interfering particles (DIPs) of viruses, represent attractive candidates for vaccine adjuvants. This review outlines some of the recent advances in vaccine development related to the use of TLR agonists, summarizes the current knowledge regarding DIP immunogenicity, and discusses the potential applications of DIPs in vaccine adjuvantation.
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Affiliation(s)
- Andri Vasou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglatzia, Nicosia 2109, Cyprus.
| | - Nazife Sultanoglu
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglatzia, Nicosia 2109, Cyprus.
| | - Stephen Goodbourn
- Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK.
| | - Richard E Randall
- School of Biology, University of St Andrews, The North Haugh, St Andrews KY16 9ST, UK.
| | - Leondios G Kostrikis
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglatzia, Nicosia 2109, Cyprus.
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22
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Influenza A Virus NS1 Protein Promotes Efficient Nuclear Export of Unspliced Viral M1 mRNA. J Virol 2017; 91:JVI.00528-17. [PMID: 28515301 PMCID: PMC5651720 DOI: 10.1128/jvi.00528-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/10/2017] [Indexed: 01/08/2023] Open
Abstract
Influenza A virus mRNAs are transcribed by the viral RNA-dependent RNA polymerase in the cell nucleus before being exported to the cytoplasm for translation. Segment 7 produces two major transcripts: an unspliced mRNA that encodes the M1 matrix protein and a spliced transcript that encodes the M2 ion channel. Export of both mRNAs is dependent on the cellular NXF1/TAP pathway, but it is unclear how they are recruited to the export machinery or how the intron-containing but unspliced M1 mRNA bypasses the normal quality-control checkpoints. Using fluorescent in situ hybridization to monitor segment 7 mRNA localization, we found that cytoplasmic accumulation of unspliced M1 mRNA was inefficient in the absence of NS1, both in the context of segment 7 RNPs reconstituted by plasmid transfection and in mutant virus-infected cells. This effect was independent of any major effect on steady-state levels of segment 7 mRNA or splicing but corresponded to a ∼5-fold reduction in the accumulation of M1. A similar defect in intronless hemagglutinin (HA) mRNA nuclear export was seen with an NS1 mutant virus. Efficient export of M1 mRNA required both an intact NS1 RNA-binding domain and effector domain. Furthermore, while wild-type NS1 interacted with cellular NXF1 and also increased the interaction of segment 7 mRNA with NXF1, mutant NS1 polypeptides unable to promote mRNA export did neither. Thus, we propose that NS1 facilitates late viral gene expression by acting as an adaptor between viral mRNAs and the cellular nuclear export machinery to promote their nuclear export.IMPORTANCE Influenza A virus is a major pathogen of a wide variety of mammalian and avian species that threatens public health and food security. A fuller understanding of the virus life cycle is important to aid control strategies. The virus has a small genome that encodes relatively few proteins that are often multifunctional. Here, we characterize a new function for the NS1 protein, showing that, as well as previously identified roles in antagonizing the innate immune defenses of the cell and directly upregulating translation of viral mRNAs, it also promotes the nuclear export of the viral late gene mRNAs by acting as an adaptor between the viral mRNAs and the cellular mRNA nuclear export machinery.
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Sánchez-Aparicio MT, Garcin D, Rice CM, Kolakofsky D, García-Sastre A, Baum A. Loss of Sendai virus C protein leads to accumulation of RIG-I immunostimulatory defective interfering RNA. J Gen Virol 2017; 98:1282-1293. [PMID: 28631605 PMCID: PMC5962894 DOI: 10.1099/jgv.0.000815] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 04/19/2017] [Indexed: 12/15/2022] Open
Abstract
Retinoic acid inducible gene (RIG-I)-mediated innate immunity plays a pivotal role in defence against virus infections. Previously we have shown that Sendai virus (SeV) defective interfering (DI) RNA functions as an exclusive and potent RIG-I ligand in DI-RNA-rich SeV-Cantell infected cells. To further understand how RIG-I is activated during SeV infection, we used a different interferon (IFN)-inducing SeV strain, recombinant SeVΔC, which, in contrast to SeV-Cantell is believed to stimulate IFN production due to the lack of the SeV IFN antagonist protein C. Surprisingly, we found that in SevΔC-infected cells, DI RNAs also functioned as an exclusive RIG-I ligand. Infections with wild-type SeV failed to generate any RIG-I-associated immunostimulatory RNA and this correlated with the lack of DI genomes in infected cells, as well as with the absence of cellular innate immune responses. Supplementation of the C protein in the context of SeVΔC infection led to a reduction in the number of DI RNAs, further supporting the potential role of the C protein as a negative regulator of DI generation and/or accumulation. Our findings indicate that limiting DI genome production is an important function of viral IFN antagonist proteins.
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Affiliation(s)
- Maria Teresa Sánchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Dominique Garcin
- Department of Genetics and Microbiology, University of Geneva School of Medicine, CMU, CH1211 Geneva, Switzerland
| | - Charles M. Rice
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Kolakofsky
- Department of Genetics and Microbiology, University of Geneva School of Medicine, CMU, CH1211 Geneva, Switzerland
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Medicine Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Alina Baum
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Present address: Regeneron Pharmaceuticals, Inc, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
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Maistriau M, Carletti T, Zakaria MK, Braga L, Faoro V, Vasileiadis V, Marcello A. A method for the detection of virus infectivity in single cells and real time: Towards an automated fluorescence neutralization test. Virus Res 2017; 237:1-6. [DOI: 10.1016/j.virusres.2017.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/08/2017] [Accepted: 05/08/2017] [Indexed: 02/04/2023]
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Ashenberg O, Padmakumar J, Doud MB, Bloom JD. Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA. PLoS Pathog 2017; 13:e1006288. [PMID: 28346537 PMCID: PMC5383324 DOI: 10.1371/journal.ppat.1006288] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 04/06/2017] [Accepted: 03/10/2017] [Indexed: 01/24/2023] Open
Abstract
The innate-immune restriction factor MxA inhibits influenza replication by targeting the viral nucleoprotein (NP). Human influenza virus is more resistant than avian influenza virus to inhibition by human MxA, and prior work has compared human and avian viral strains to identify amino-acid differences in NP that affect sensitivity to MxA. However, this strategy is limited to identifying sites in NP where mutations that affect MxA sensitivity have fixed during the small number of documented zoonotic transmissions of influenza to humans. Here we use an unbiased deep mutational scanning approach to quantify how all single amino-acid mutations to NP affect MxA sensitivity in the context of replication-competent virus. We both identify new sites in NP where mutations affect MxA resistance and re-identify mutations known to have increased MxA resistance during historical adaptations of influenza to humans. Most of the sites where mutations have the greatest effect are almost completely conserved across all influenza A viruses, and the amino acids at these sites confer relatively high resistance to MxA. These sites cluster in regions of NP that appear to be important for its recognition by MxA. Overall, our work systematically identifies the sites in influenza nucleoprotein where mutations affect sensitivity to MxA. We also demonstrate a powerful new strategy for identifying regions of viral proteins that affect inhibition by host factors. During viral infection, human cells express proteins that can restrict virus replication. However, in many cases it remains unclear what determines the sensitivity of a given viral strain to a particular restriction factor. Here we use a high-throughput approach to measure how all amino-acid mutations to the nucleoprotein of influenza virus affect restriction by the human protein MxA. We find several dozen sites where mutations substantially affect the sensitivity of influenza virus to MxA. While a few of these sites are known to have fixed mutations during past adaptations of influenza virus to humans, most of the sites are broadly conserved across all influenza strains and have never previously been described as affecting MxA resistance. Our results therefore show that the known historical evolution of influenza has only involved substitutions at a small fraction of the sites where mutations can in principle affect MxA resistance. We suggest that this is because many sites are already broadly fixed at amino acids that confer high resistance.
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Affiliation(s)
- Orr Ashenberg
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jai Padmakumar
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael B. Doud
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA, USA
| | - Jesse D. Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- * E-mail:
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Killip MJ, Jackson D, Pérez-Cidoncha M, Fodor E, Randall RE. Single-cell studies of IFN-β promoter activation by wild-type and NS1-defective influenza A viruses. J Gen Virol 2017; 98:357-363. [PMID: 27983470 PMCID: PMC5721924 DOI: 10.1099/jgv.0.000687] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Deletion or truncation of NS1, the principal IFN antagonist of influenza viruses, leads to increased IFN induction during influenza virus infection. We have studied activation of the IFN induction cascade by both wild-type and NS1-defective viruses at the single-cell level using a cell line expressing GFP under the control of the IFN-β promoter and by examining MxA expression. The IFN-β promoter was not activated in all infected cells even during NS1-defective virus infections. Loss of NS1 expression is therefore insufficient per se to induce IFN in an infected cell, and factors besides NS1 expression status must dictate whether the IFN response is activated. The IFN response was efficiently stimulated in these cells following infection with other viruses; the differential IFN response we observe with influenza viruses is therefore not cell specific but is likely due to differences in the nature of the infecting virus particles and their subsequent replication.
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Affiliation(s)
- M. J Killip
- School of Biology, Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife KY16 9ST, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- *Correspondence: M. J. Killip,
| | - D Jackson
- School of Biology, Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife KY16 9ST, UK
| | - M Pérez-Cidoncha
- School of Biology, Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife KY16 9ST, UK
| | - E Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - R. E Randall
- School of Biology, Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife KY16 9ST, UK
- R. E. Randall,
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Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family. J Virol 2016; 90:9446-56. [PMID: 27512068 PMCID: PMC5044818 DOI: 10.1128/jvi.01056-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/03/2016] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED We have previously shown that IFIT1 is primarily responsible for the antiviral action of interferon (IFN) alpha/beta against parainfluenza virus type 5 (PIV5), selectively inhibiting the translation of PIV5 mRNAs. Here we report that while PIV2, PIV5, and mumps virus (MuV) are sensitive to IFIT1, nonrubulavirus members of the paramyxoviridae such as PIV3, Sendai virus (SeV), and canine distemper virus (CDV) are resistant. The IFIT1 sensitivity of PIV5 was not rescued by coinfection with an IFIT1-resistant virus (PIV3), demonstrating that PIV3 does not specifically inhibit the antiviral activity of IFIT1 and that the inhibition of PIV5 mRNAs is regulated by cis-acting elements. We developed an in vitro translation system using purified human IFIT1 to further investigate the mechanism of action of IFIT1. While the translations of PIV2, PIV5, and MuV mRNAs were directly inhibited by IFIT1, the translations of PIV3, SeV, and CDV mRNAs were not. Using purified human mRNA-capping enzymes, we show biochemically that efficient inhibition by IFIT1 is dependent upon a 5' guanosine nucleoside cap (which need not be N7 methylated) and that this sensitivity is partly abrogated by 2'O methylation of the cap 1 ribose. Intriguingly, PIV5 M mRNA, in contrast to NP mRNA, remained sensitive to inhibition by IFIT1 following in vitro 2'O methylation, suggesting that other structural features of mRNAs may influence their sensitivity to IFIT1. Thus, surprisingly, the viral polymerases (which have 2'-O-methyltransferase activity) of rubulaviruses do not protect these viruses from inhibition by IFIT1. Possible biological consequences of this are discussed. IMPORTANCE Paramyxoviruses cause a wide variety of diseases, and yet most of their genes encode structural proteins and proteins involved in their replication cycle. Thus, the amount of genetic information that determines the type of disease that paramyxoviruses cause is relatively small. One factor that will influence disease outcomes is how they interact with innate host cell defenses, including the interferon (IFN) system. Here we show that different paramyxoviruses interact in distinct ways with cells in a preexisting IFN-induced antiviral state. Strikingly, all the rubulaviruses tested were sensitive to the antiviral action of ISG56/IFIT1, while all the other paramyxoviruses tested were resistant. We developed novel in vitro biochemical assays to investigate the mechanism of action of IFIT1, demonstrating that the mRNAs of rubulaviruses can be directly inhibited by IFIT1 and that this is at least partially because their mRNAs are not correctly methylated.
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Gage ZO, Vasou A, Gray DW, Randall RE, Adamson CS. Identification of Novel Inhibitors of the Type I Interferon Induction Pathway Using Cell-Based High-Throughput Screening. ACTA ACUST UNITED AC 2016; 21:978-88. [PMID: 27358388 PMCID: PMC5030734 DOI: 10.1177/1087057116656314] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/01/2016] [Indexed: 12/24/2022]
Abstract
Production of type I interferon (IFN) is an essential component of the innate immune response against invading pathogens. However, its production must be tightly regulated to avoid harmful effects. Compounds that modulate the IFN response are potentially valuable for a variety of applications due to IFN’s beneficial and detrimental roles. We developed and executed a cell-based high-throughput screen (HTS) targeting components that participate in and/or regulate the IRF3 and nuclear factor (NF)–κB branches of the IFN induction pathway. The assay detects activation of the IFN induction pathway via an enhanced green fluorescent protein (eGFP) reporter gene under the control of the IFNβ promoter and was optimized, miniaturized, and demonstrated suitable for HTS as robust Z′ factor scores of >0.6 were consistently achieved. A diversity screening set of 15,667 small molecules was assayed and two novel hit compounds validated that specifically inhibit the IFN induction pathway. We demonstrate that one of these compounds acts at or upstream of IRF3 phosphorylation. A second cell-based assay to detect activation of the IFN signaling (Jak-Stat) pathway via an eGFP reporter gene under the control of an IFN-stimulated response element (ISRE) containing MxA promoter also performed well (robust Z′ factor >0.7) and may therefore be similarly used to identify small molecules that modulate the IFN signaling pathway.
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Affiliation(s)
- Zoe O Gage
- School of Biology, University of St Andrews, St Andrews, Fife, UK Biomedical Sciences Research Complex (BSRC), University of St Andrews, St Andrews, Fife, UK
| | - Andri Vasou
- School of Biology, University of St Andrews, St Andrews, Fife, UK Biomedical Sciences Research Complex (BSRC), University of St Andrews, St Andrews, Fife, UK
| | - David W Gray
- Drug Discovery Unit, University of Dundee, Dundee, UK
| | - Richard E Randall
- School of Biology, University of St Andrews, St Andrews, Fife, UK Biomedical Sciences Research Complex (BSRC), University of St Andrews, St Andrews, Fife, UK
| | - Catherine S Adamson
- School of Biology, University of St Andrews, St Andrews, Fife, UK Biomedical Sciences Research Complex (BSRC), University of St Andrews, St Andrews, Fife, UK
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Voigt EA, Swick A, Yin J. Rapid induction and persistence of paracrine-induced cellular antiviral states arrest viral infection spread in A549 cells. Virology 2016; 496:59-66. [PMID: 27254596 DOI: 10.1016/j.virol.2016.05.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 12/31/2022]
Abstract
The virus/host interaction is a complex interplay between pro- and anti-viral factors that ultimately determines the spread or halt of virus infections in tissues. This interplay develops over multiple rounds of infection. The purpose of this study was to determine how cellular-level processes combine to impact the spatial spread of infection. We measured the kinetics of virus replication (VSV), antiviral paracrine signal upregulation and secretion, spatial spread of virus and paracrine antiviral signaling, and inhibition of virus production in antiviral-exposed A549 human lung epithelial cells. We found that initially infected cells released antiviral signals 4-to-7h following production of virus. However, the subsequent rapid dissemination of signal and fast induction of a robust and persistent antiviral state ultimately led to a suppression of infection spread. This work shows how cellular responses to infection and activation of antiviral responses can integrate to ultimately control infection spread across host cell populations.
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Affiliation(s)
- Emily A Voigt
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam Swick
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - John Yin
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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Upregulated LINE-1 Activity in the Fanconi Anemia Cancer Susceptibility Syndrome Leads to Spontaneous Pro-inflammatory Cytokine Production. EBioMedicine 2016; 8:184-194. [PMID: 27428429 PMCID: PMC4919473 DOI: 10.1016/j.ebiom.2016.05.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/08/2016] [Accepted: 05/05/2016] [Indexed: 11/30/2022] Open
Abstract
Fanconi Anemia (FA) is a genetic disorder characterized by elevated cancer susceptibility and pro-inflammatory cytokine production. Using SLX4FANCP deficiency as a working model, we questioned the trigger for chronic inflammation in FA. We found that absence of SLX4 caused cytoplasmic DNA accumulation, including sequences deriving from active Long INterspersed Element-1 (LINE-1), triggering the cGAS-STING pathway to elicit interferon (IFN) expression. In agreement, absence of SLX4 leads to upregulated LINE-1 retrotransposition. Importantly, similar results were obtained with the FANCD2 upstream activator of SLX4. Furthermore, treatment of FA cells with the Tenofovir reverse transcriptase inhibitor (RTi), that prevents endogenous retrotransposition, decreased both accumulation of cytoplasmic DNA and pro-inflammatory signaling. Collectively, our data suggest a contribution of endogenous RT activities to the generation of immunogenic cytoplasmic nucleic acids responsible for inflammation in FA. The additional observation that RTi decreased pro-inflammatory cytokine production induced by DNA replication stress-inducing drugs further demonstrates the contribution of endogenous RTs to sustaining chronic inflammation. Altogether, our data open perspectives in the prevention of adverse effects of chronic inflammation in tumorigenesis. Cytoplasmic DNA, comprising LINE-1-derived sequences, elicits IFN expression via the cGAS-STING pathway in SLX4-deficiency. Members of the Fanconi Anemia DNA repair pathway negatively regulate LINE-1 retrotransposition. Endogenous reverse transcriptase activities contribute to spontaneous and chemotherapy-induced inflammation.
Chronic inflammation favors tumorigenesis, negatively influencing patient prognosis. Yet, the underlying molecular mechanisms are poorly understood. Here, we show that increased endogenous retroelement-associated reverse transcriptase activity contributes to generate immunogenic cytoplasmic nucleic acids susceptible of triggering a pro-inflammatory response in the Fanconi Anemia (FA) cancer susceptibility syndrome. In addition, treatment of FA cells or of cells exposed to replication stress inducing drugs, with a reverse transcriptase inhibitor, decreases pro-inflammatory signals. Altogether our data suggest the involvement of endogenous reverse transcriptase activities in sustaining pervasive chronic inflammation, opening therapeutic perspectives for preventing its impact on tumorigenesis.
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Anchisi S, Guerra J, Mottet-Osman G, Garcin D. Mismatches in the Influenza A Virus RNA Panhandle Prevent Retinoic Acid-Inducible Gene I (RIG-I) Sensing by Impairing RNA/RIG-I Complex Formation. J Virol 2016; 90:586-90. [PMID: 26446607 PMCID: PMC4702558 DOI: 10.1128/jvi.01671-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/05/2015] [Indexed: 11/20/2022] Open
Abstract
Influenza virus RNA (vRNA) promoter panhandle structures are believed to be sensed by retinoic acid-inducible gene I (RIG-I). The occurrence of mismatches in this double-stranded RNA structure raises questions about their effect on innate sensing. Our results suggest that mismatches in vRNA promoters decrease binding to RIG-I in vivo, affecting RNA/RIG-I complex formation and preventing RIG-I activation. These results can be inferred to apply to other viruses and suggest that mismatches may represent a general viral strategy to escape RIG-I sensing.
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Affiliation(s)
- Stéphanie Anchisi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jessica Guerra
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Geneviève Mottet-Osman
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Dominique Garcin
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Fluorescence-Activated Cell Sorting-Based Analysis Reveals an Asymmetric Induction of Interferon-Stimulated Genes in Response to Seasonal Influenza A Virus. J Virol 2015; 89:6982-93. [PMID: 25903337 DOI: 10.1128/jvi.00857-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/18/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Influenza A virus (IAV) infection provokes an antiviral response involving the expression of type I and III interferons (IFN) and IFN-stimulated genes (ISGs) in infected cell cultures. However, the spatiotemporal dynamics of the IFN reaction are incompletely understood, as previous studies investigated mainly the population responses of virus-infected cultures, although substantial cell-to-cell variability has been documented. We devised a fluorescence-activated cell sorting-based assay to simultaneously quantify expression of viral antigens and ISGs, such as ISG15, MxA, and IFIT1, in IAV-infected cell cultures at the single-cell level. This approach revealed that seasonal IAV triggers an unexpected asymmetric response, as the major cell populations expressed either viral antigen or ISG, but rarely both. Further investigations identified a role of the viral NS1 protein in blocking ISG expression in infected cells, which surprisingly did not reduce paracrine IFN signaling to noninfected cells. Interestingly, viral ISG control was impaired in cultures infected with avian-origin IAV, including the H7N9 virus from eastern China. This phenotype was traced back to polymorphic NS1 amino acids known to be important for stable binding of the polyadenylation factor CPSF30 and concomitant suppression of host cell gene expression. Most significantly, mutation of two amino acids within the CPSF30 attachment site of NS1 from seasonal IAV diminished the strict control of ISG expression in infected cells and substantially attenuated virus replication. In conclusion, our approach revealed an asymmetric, NS1-dependent ISG induction in cultures infected with seasonal IAV, which appears to be essential for efficient virus propagation. IMPORTANCE Interferons are expressed by infected cells in response to IAV infection and play important roles in the antiviral immune response by inducing hundreds of interferon-stimulated genes (ISGs). Unlike many previous studies, we investigated the ISG response at the single-cell level, enabling novel insights into this virus-host interaction. Hence, cell cultures infected with seasonal IAV displayed an asymmetric ISG induction that was confined almost exclusively to noninfected cells. In comparison, ISG expression was observed in larger cell populations infected with avian-origin IAV, suggesting a more resolute antiviral response to these strains. Strict control of ISG expression by seasonal IAV was explained by the binding of the viral NS1 protein to the polyadenylation factor CPSF30, which reduces host cell gene expression. Mutational disruption of CPSF30 binding within NS1 concomitantly attenuated ISG control and replication of seasonal IAV, illustrating the importance of maintaining an asymmetric ISG response for efficient virus propagation.
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Anchisi S, Guerra J, Garcin D. RIG-I ATPase activity and discrimination of self-RNA versus non-self-RNA. mBio 2015; 6:e02349. [PMID: 25736886 PMCID: PMC4358010 DOI: 10.1128/mbio.02349-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 01/21/2015] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Many RNA viruses are detected by retinoic acid-inducible gene i (RIG-I), a cytoplasmic sensor that triggers an antiviral response upon binding non-self-RNA that contains a stretch of double-stranded RNA (dsRNA) bearing a base-paired 5' ppp nucleotide. To gain insight into how RIG-I discriminates between self-RNA and non-self-RNA, we used duplexes whose complementary bottom strand contained both ribo- and deoxynucleotides. These duplexes were examined for their binding to RIG-I and their relative abilities to stimulate ATPase activity, to induce RIG-I dimerization on the duplex, and to induce beta interferon (IFN-β) expression. We show that the chemical nature of the bottom strand is not critical for RIG-I binding. However, two key ribonucleotides, at positions 2 and 5 on the bottom strand, are minimally required for the RIG-I ATPase activity, which is necessary but not sufficient for IFN-β stimulation. We find that duplexes with shorter stretches of dsRNA, as model self-RNAs, bind less stably to RIG-I but nevertheless have an enhanced ability to stimulate the ATPase. Moreover, ATPase activity promotes RIG-I recycling on RIG-I/dsRNA complexes. Since pseudo-self-RNAs bind to RIG-I less stably, they are preferentially recycled by ATP hydrolysis that weakens the helicase domain binding of dsRNA. Our results suggest that one function of the ATPase is to restrict RIG-I signaling to its interaction with non-self-RNA. A model of how this discrimination occurs as a function of dsRNA length is presented. IMPORTANCE The innate immune response to pathogens is based on the discrimination between self-RNA and non-self-RNA. The main determinants of this detection for RNA viruses are specific pathogen-associated molecular patterns (PAMPs) of RNA, which are detected by dedicated cytoplasmic pattern recognition receptors (PRRs). RIG-I is a PRR that specifically detects short viral dsRNAs amid a sea of cellular RNAs. Here we study the determinants of this discrimination and how RIG-I ATPase activity, the only enzymatic activity of this sensor, contributes to its activation in a manner restricted to its interaction with non-self-RNAs. We also show how the innate immune response evolves during infection via IFN expression, from a state in which discrimination of self-RNA from non-self-RNA is most important to one in which this discrimination is sacrificed for the effectiveness of the antiviral response.
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Affiliation(s)
- Stéphanie Anchisi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jessica Guerra
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Dominique Garcin
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Patil S, Fribourg M, Ge Y, Batish M, Tyagi S, Hayot F, Sealfon SC. Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-β response to viral infection. Sci Signal 2015; 8:ra16. [PMID: 25670204 DOI: 10.1126/scisignal.2005728] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Immune responses to viral infection are stochastic processes, which initiate in a limited number of cells that then propagate the response. A key component of the response to viral infection entails the synthesis and secretion of type I interferons (IFNs), including the early induction of the gene encoding IFN-β (Ifnb1). With single-cell analysis and mathematical modeling, we investigated the mechanisms underlying how increases in the amount of Ifnb1 mRNA per cell and in the numbers of cells expressing Ifnb1 calibrate the response to viral infection. We used single-cell, single-molecule assays to quantify the early induction of Ifnb1 expression (the Ifnb1 response) in human monocyte-derived dendritic cells infected with Newcastle disease virus, thus retaining the physiological stoichiometry of transcriptional regulators to both alleles of the Ifnb1 gene. We applied computational methods to extract the stochastic features that underlie the cell-to-cell variations in gene expression over time. Integration of simulations and experiments identified the role of paracrine signaling in increasing the number of cells that express Ifnb1 over time and in calibrating the immune response to viral infection.
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Affiliation(s)
- Sonali Patil
- Department of Neurology and Center for Translational Systems Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel Fribourg
- Department of Neurology and Center for Translational Systems Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology and Center for Translational Systems Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mona Batish
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Fernand Hayot
- Department of Neurology and Center for Translational Systems Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stuart C Sealfon
- Department of Neurology and Center for Translational Systems Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Killip MJ, Fodor E, Randall RE. Influenza virus activation of the interferon system. Virus Res 2015; 209:11-22. [PMID: 25678267 PMCID: PMC4638190 DOI: 10.1016/j.virusres.2015.02.003] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 12/24/2022]
Abstract
We summarise the literature regarding activation of the IFN response by influenza viruses. We consider evidence concerning the identity of the viral RNA responsible for IFN induction. The link between IFN induction and defective virus genomes is discussed.
The host interferon (IFN) response represents one of the first barriers that influenza viruses must surmount in order to establish an infection. Many advances have been made in recent years in understanding the interactions between influenza viruses and the interferon system. In this review, we summarise recent work regarding activation of the type I IFN response by influenza viruses, including attempts to identify the viral RNA responsible for IFN induction, the stage of the virus life cycle at which it is generated and the role of defective viruses in this process.
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Affiliation(s)
- Marian J Killip
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK; Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Richard E Randall
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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Stewart CE, Randall RE, Adamson CS. Inhibitors of the interferon response enhance virus replication in vitro. PLoS One 2014; 9:e112014. [PMID: 25390891 PMCID: PMC4229124 DOI: 10.1371/journal.pone.0112014] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/11/2014] [Indexed: 12/24/2022] Open
Abstract
Virus replication efficiency is influenced by two conflicting factors, kinetics of the cellular interferon (IFN) response and induction of an antiviral state versus speed of virus replication and virus-induced inhibition of the IFN response. Disablement of a virus's capacity to circumvent the IFN response enables both basic research and various practical applications. However, such IFN-sensitive viruses can be difficult to grow to high-titer in cells that produce and respond to IFN. The current default option for growing IFN-sensitive viruses is restricted to a limited selection of cell-lines (e.g. Vero cells) that have lost their ability to produce IFN. This study demonstrates that supplementing tissue-culture medium with an IFN inhibitor provides a simple, effective and flexible approach to increase the growth of IFN-sensitive viruses in a cell-line of choice. We report that IFN inhibitors targeting components of the IFN response (TBK1, IKK2, JAK1) significantly increased virus replication. More specifically, the JAK1/2 inhibitor Ruxolitinib enhances the growth of viruses that are sensitive to IFN due to (i) loss of function of the viral IFN antagonist (due to mutation or species-specific constraints) or (ii) mutations/host cell constraints that slow virus spread such that it can be controlled by the IFN response. This was demonstrated for a variety of viruses, including, viruses with disabled IFN antagonists that represent live-attenuated vaccine candidates (Respiratory Syncytial Virus (RSV), Influenza Virus), traditionally attenuated vaccine strains (Measles, Mumps) and a slow-growing wild-type virus (RSV). In conclusion, supplementing tissue culture-medium with an IFN inhibitor to increase the growth of IFN-sensitive viruses in a cell-line of choice represents an approach, which is broadly applicable to research investigating the importance of the IFN response in controlling virus infections and has utility in a number of practical applications including vaccine and oncolytic virus production, virus diagnostics and techniques to isolate newly emerging viruses.
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Affiliation(s)
- Claire E. Stewart
- School of Biology, University of St Andrews, Fife, Scotland, United Kingdom
| | - Richard E. Randall
- School of Biology, University of St Andrews, Fife, Scotland, United Kingdom
| | - Catherine S. Adamson
- School of Biology, University of St Andrews, Fife, Scotland, United Kingdom
- * E-mail:
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Pérez-Cidoncha M, Killip MJ, Asensio VJ, Fernández Y, Bengoechea JA, Randall RE, Ortín J. Generation of replication-proficient influenza virus NS1 point mutants with interferon-hyperinducer phenotype. PLoS One 2014; 9:e98668. [PMID: 24887174 PMCID: PMC4041880 DOI: 10.1371/journal.pone.0098668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/05/2014] [Indexed: 12/24/2022] Open
Abstract
The NS1 protein of influenza A viruses is the dedicated viral interferon (IFN)-antagonist. Viruses lacking NS1 protein expression cannot multiply in normal cells but are viable in cells deficient in their ability to produce or respond to IFN. Here we report an unbiased mutagenesis approach to identify positions in the influenza A NS1 protein that modulate the IFN response upon infection. A random library of virus ribonucleoproteins containing circa 40 000 point mutants in NS1 were transferred to infectious virus and amplified in MDCK cells unable to respond to interferon. Viruses that activated the interferon (IFN) response were subsequently selected by their ability to induce expression of green-fluorescent protein (GFP) following infection of A549 cells bearing an IFN promoter-dependent GFP gene. Using this approach we isolated individual mutant viruses that replicate to high titers in IFN-compromised cells but, compared to wild type viruses, induced higher levels of IFN in IFN-competent cells and had a reduced capacity to counteract exogenous IFN. Most of these viruses contained not previously reported NS1 mutations within either the RNA-binding domain, the effector domain or the linker region between them. These results indicate that subtle alterations in NS1 can reduce its effectiveness as an IFN antagonist without affecting the intrinsic capacity of the virus to multiply. The general approach reported here may facilitate the generation of replication-proficient, IFN-inducing virus mutants, that potentially could be developed as attenuated vaccines against a variety of viruses.
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Affiliation(s)
- Maite Pérez-Cidoncha
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
- Ciber de Enfermedades Respiratorias (ISCIII), Madrid, Spain
| | - Marian J. Killip
- School of Biology, Centre for Biomolecular Sciences, University of St Andrews, St Andrews, United Kingdom
| | - Víctor J. Asensio
- Fundació d'Investigació Sanitària de les Illes Balears (FISIB), Bunyola, Mallorca, Spain
| | - Yolanda Fernández
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
- Ciber de Enfermedades Respiratorias (ISCIII), Madrid, Spain
| | - José A. Bengoechea
- Laboratory Microbial Pathogenesis, Fundació d'Investigació Sanitària de les Illes Balears (FISIB), Bunyola, Mallorca, Spain
- Ciber de Enfermedades Respiratorias (ISCIII), Madrid, Spain
| | - Richard E. Randall
- School of Biology, Centre for Biomolecular Sciences, University of St Andrews, St Andrews, United Kingdom
| | - Juan Ortín
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
- Ciber de Enfermedades Respiratorias (ISCIII), Madrid, Spain
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Witteveldt J, Blundell R, Maarleveld JJ, McFadden N, Evans DJ, Simmonds P. The influence of viral RNA secondary structure on interactions with innate host cell defences. Nucleic Acids Res 2014; 42:3314-29. [PMID: 24335283 PMCID: PMC3950689 DOI: 10.1093/nar/gkt1291] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 12/21/2022] Open
Abstract
RNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts. Although interactions with host innate and adaptive responses are complex and persistence mechanisms likely multi-factorial, we previously observed associations between bioinformatically predicted RNA secondary formation in genomes of positive-stranded RNA viruses with their in vivo fitness and persistence. To analyse this interactions functionally, we transfected fibroblasts with non-replicating, non-translated RNA transcripts from RNA viral genomes with differing degrees of genome-scale ordered RNA structure (GORS). Single-stranded RNA transcripts induced interferon-β mediated though RIG-I and PKR activation, the latter associated with rapid induction of antiviral stress granules. A striking inverse correlation was observed between induction of both cellular responses with transcript RNA structure formation that was independent of both nucleotide composition and sequence length. The consistent inability of cells to recognize RNA transcripts possessing GORS extended to downstream differences from unstructured transcripts in expression of TNF-α, other interferon-stimulated genes and induction of apoptosis. This functional association provides novel insights into interactions between virus and host early after infection and provides evidence for a novel mechanism for evading intrinsic and innate immune responses.
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Affiliation(s)
- Jeroen Witteveldt
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard Blundell
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Joris J. Maarleveld
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Nora McFadden
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - David J. Evans
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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An unbiased genetic screen reveals the polygenic nature of the influenza virus anti-interferon response. J Virol 2014; 88:4632-46. [PMID: 24574395 PMCID: PMC3993829 DOI: 10.1128/jvi.00014-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Influenza A viruses counteract the cellular innate immune response at several steps, including blocking RIG I-dependent activation of interferon (IFN) transcription, interferon (IFN)-dependent upregulation of IFN-stimulated genes (ISGs), and the activity of various ISG products; the multifunctional NS1 protein is responsible for most of these activities. To determine the importance of other viral genes in the interplay between the virus and the host IFN response, we characterized populations and selected mutants of wild-type viruses selected by passage through non-IFN-responsive cells. We reasoned that, by allowing replication to occur in the absence of the selection pressure exerted by IFN, the virus could mutate at positions that would normally be restricted and could thus find new optimal sequence solutions. Deep sequencing of selected virus populations and individual virus mutants indicated that nonsynonymous mutations occurred at many phylogenetically conserved positions in nearly all virus genes. Most individual mutants selected for further characterization induced IFN and ISGs and were unable to counteract the effects of exogenous IFN, yet only one contained a mutation in NS1. The relevance of these mutations for the virus phenotype was verified by reverse genetics. Of note, several virus mutants expressing intact NS1 proteins exhibited alterations in the M1/M2 proteins and accumulated large amounts of deleted genomic RNAs but nonetheless replicated to high titers. This suggests that the overproduction of IFN inducers by these viruses can override NS1-mediated IFN modulation. Altogether, the results suggest that influenza viruses replicating in IFN-competent cells have tuned their complete genomes to evade the cellular innate immune system and that serial replication in non-IFN-responsive cells allows the virus to relax from these constraints and find a new genome consensus within its sequence space. IMPORTANCE In natural virus infections, the production of interferons leads to an antiviral state in cells that effectively limits virus replication. The interferon response places considerable selection pressure on viruses, and they have evolved a variety of ways to evade it. Although the influenza virus NS1 protein is a powerful interferon antagonist, the contributions of other viral genes to interferon evasion have not been well characterized. Here, we examined the effects of alleviating the selection pressure exerted by interferon by serially passaging influenza viruses in cells unable to respond to interferon. Viruses that grew to high titers had mutations at many normally conserved positions in nearly all genes and were not restricted to the NS1 gene. Our results demonstrate that influenza viruses have fine-tuned their entire genomes to evade the interferon response, and by removing interferon-mediated constraints, viruses can mutate at genome positions normally restricted by the interferon response.
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Activation of the interferon induction cascade by influenza a viruses requires viral RNA synthesis and nuclear export. J Virol 2014; 88:3942-52. [PMID: 24478437 PMCID: PMC3993719 DOI: 10.1128/jvi.03109-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We have examined the requirements for virus transcription and replication and thus the roles of input and progeny genomes in the generation of interferon (IFN)-inducing pathogen-associated molecular patterns (PAMPs) by influenza A viruses using inhibitors of these processes. Using IFN regulatory factor 3 (IRF3) phosphorylation as a marker of activation of the IFN induction cascade that occurs upstream of the IFN-β promoter, we demonstrate strong activation of the IFN induction cascade in A549 cells infected with a variety of influenza A viruses in the presence of cycloheximide or nucleoprotein (NP) small interfering RNA (siRNA), which inhibits viral protein synthesis and thus complementary ribonucleoprotein (cRNP) and progeny viral RNP (vRNP) synthesis. In contrast, activation of the IFN induction cascade by influenza viruses was very effectively abrogated by treatment with actinomycin D and other transcription inhibitors, which correlated with the inhibition of the synthesis of all viral RNA species. Furthermore, 5,6-dichloro-1-β-d-ribofuranosyl-benzimidazole, an inhibitor that prevents viral RNA export from the nucleus, was also a potent inhibitor of IRF3 activation; thus, both viral RNA synthesis and nuclear export are required for IFN induction by influenza A viruses. While the exact nature of the viral PAMPs remains to be determined, our data suggest that in this experimental system the major influenza A virus PAMPs are distinct from those of incoming genomes or progeny vRNPs. IMPORTANCE The host interferon system exerts an extremely potent antiviral response that efficiently restricts virus replication and spread; the interferon response can thus dictate the outcome of a virus infection, and it is therefore important to understand how viruses induce interferon. Both input and progeny genomes have been linked to interferon induction by influenza viruses. However, our experiments in tissue culture cells show that viral RNA synthesis and nuclear export are required to activate this response. Furthermore, the interferon induction cascade is activated under conditions in which the synthesis of progeny genomes is inhibited. Therefore, in tissue culture cells, input and progeny genomes are not the predominant inducers of interferon generated by influenza A viruses; the major viral interferon inducer(s) still remains to be identified.
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Swick A, Baltes A, Yin J. Visualizing infection spread: dual-color fluorescent reporting of virus-host interactions. Biotechnol Bioeng 2013; 111:1200-9. [PMID: 24338628 DOI: 10.1002/bit.25170] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/22/2013] [Accepted: 12/02/2013] [Indexed: 12/24/2022]
Abstract
Although the molecular mechanisms by which host cells defend themselves against viral infection have been studied in great depth, and countermeasures viruses employ to suppress such defensive responses have been widely documented, relatively little attention has been devoted toward elucidating how such interactions between virus and host are resolved over multiple rounds of infection. Here, we describe the design, synthesis, and validation of a dual-color fluorescent reporter system to study how viral infections spread through a host cell monolayer and how the cellular innate immune system mounts an antiviral response. We employed recombinant, red fluorescent protein expressing mutants of a prototypical RNA virus, vesicular stomatitis virus to enable identification and tracking of infected cells. Further, we generated stable reporter cells that use green fluorescent protein to report on the expression of IFIT2, an interferon stimulated gene involved in the interference of viral protein translation, and a marker of antiviral defense activation. The presence of the fluorescent protein reporters had minimal effects on the normal behavior of the cells or viruses. Moreover, expression of the virus and cell reporters correlated with the kinetics of viral replication and activation of an anti-viral response, respectively. This two-color system enabled us to track and quantify in live cells how viral replication and activation of host defensive responses play out over multiple rounds of infection. Initial study of propagating infections demonstrated that antiviral activation over multiple rounds was critical for slowing and ultimately halting the spread of infection.
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Affiliation(s)
- Adam Swick
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin, 53706-1607; Wisconsin Institute for Discovery-Systems Biology Theme, University of Wisconsin-Madison, Madison, Wisconsin
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The human interferon-induced MxA protein inhibits early stages of influenza A virus infection by retaining the incoming viral genome in the cytoplasm. J Virol 2013; 87:13053-8. [PMID: 24049170 PMCID: PMC3838145 DOI: 10.1128/jvi.02220-13] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The induction of an interferon-induced antiviral state is a powerful cellular response against viral infection that limits viral spread. Here, we show that a preexisting antiviral state inhibits the replication of influenza A viruses in human A549 cells by preventing transport of the viral genome to the nucleus and that the interferon-induced MxA protein is necessary but not sufficient for this process. This represents a previously unreported antiviral function of MxA against influenza A virus infection.
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Recent Progress in Lab-on-a-Chip Technology and Its Potential Application to Clinical Diagnoses. Int Neurourol J 2013; 17:2-10. [PMID: 23610705 PMCID: PMC3627994 DOI: 10.5213/inj.2013.17.1.2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 03/26/2013] [Indexed: 12/02/2022] Open
Abstract
We present the construction of the lab-on-a-chip (LOC) system, a state-of-the-art technology that uses polymer materials (i.e., poly[dimethylsiloxane]) for the miniaturization of conventional laboratory apparatuses, and show the potential use of these microfluidic devices in clinical applications. In particular, we introduce the independent unit components of the LOC system and demonstrate how each component can be functionally integrated into one monolithic system for the realization of a LOC system. In specific, we demonstrate microscale polymerase chain reaction with the use of a single heater, a microscale sample injection device with a disposable plastic syringe and a strategy for device assembly under environmentally mild conditions assisted by surface modification techniques. In this way, we endeavor to construct a totally integrated, disposable microfluidic system operated by a single mode, the pressure, which can be applied on-site with enhanced device portability and disposability and with simple and rapid operation for medical and clinical diagnoses, potentially extending its application to urodynamic studies in molecular level.
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Abstract
Cache Valley virus (CVV)-induced malformations have been previously reproduced in ovine fetuses. To evaluate the development of the antiviral response by the early, infected fetus, before the development of immunocompetency, ovine fetuses at 35 days of gestation were inoculated in utero with CVV and euthanized at 7, 10, 14, 21, and 28 days postinfection. The antiviral immune response in immature fetuses infected with CVV was evaluated. Gene expression associated with an innate, immune response was quantified by real-time quantitative PCR. The upregulated genes in infected fetuses included ISG15, Mx1, Mx2, IL-1, IL-6, TNF-α, TLR-7, and TLR-8. The amount of Mx1 protein, an interferon-stimulated GTPase capable of restricting growth of bunyaviruses, was elevated in the allantoic and amniotic fluid in infected fetuses. ISG15 protein expression was significantly increased in target tissues of infected animals. B lymphocytes and immunoglobulin-positive cells were detected in lymphoid tissues and in the meninges of infected animals. These results demonstrated that the infected ovine fetus is able to initiate an innate and adaptive immune response much earlier than previously known, which presumably contributes to viral clearance in infected animals.
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45
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Deep sequencing analysis of defective genomes of parainfluenza virus 5 and their role in interferon induction. J Virol 2013; 87:4798-807. [PMID: 23449801 DOI: 10.1128/jvi.03383-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Preparations of parainfluenza virus 5 (PIV5) that are potent activators of the interferon (IFN) induction cascade were generated by high-multiplicity passage in order to accumulate defective interfering virus genomes (DIs). Nucleocapsid RNA from these virus preparations was extracted and subjected to deep sequencing. Sequencing data were analyzed using methods designed to detect internal deletion and "copyback" DIs in order to identify and characterize the different DIs present and to approximately quantify the ratio of defective to nondefective genomes. Trailer copybacks dominated the DI populations in IFN-inducing preparations of both the PIV5 wild type (wt) and PIV5-VΔC (a recombinant virus that does not encode a functional V protein). Although the PIV5 V protein is an efficient inhibitor of the IFN induction cascade, we show that nondefective PIV5 wt is unable to prevent activation of the IFN response by coinfecting copyback DIs due to the interfering effects of copyback DIs on nondefective virus protein expression. As a result, copyback DIs are able to very rapidly activate the IFN induction cascade prior to the expression of detectable levels of V protein by coinfecting nondefective virus.
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46
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STAT2 deficiency and susceptibility to viral illness in humans. Proc Natl Acad Sci U S A 2013; 110:3053-8. [PMID: 23391734 DOI: 10.1073/pnas.1220098110] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Severe infectious disease in children may be a manifestation of primary immunodeficiency. These genetic disorders represent important experiments of nature with the capacity to elucidate nonredundant mechanisms of human immunity. We hypothesized that a primary defect of innate antiviral immunity was responsible for unusually severe viral illness in two siblings; the proband developed disseminated vaccine strain measles following routine immunization, whereas an infant brother died after a 2-d febrile illness from an unknown viral infection. Patient fibroblasts were indeed abnormally permissive for viral replication in vitro, associated with profound failure of type I IFN signaling and absence of STAT2 protein. Sequencing of genomic DNA and RNA revealed a homozygous mutation in intron 4 of STAT2 that prevented correct splicing in patient cells. Subsequently, other family members were identified with the same genetic lesion. Despite documented infection by known viral pathogens, some of which have been more severe than normal, surviving STAT2-deficient individuals have remained generally healthy, with no obvious defects in their adaptive immunity or developmental abnormalities. These findings imply that type I IFN signaling [through interferon-stimulated gene factor 3 (ISGF3)] is surprisingly not essential for host defense against the majority of common childhood viral infections.
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Levy DE, Marié IJ, Durbin JE. Induction and function of type I and III interferon in response to viral infection. Curr Opin Virol 2012; 1:476-86. [PMID: 22323926 DOI: 10.1016/j.coviro.2011.11.001] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The type I and III interferon (IFN) families consist of cytokines rapidly induced during viral infection that confer antiviral protection on target cells and are critical components of innate immune responses and the transition to effective adaptive immunity. The regulation of their expression involves an intricate and stringently regulated signaling cascade, initiated by recognition most often of viral nucleic acid in cytoplasmic and endosomal compartments and involving a series of protein conformational rearrangements and interactions regulated by helicase action, ubiquitin modification, and protein aggregation, culminating in kinase activation and phosphorylation of critical transcription factors and their regulators. The many IFN subtypes induced by viruses confer amplification, diversification, and cell-type specificity to the host response to infection, providing fertile ground for development of antiviral therapeutics and vaccines.
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Affiliation(s)
- David E Levy
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
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48
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Andrejeva J, Norsted H, Habjan M, Thiel V, Goodbourn S, Randall RE. ISG56/IFIT1 is primarily responsible for interferon-induced changes to patterns of parainfluenza virus type 5 transcription and protein synthesis. J Gen Virol 2012; 94:59-68. [PMID: 23052390 PMCID: PMC3542720 DOI: 10.1099/vir.0.046797-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Interferon (IFN) induces an antiviral state in cells that results in alterations of the patterns and levels of parainfluenza virus type 5 (PIV5) transcripts and proteins. This study reports that IFN-stimulated gene 56/IFN-induced protein with tetratricopeptide repeats 1 (ISG56/IFIT1) is primarily responsible for these effects of IFN. It was shown that treating cells with IFN after infection resulted in an increase in virus transcription but an overall decrease in virus protein synthesis. As there was no obvious decrease in the overall levels of cellular protein synthesis in infected cells treated with IFN, these results suggested that ISG56/IFIT1 selectively inhibits the translation of viral mRNAs. This conclusion was supported by in vitro translation studies. Previous work has shown that ISG56/IFIT1 can restrict the replication of viruses lacking a 2′-O-methyltransferase activity, an enzyme that methylates the 2′-hydroxyl group of ribose sugars in the 5′-cap structures of mRNA. However, the data in the current study strongly suggested that PIV5 mRNAs are methylated at the 2′-hydroxyl group and thus that ISG56/IFIT1 selectively inhibits the translation of PIV5 mRNA by some as yet unrecognized mechanism. It was also shown that ISG56/IFIT1 is primarily responsible for the IFN-induced inhibition of PIV5.
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Affiliation(s)
- J Andrejeva
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - H Norsted
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - M Habjan
- Kantonal Hospital St Gallen, Institute of Immunobiology, CH-9007 St Gallen, Switzerland
| | - V Thiel
- Kantonal Hospital St Gallen, Institute of Immunobiology, CH-9007 St Gallen, Switzerland
| | - S Goodbourn
- Division of Basic Medical Sciences, St George's, University of London, London SW17 0RE, UK
| | - R E Randall
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
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Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response. Mol Syst Biol 2012; 8:584. [PMID: 22617958 PMCID: PMC3377992 DOI: 10.1038/msb.2012.17] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 04/24/2012] [Indexed: 12/12/2022] Open
Abstract
The cellular recognition of viruses evokes the secretion of type-I interferons (IFNs) that induce an antiviral protective state. By live-cell imaging, we show that key steps of virus-induced signal transduction, IFN-β expression, and induction of IFN-stimulated genes (ISGs) are stochastic events in individual cells. The heterogeneity in IFN production is of cellular-and not viral-origin, and temporal unpredictability of IFN-β expression is largely due to cell-intrinsic noise generated both upstream and downstream of the activation of nuclear factor-κB and IFN regulatory factor transcription factors. Subsequent ISG induction occurs as a stochastic all-or-nothing switch, where the responding cells are protected against virus replication. Mathematical modelling and experimental validation show that reliable antiviral protection in the face of multi-layered cellular stochasticity is achieved by paracrine response amplification. Achieving coherent responses through intercellular communication is likely to be a more widely used strategy by mammalian cells to cope with pervasive stochasticity in signalling and gene expression.
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Childs K, Randall R, Goodbourn S. Paramyxovirus V proteins interact with the RNA Helicase LGP2 to inhibit RIG-I-dependent interferon induction. J Virol 2012; 86:3411-21. [PMID: 22301134 PMCID: PMC3302505 DOI: 10.1128/jvi.06405-11] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/16/2012] [Indexed: 12/24/2022] Open
Abstract
RIG-I and mda-5 are activated by viral RNA and stimulate type I interferon production. Laboratory of genetics and physiology 2 (LGP2) shares homology with RIG-I and mda-5 but lacks the CARD domains required for signaling. The V proteins of paramyxoviruses limit interferon induction by binding mda-5 and preventing its activation; however, they do not bind RIG-I and have not been considered inhibitors of RIG-I signaling. Here we uncover a novel mechanism of RIG-I inhibition in which the V protein of parainfluenzavirus type 5 (PIV5; formerly known as simian virus type 5 [SV5]) interacts with LGP2 and cooperatively inhibits induction by RIG-I ligands. A complex between RIG-I and LGP2 is observed in the presence of PIV5-V, and we propose that this complex is refractory to activation by RIG-I ligands. The V proteins from other paramyxoviruses also bind LGP2 and demonstrate LGP2-dependent inhibition of RIG-I signaling. This is significant, because it demonstrates a general mechanism for the targeting of the RIG-I pathway by paramyxoviruses.
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Affiliation(s)
- Kay Childs
- Division of Basic Medical Sciences, St. George’s, University of London, London, United Kingdom.
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