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Khalil AM, Nogales A, Martínez-Sobrido L, Mostafa A. Antiviral responses versus virus-induced cellular shutoff: a game of thrones between influenza A virus NS1 and SARS-CoV-2 Nsp1. Front Cell Infect Microbiol 2024; 14:1357866. [PMID: 38375361 PMCID: PMC10875036 DOI: 10.3389/fcimb.2024.1357866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Following virus recognition of host cell receptors and viral particle/genome internalization, viruses replicate in the host via hijacking essential host cell machinery components to evade the provoked antiviral innate immunity against the invading pathogen. Respiratory viral infections are usually acute with the ability to activate pattern recognition receptors (PRRs) in/on host cells, resulting in the production and release of interferons (IFNs), proinflammatory cytokines, chemokines, and IFN-stimulated genes (ISGs) to reduce virus fitness and mitigate infection. Nevertheless, the game between viruses and the host is a complicated and dynamic process, in which they restrict each other via specific factors to maintain their own advantages and win this game. The primary role of the non-structural protein 1 (NS1 and Nsp1) of influenza A viruses (IAV) and the pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respectively, is to control antiviral host-induced innate immune responses. This review provides a comprehensive overview of the genesis, spatial structure, viral and cellular interactors, and the mechanisms underlying the unique biological functions of IAV NS1 and SARS-CoV-2 Nsp1 in infected host cells. We also highlight the role of both non-structural proteins in modulating viral replication and pathogenicity. Eventually, and because of their important role during viral infection, we also describe their promising potential as targets for antiviral therapy and the development of live attenuated vaccines (LAV). Conclusively, both IAV NS1 and SARS-CoV-2 Nsp1 play an important role in virus-host interactions, viral replication, and pathogenesis, and pave the way to develop novel prophylactic and/or therapeutic interventions for the treatment of these important human respiratory viral pathogens.
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Affiliation(s)
- Ahmed Magdy Khalil
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Aitor Nogales
- Center for Animal Health Research, CISA-INIA-CSIC, Madrid, Spain
| | - Luis Martínez-Sobrido
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ahmed Mostafa
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
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Cellular PSMB4 Protein Suppresses Influenza A Virus Replication through Targeting NS1 Protein. Viruses 2022; 14:v14102277. [DOI: 10.3390/v14102277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
The nonstructural protein 1 (NS1) of influenza A virus (IAV) possesses multiple functions, such as the inhibition of the host antiviral immune responses, to facilitate viral infection. To search for cellular proteins interacting with the IAV NS1 protein, the yeast two-hybrid system was adopted. Proteasome family member PSMB4 (proteasome subunit beta type 4) was found to interact with the NS1 protein in this screening experiment. The binding domains of these two proteins were also determined using this system. The physical interactions between the NS1 and cellular PSMB4 proteins were further confirmed by co-immunoprecipitation assay and confocal microscopy in mammalian cells. Neither transiently nor stably expressed NS1 protein affected the PSMB4 expression in cells. In contrast, PSMB4 reduced the NS1 protein expression level, especially in the presence of MG132. As expected, the functions of the NS1 protein, such as inhibition of interferon activity and enhancement of transient gene expression, were suppressed by PSMB4. PSMB4 knockdown enhances IAV replication, while its overexpression attenuates IAV replication. Thus, the results of this study suggest that the cellular PSMB4 protein interacts with and possibly facilitates the degradation of the NS1 protein, which in turn suppresses IAV replication.
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Huang CH, Lei KF. Cell marathon: long-distance cell migration and metastasis-associated gene analysis using a folding paper system. LAB ON A CHIP 2022; 22:3827-3836. [PMID: 36093980 DOI: 10.1039/d2lc00663d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A high mortality rate was found in cancer patients with distant metastasis. Development of targeted drugs for effectively inhibiting cancer metastasis is the key for increasing therapeutic success. In the current study, a folding paper system was developed to mimic a tumor-vascular interface for the study of long-distance cell migration. Correlation between the cell migration distance and metastasis-associated gene was successfully analyzed by disassembling the stacked paper construct. The result revealed that the migration distance and number of migrated cells were highly correlated to cell characteristics. Moreover, immunocytochemistry was directly conducted on the paper layer to study the signaling pathway. Kelch-like and protein tyrosine phosphatase families were examined and the PTPN13 gene was shown to regulate long-distance cell migration. By analyzing the phosphorylated mTOR, the PTPN13 gene was further confirmed to be a tumor suppressor gene that inhibits long-distance cell migration. The folding paper system provides an alternative approach for long-distance cell migration. Metastasis-associated gene expression can be analyzed to potentially develop targeted drugs for cancer metastasis inhibition.
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Affiliation(s)
- Chia-Hao Huang
- Department of Biomedical Engineering, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333 Taiwan.
| | - Kin Fong Lei
- Department of Biomedical Engineering, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333 Taiwan.
- Department of Radiation Oncology, Chang Gung Memorial Hospital, Linkou, Taiwan
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Kim I, Dubrow A, Zuniga B, Zhao B, Sherer N, Bastiray A, Li P, Cho JH. Energy landscape reshaped by strain-specific mutations underlies epistasis in NS1 evolution of influenza A virus. Nat Commun 2022; 13:5775. [PMID: 36182933 PMCID: PMC9526705 DOI: 10.1038/s41467-022-33554-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022] Open
Abstract
Elucidating how individual mutations affect the protein energy landscape is crucial for understanding how proteins evolve. However, predicting mutational effects remains challenging because of epistasis—the nonadditive interactions between mutations. Here, we investigate the biophysical mechanism of strain-specific epistasis in the nonstructural protein 1 (NS1) of influenza A viruses (IAVs). We integrate structural, kinetic, thermodynamic, and conformational dynamics analyses of four NS1s of influenza strains that emerged between 1918 and 2004. Although functionally near-neutral, strain-specific NS1 mutations exhibit long-range epistatic interactions with residues at the p85β-binding interface. We reveal that strain-specific mutations reshaped the NS1 energy landscape during evolution. Using NMR spin dynamics, we find that the strain-specific mutations altered the conformational dynamics of the hidden network of tightly packed residues, underlying the evolution of long-range epistasis. This work shows how near-neutral mutations silently alter the biophysical energy landscapes, resulting in diverse background effects during molecular evolution. Influenza A virus (IAV) nonstructural protein 1 (NS1) is a multifunctional virulence factor that interacts with several host factors such as phosphatidylinositol-3-kinase (PI3K). NS1 binds specifically to the p85β regulatory subunit of PI3K and subsequently activates PI3K signaling. Here, Kim et al. show that functionally near-neutral, strain-specific NS1 mutations lead to variations in binding kinetics to p85β exhibit long-range epistatic interactions. Applying NMR they provide evidence that the structural dynamics of the NS1 hydrophobic core have evolved over time and contributed to epistasis.
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Affiliation(s)
- Iktae Kim
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Alyssa Dubrow
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Bryan Zuniga
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Baoyu Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Noah Sherer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Abhishek Bastiray
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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Chung YT, Kuan CY, Liao GR, Albrecht RA, Tseng YY, Hsu YC, Ou SC, Hsu WL. A variant NS1 protein from H5N2 avian influenza virus suppresses PKR activation and promotes replication and virulence in mammals. Emerg Microbes Infect 2022; 11:2291-2303. [PMID: 35979918 PMCID: PMC9559317 DOI: 10.1080/22221751.2022.2114853] [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: 12/04/2022]
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) frequently receive global attention as threats to public health. The NS1 protein is a key virulence factor known to impair host antiviral responses. The study herein revealed HPAIV H5N2 NS gene encoded additional protein; a truncated NS1 variant, designated NS3, produced by alternative splicing of the NS transcript. To examine the function of NS3 during infection, we generated recombinant viruses expressing either full-length NS1 (RG-AIV-T375G) or NS3 (RG-AIV-NS3). Interestingly, RG-AIV-NS3 virus produced higher titres than RG-AIV-T375G in multiple mammalian cell lines. However, RG-AIV-T375G exhibited a replication advantage over RG-AIV-NS3 in chicken DF-1 cells, indicating that host cell identity dictates the effect of NS3 on viral replication. In mice and mammalian cells, RG-AIV-NS3 infection elicited higher level of cytokines, including IFN-β, MX and TNF-α, potentially due to its higher replication activity. Based on mini-genome assay, NS3 had pronounced effects on viral replication machinery. Surprisingly, NS3 retained an interaction with PKR and suppressed PKR activation despite its lack of amino-acid residues 126-167. The poor replication ability of RG-AIV-T375G was partially restored in cells deficient in PKR suggesting that full-length NS1 may be insufficient to suppress PKR function. Notably, virulence of the full-length NS1-expressing RG-AIV-T375G virus was highly attenuated in mice when compared to RG-AIV-NS3. In summary, our study reveals the existence and function of a previously unidentified H5N2 viral protein, NS3. We found that NS3 is functionally distinct from NS1 protein, as it enhances viral replication and pathogenicity in mammalian systems, potentially via suppression of PKR activity.
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Affiliation(s)
- Yun-Ting Chung
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Ying Kuan
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Guan-Ru Liao
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Randy A Albrecht
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yeu-Yang Tseng
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Yu-Chen Hsu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Shan-Chia Ou
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
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Interactome Profiling of N-Terminus-Truncated NS1 Protein of Influenza A Virus Reveals Role of 14-3-3γ in Virus Replication. Pathogens 2022; 11:pathogens11070733. [PMID: 35889979 PMCID: PMC9321973 DOI: 10.3390/pathogens11070733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 12/03/2022] Open
Abstract
Influenza A virus is transmitted through a respiratory route and has caused several pandemics throughout history. The NS1 protein of influenza A virus, which consists of an N-terminal RNA-binding domain and a C-terminal effector domain, is considered one of the critical virulence factors during influenza A virus infection because the viral protein can downregulate the antiviral response of the host cell and facilitate viral replication. Our previous study identified an N-terminus-truncated NS1 protein that covers the C-terminus effector domain. To comprehensively explore the role of the truncated NS1 in cells, we conducted immunoprecipitation coupled with LC-MS/MS to identify its interacting cellular proteins. There were 46 cellular proteins identified as the components of the truncated NS1 protein complex. As for our previous results for the identification of the full-length NS1-interacting host proteins, we discovered that the truncated NS1 protein interacts with the γ isoform of the 14-3-3 protein family. In addition, we found that the knockdown of 14-3-3γ in host cells reduced the replication of the influenza A/PR8 wild-type virus but not that of the PR8-NS1/1-98 mutant virus, which lacks most of the effector domain of NS1. This research highlights the role of 14-3-3γ, which interacts with the effector domain of NS1 protein, in influenza A viral replication.
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Hu Y, Pan Q, Zhou K, Ling Y, Wang H, Li Y. RUNX1 inhibits the antiviral immune response against influenza A virus through attenuating type I interferon signaling. Virol J 2022; 19:39. [PMID: 35248104 PMCID: PMC8897766 DOI: 10.1186/s12985-022-01764-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background Influenza A viruses (IAVs) are zoonotic, segmented negative-stranded RNA viruses. The rapid mutation of IAVs results in host immune response escape and antiviral drug and vaccine resistance. RUNX1 is a transcription factor that not only plays essential roles in hematopoiesis, but also functions as a regulator in inflammation. However, its role in the innate immunity to IAV infection has not been well studied. Methods To investigate the effects of RUNX1 on IAV infection and explore the mechanisms that RUNX1 uses during IAV infection. We infected the human alveolar epithelial cell line (A549) with influenza virus A/Puerto Rico/8/34 (H1N1) (PR8) and examined RUNX1 expression by Western blot and qRT-PCR. We also knocked down or overexpressed RUNX1 in A549 cells, then evaluated viral replication by Western blot, qRT-PCR, and viral titration. Results We found RUNX1 expression is induced by IAV H1N1 PR8 infection, but not by poly(I:C) treatment, in the human alveolar epithelial cell line A549. Knockdown of RUNX1 significantly inhibited IAV infection. Conversely, overexpression of RUNX1 efficiently promoted production of progeny viruses. Additionally, RUNX1 knockdown increased IFN-β and ISGs production while RUNX1 overexpression compromised IFN-β and ISGs production upon PR8 infection in A549 cells. We further showed that RUNX1 may attenuate the interferon signaling transduction by hampering the expression of IRF3 and STAT1 during IAV infection. Conclusions Taken together, we found RUNX1 attenuates type I interferon signaling to facilitate IAV infection in A549 cells.
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Abstract
Influenza A virus has long been known to encode 10 major polypeptides, produced, almost without exception, by every natural isolate of the virus. These polypeptides are expressed in readily detectable amounts during infection and are either fully essential or their loss severely attenuates virus replication. More recent work has shown that this core proteome is elaborated by expression of a suite of accessory gene products that tend to be expressed at lower levels through noncanonical transcriptional and/or translational events. Expression and activity of these accessory proteins varies between virus strains and is nonessential (sometimes inconsequential) for virus replication in cell culture, but in many cases has been shown to affect virulence and/or transmission in vivo. This review describes, when known, the expression mechanisms and functions of this influenza A virus accessory proteome and discusses its significance and evolution.
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Affiliation(s)
- Rute M Pinto
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Eleanor Gaunt
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Paul Digard
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
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9
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How Influenza A Virus NS1 Deals with the Ubiquitin System to Evade Innate Immunity. Viruses 2021; 13:v13112309. [PMID: 34835115 PMCID: PMC8619935 DOI: 10.3390/v13112309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/14/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
Ubiquitination is a post-translational modification regulating critical cellular processes such as protein degradation, trafficking and signaling pathways, including activation of the innate immune response. Therefore, viruses, and particularly influenza A virus (IAV), have evolved different mechanisms to counteract this system to perform proper infection. Among IAV proteins, the non-structural protein NS1 is shown to be one of the main virulence factors involved in these viral hijackings. NS1 is notably able to inhibit the host's antiviral response through the perturbation of ubiquitination in different ways, as discussed in this review.
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10
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Rathnasinghe R, Salvatore M, Zheng H, Jangra S, Kehrer T, Mena I, Schotsaert M, Muster T, Palese P, García-Sastre A. Interferon mediated prophylactic protection against respiratory viruses conferred by a prototype live attenuated influenza virus vaccine lacking non-structural protein 1. Sci Rep 2021; 11:22164. [PMID: 34773048 PMCID: PMC8589955 DOI: 10.1038/s41598-021-01780-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/19/2021] [Indexed: 12/29/2022] Open
Abstract
The influenza A non-structural protein 1 (NS1) is known for its ability to hinder the synthesis of type I interferon (IFN) during viral infection. Influenza viruses lacking NS1 (ΔNS1) are under clinical development as live attenuated human influenza virus vaccines and induce potent influenza virus-specific humoral and cellular adaptive immune responses. Attenuation of ΔNS1 influenza viruses is due to their high IFN inducing properties, that limit their replication in vivo. This study demonstrates that pre-treatment with a ΔNS1 virus results in an antiviral state which prevents subsequent replication of homologous and heterologous viruses, preventing disease from virus respiratory pathogens, including SARS-CoV-2. Our studies suggest that ΔNS1 influenza viruses could be used for the prophylaxis of influenza, SARS-CoV-2 and other human respiratory viral infections, and that an influenza virus vaccine based on ΔNS1 live attenuated viruses would confer broad protection against influenza virus infection from the moment of administration, first by non-specific innate immune induction, followed by specific adaptive immunity.
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Affiliation(s)
- Raveen Rathnasinghe
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 100229 USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Mirella Salvatore
- grid.5386.8000000041936877XDepartment of Medicine, Weill Cornell Medical College, New York, NY USA
| | - Hongyong Zheng
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 100229 USA
| | - Sonia Jangra
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 100229 USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Thomas Kehrer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 100229 USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Ignacio Mena
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 100229 USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Michael Schotsaert
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 100229 USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Thomas Muster
- grid.22937.3d0000 0000 9259 8492Department of Dermatology, University of Vienna Medical School, 1090 Wien, Austria
| | - Peter Palese
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY 100229 USA ,grid.59734.3c0000 0001 0670 2351Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, NY, 100229, USA. .,Global Health and Emerging Pathogens Institute, 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. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Chathuranga K, Weerawardhana A, Dodantenna N, Lee JS. Regulation of antiviral innate immune signaling and viral evasion following viral genome sensing. Exp Mol Med 2021; 53:1647-1668. [PMID: 34782737 PMCID: PMC8592830 DOI: 10.1038/s12276-021-00691-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/15/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
A harmonized balance between positive and negative regulation of pattern recognition receptor (PRR)-initiated immune responses is required to achieve the most favorable outcome for the host. This balance is crucial because it must not only ensure activation of the first line of defense against viral infection but also prevent inappropriate immune activation, which results in autoimmune diseases. Recent studies have shown how signal transduction pathways initiated by PRRs are positively and negatively regulated by diverse modulators to maintain host immune homeostasis. However, viruses have developed strategies to subvert the host antiviral response and establish infection. Viruses have evolved numerous genes encoding immunomodulatory proteins that antagonize the host immune system. This review focuses on the current state of knowledge regarding key host factors that regulate innate immune signaling molecules upon viral infection and discusses evidence showing how specific viral proteins counteract antiviral responses via immunomodulatory strategies.
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Affiliation(s)
- Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Korea
| | - Asela Weerawardhana
- College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Korea
| | - Niranjan Dodantenna
- College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Korea
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Korea.
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Tam EH, Liu YC, Woung CH, Liu HM, Wu GH, Wu CC, Kuo RL. Role of the Chaperone Protein 14-3-3ε in the Regulation of Influenza A Virus-Activated Beta Interferon. J Virol 2021; 95:e0023121. [PMID: 34379499 PMCID: PMC8475545 DOI: 10.1128/jvi.00231-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
The NS1 protein of the influenza A virus plays a critical role in regulating several biological processes in cells, including the type I interferon (IFN) response. We previously profiled the cellular factors that interact with the NS1 protein of influenza A virus and found that the NS1 protein interacts with proteins involved in RNA splicing/processing, cell cycle regulation, and protein targeting processes, including 14-3-3ε. Since 14-3-3ε plays an important role in retinoic acid-inducible gene I (RIG-I) translocation to mitochondrial antiviral-signaling protein (MAVS) to activate type I IFN expression, the interaction of the NS1 and 14-3-3ε proteins may prevent the RIG-I-mediated IFN response. In this study, we confirmed that the 14-3-3ε protein interacts with the N-terminal domain of the NS1 protein and that the NS1 protein inhibits RIG-I-mediated IFN-β promoter activation in 14-3-3ε-overexpressing cells. In addition, our results showed that knocking down 14-3-3ε can reduce IFN-β expression elicited by influenza A virus and enhance viral replication. Furthermore, we found that threonine in the 49th amino acid position of the NS1 protein plays a role in the interaction with 14-3-3ε. Influenza A virus expressing C terminus-truncated NS1 with a T49A mutation dramatically increases IFN-β mRNA in infected cells and causes slower replication than that of virus without the T-to-A mutation. Collectively, this study demonstrates that 14-3-3ε is involved in influenza A virus-initiated IFN-β expression and that the interaction of the NS1 protein and 14-3-3ε may be one of the mechanisms for inhibiting type I IFN activation during influenza A virus infection. IMPORTANCE Influenza A virus is an important human pathogen causing severe respiratory disease. The virus has evolved several strategies to dysregulate the innate immune response and facilitate its replication. We demonstrate that the NS1 protein of influenza A virus interacts with the cellular chaperone protein 14-3-3ε, which plays a critical role in retinoic acid-inducible gene I (RIG-I) translocation that induces type I interferon (IFN) expression, and that NS1 protein prevents RIG-I translocation to the mitochondrial membrane. The interaction site for 14-3-3ε is the RNA-binding domain (RBD) of the NS1 protein. Therefore, this research elucidates a novel mechanism by which the NS1 RBD mediates IFN-β suppression to facilitate influenza A viral replication. Additionally, the findings reveal the antiviral role of 14-3-3ε during influenza A virus infection.
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Affiliation(s)
- Ee-Hong Tam
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yen-Chin Liu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chian-Huey Woung
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Helene Minyi Liu
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Guan-Hong Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Rei-Lin Kuo
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taiwan
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13
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Rathnasinghe R, Salvatore M, Zheng H, Jangra S, Kehrer T, Mena I, Schotsaert M, Muster T, Palese P, García-Sastre A. Prophylactic protection against respiratory viruses conferred by a prototype live attenuated influenza virus vaccine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.28.441797. [PMID: 33948589 PMCID: PMC8095196 DOI: 10.1101/2021.04.28.441797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The influenza A non-structural protein 1 (NS1) is known for its ability to hinder the synthesis of type I interferon (IFN) during viral infection. Influenza viruses lacking NS1 (ΔNS1) are under clinical development as live attenuated human influenza virus vaccines and induce potent influenza virus-specific humoral and cellular adaptive immune responses. Attenuation of ΔNS1 influenza viruses is due to their high IFN inducing properties, that limit their replication in vivo. This study demonstrates that pre-treatment with a ΔNS1 virus results in an immediate antiviral state which prevents subsequent replication of homologous and heterologous viruses, preventing disease from virus respiratory pathogens, including SARS-CoV-2. Our studies suggest that ΔNS1 influenza viruses could be used for the prophylaxis of influenza, SARS-CoV-2 and other human respiratory viral infections, and that an influenza virus vaccine based on ΔNS1 live attenuated viruses would confer broad protection against influenza virus infection from the moment of administration, first by non-specific innate immune induction, followed by specific adaptive immunity.
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14
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Lei KF, Ho YC, Huang CH, Huang CH, Pai PC. Characterization of stem cell-like property in cancer cells based on single-cell impedance measurement in a microfluidic platform. Talanta 2021; 229:122259. [PMID: 33838770 DOI: 10.1016/j.talanta.2021.122259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/01/2021] [Accepted: 02/24/2021] [Indexed: 11/20/2022]
Abstract
Investigation of stem cell-like property in cancer cells is important for the development of new therapeutic drugs targeting at malignant tumors. Currently, the standard approach for identifying cancer stem cell-like cells relies on the recognition of stem cell surface markers. However, the reliability remains controversial among biologists. In the current work, a dielectrophoretic and impedimetric hybrid microfluidic platform was developed for capturing single cells and characterizing their stem cell-like property. Single cells were captured in 20 μm trapping wells by dielectrophoretic force and their impedance spectra were measured by an impedance analyzer. The result showed that different cancer cell lines could be differentiated by impedance magnitude ranging between 2 and 20 kHz. Moreover, cancer cells and cancer stem cell-like cells could be categorized by a 2-dimensional graph of the impedance magnitudes at 2 and 20 kHz. The stem cell-like property in cancer cells was verified by stem cell surface markers and single-cell derived colony assay. Comparing with bio-chemical approach, i.e., surface markers, bio-physical approach, i.e., cell impedance, is a label-free technique to identify cancer stem cell-like cells.
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Affiliation(s)
- Kin Fong Lei
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan; Department of Radiation Oncology, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Yu-Chen Ho
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Hao Huang
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Hao Huang
- PhD Program in Biomedical Engineering, College of Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Ping Ching Pai
- Department of Radiation Oncology, Chang Gung Memorial Hospital, Linkou, Taiwan
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15
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Huang CH, Lei KF. Impedimetric quantification of migration speed of cancer cells migrating along a Matrigel-filled microchannel. Anal Chim Acta 2020; 1121:67-73. [DOI: 10.1016/j.aca.2020.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/29/2020] [Accepted: 05/03/2020] [Indexed: 12/21/2022]
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16
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Wang WC, Kuan CY, Tseng YJ, Chang CH, Liu YC, Chang YC, Hsu YC, Hsieh MK, Ou SC, Hsu WL. The Impacts of Reassortant Avian Influenza H5N2 Virus NS1 Proteins on Viral Compatibility and Regulation of Immune Responses. Front Microbiol 2020; 11:280. [PMID: 32226416 PMCID: PMC7080822 DOI: 10.3389/fmicb.2020.00280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/06/2020] [Indexed: 11/25/2022] Open
Abstract
Avian influenza virus (AIV) can cause severe diseases in poultry worldwide. H6N1 AIV was the dominant enzootic subtype in 1985 in the chicken farms of Taiwan until the initial outbreak of a low pathogenic avian influenza (LPAI) H5N2 virus in 2003; thereafter, this and other LPAIs have been sporadically detected. In 2015, the outbreak of three novel H5Nx viruses of highly pathogenic avian influenza (HPAI) emerged and devastated Taiwanese chicken and waterfowl industries. The mechanism of variation in pathogenicity among these viruses is unclear; but, in light of the many biological functions of viral non-structural protein 1 (NS1), including interferon (IFN) antagonist and host range determinant, we hypothesized that NS genetic diversity contributes to AIV pathogenesis. To determine the impact of NS1 variants on viral infection dynamics, we established a reverse genetics system with the genetic backbone of the enzootic Taiwanese H6N1 for generation of reassortant AIVs carrying exogenous NS segments of three different Taiwanese H5N2 strains. We observed distinct cellular distributions of NS1 among the reassortant viruses. Moreover, exchange of the NS segment significantly influenced growth kinetics and induction of cytokines [IFN-α, IFN-β, and tumor necrosis factor alpha (TNF-α)] in an NS1- and host-specific manner. The impact of NS1 variants on viral replication appears related to their synergic effects on viral RNA-dependent RNA polymerase activity and IFN response. With these approaches, we revealed that NS1 is a key factor responsible for the diverse characteristics of AIVs in Taiwan.
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Affiliation(s)
- Wen-Chien Wang
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Ying Kuan
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Jing Tseng
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Hsuan Chang
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yee-Chen Liu
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chih Chang
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chen Hsu
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Ming-Kun Hsieh
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Shan-Chia Ou
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
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17
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Goh A, Yeh CC, Lei KF. Visualization and Quantification of 3D Tumor Cell Migration under Extracellular Stimulation. ACS APPLIED BIO MATERIALS 2020; 3:1506-1513. [DOI: 10.1021/acsabm.9b01134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrew Goh
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Chih Yeh
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Kin Fong Lei
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan
- Department of Radiation Oncology, Chang Gung Memorial Hospital, Linkou, Taiwan
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18
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Li YH, Hu CY, Wu NP, Yao HP, Li LJ. Molecular Characteristics, Functions, and Related Pathogenicity of MERS-CoV Proteins. ENGINEERING (BEIJING, CHINA) 2019; 5:940-947. [PMID: 32288963 PMCID: PMC7104727 DOI: 10.1016/j.eng.2018.11.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/24/2018] [Accepted: 11/12/2018] [Indexed: 05/02/2023]
Abstract
Middle East respiratory syndrome (MERS) is a viral respiratory disease caused by a de novo coronavirus-MERS-CoV-that is associated with high mortality. However, the mechanism by which MERS-CoV infects humans remains unclear. To date, there is no effective vaccine or antibody for human immunity and treatment, other than the safety and tolerability of the fully human polyclonal Immunoglobulin G (IgG) antibody (SAB-301) as a putative therapeutic agent specific for MERS. Although rapid diagnostic and public health measures are currently being implemented, new cases of MERS-CoV infection are still being reported. Therefore, various effective measures should be taken to prevent the serious impact of similar epidemics in the future. Further investigation of the epidemiology and pathogenesis of the virus, as well as the development of effective therapeutic and prophylactic anti-MERS-CoV infections, is necessary. For this purpose, detailed information on MERS-CoV proteins is needed. In this review, we describe the major structural and nonstructural proteins of MERS-CoV and summarize different potential strategies for limiting the outbreak of MERS-CoV. The combination of computational biology and virology can accelerate the advanced design and development of effective peptide therapeutics against MERS-CoV. In summary, this review provides important information about the progress of the elimination of MERS, from prevention to treatment.
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Affiliation(s)
- Yan-Hua Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
| | - Chen-Yu Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
| | - Nan-Ping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
| | - Lan-Juan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 31003, China
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19
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Dawson WK, Lazniewski M, Plewczynski D. RNA structure interactions and ribonucleoprotein processes of the influenza A virus. Brief Funct Genomics 2019; 17:402-414. [PMID: 29040388 PMCID: PMC6252904 DOI: 10.1093/bfgp/elx028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In one more years, we will ‘celebrate’ an exact centenary of the Spanish flu pandemic. With the rapid evolution of the influenza virus, the possibility of novel pandemic remains ever a concern. This review covers our current knowledge of the influenza A virus: on the role of RNA in translation, replication, what is known of the expressed proteins and the protein products generated from alternative splicing, and on the role of base pairing in RNA structure. We highlight the main events associated with viral entry into the cell, the transcription and replication process, an export of the viral genetic material from the nucleus and the final release of the virus. We discuss the observed potential roles of RNA secondary structure (the RNA base-pairing arrangement) and RNA/RNA interactions in this scheme.
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Affiliation(s)
- Wayne K Dawson
- Bio-information Lab, University of Tokyo.,University of Warsaw, Center of New Technologies (CeNT), Warsaw, Poland
| | - Michal Lazniewski
- University of Warsaw, Center of New Technologies (CeNT), Warsaw, Poland
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20
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Trigueiro-Louro JM, Correia V, Santos LA, Guedes RC, Brito RMM, Rebelo-de-Andrade H. To hit or not to hit: Large-scale sequence analysis and structure characterization of influenza A NS1 unlocks new antiviral target potential. Virology 2019; 535:297-307. [PMID: 31104825 DOI: 10.1016/j.virol.2019.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/13/2022]
Abstract
Influenza NS1 protein is among the most promising novel druggable anti-influenza target, based on its structure; multiple interactions; and global function in influenza replication and pathogenesis. Notwithstanding, drug development guidance based on NS1 structural biology is lacking. Here, we design a promising strategy directed to highly conserved druggable regions as a result of an exhaustive large-scale sequence analysis and structure characterization of NS1 protein across human-infecting influenza A subtypes, over the past 100 years. We have identified 3 druggable pockets and 8 new potential hot spot residues in the NS1 protein, not described before, additionally to other 16 sites previously identified, which represent attractive targets for pharmacological modulation. This study provides a rationale towards structure-function studies of NS1 druggable sites, which have the potential to accelerate the NS1 target validation. This research also contributes to a deeper comprehension and insight into the evolutionary dynamics of influenza A NS1 protein.
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Affiliation(s)
- João M Trigueiro-Louro
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Vanessa Correia
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Luís A Santos
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Rita C Guedes
- Medicinal Chemistry Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal
| | - Rui M M Brito
- Chemistry Department and Coimbra Chemistry Centre, Faculty of Science and Technology, University of Coimbra, 3004-535, Coimbra, Portugal
| | - Helena Rebelo-de-Andrade
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
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21
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Proliferation arrest, selectivity, and chemosensitivity enhancement of cancer cells treated by a low-intensity alternating electric field. Biomed Microdevices 2018; 20:90. [DOI: 10.1007/s10544-018-0339-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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22
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Tombácz D, Balázs Z, Csabai Z, Snyder M, Boldogkői Z. Long-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses. Front Genet 2018; 9:259. [PMID: 30065753 PMCID: PMC6056645 DOI: 10.3389/fgene.2018.00259] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/27/2018] [Indexed: 12/28/2022] Open
Abstract
Long-read sequencing (LRS) techniques are very recent advancements, but they have already been used for transcriptome research in all of the three subfamilies of herpesviruses. These techniques have multiplied the number of known transcripts in each of the examined viruses. Meanwhile, they have revealed a so far hidden complexity of the herpesvirus transcriptome with the discovery of a large number of novel RNA molecules, including coding and non-coding RNAs, as well as transcript isoforms, and polycistronic RNAs. Additionally, LRS techniques have uncovered an intricate meshwork of transcriptional overlaps between adjacent and distally located genes. Here, we review the contribution of LRS to herpesvirus transcriptomics and present the complexity revealed by this technology, while also discussing the functional significance of this phenomenon.
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Affiliation(s)
- Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, United States
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
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23
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Zheng J, Perlman S. Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host. Curr Opin Virol 2018; 28:43-52. [PMID: 29172107 PMCID: PMC5835172 DOI: 10.1016/j.coviro.2017.11.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/02/2017] [Indexed: 12/25/2022]
Abstract
Respiratory viruses, especially influenza A viruses and coronaviruses such as MERS-CoV, represent continuing global threats to human health. Despite significant advances, much needs to be learned. Recent studies in virology and immunology have improved our understanding of the role of the immune system in protection and in the pathogenesis of these infections and of co-evolution of viruses and their hosts. These findings, together with sophisticated molecular structure analyses, omics tools and computer-based models, have helped delineate the interaction between respiratory viruses and the host immune system, which will facilitate the development of novel treatment strategies and vaccines with enhanced efficacy.
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Affiliation(s)
- Jian Zheng
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, United States
| | - Stanley Perlman
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, United States.
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24
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Chang CK, Chen CJ, Wu CC, Chen SW, Shih SR, Kuo RL. Cellular hnRNP A2/B1 interacts with the NP of influenza A virus and impacts viral replication. PLoS One 2017; 12:e0188214. [PMID: 29145464 PMCID: PMC5690641 DOI: 10.1371/journal.pone.0188214] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/02/2017] [Indexed: 12/23/2022] Open
Abstract
The viral ribonucleoprotein (vRNP) of influenza A virus is formed by virion RNA (vRNA), viral polymerase complex, and nucleoprotein (NP). The NP plays an important role in facilitating the replication and stabilization of viral RNA. To explore host factors that may be involved in the regulation of viral replication through interactions with NP, we conducted an immunoprecipitation experiment followed by mass spectrometry to identify NP-associated cellular proteins. Here, we demonstrate that NP can interact and colocalize with heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 in mammalian cells and that the interaction may occur via direct binding to the glycine-rich domain (GRD) of hnRNP A2/B1. In addition, two residues in the tail loop of NP, F412 and R422, are required for the interaction of hnRNP A2/B1. Because the knockdown of hnRNP A2/B1 expression reduces viral RNP activity, hnRNP A2/B1 may act as a positive regulator in viral RNA synthesis of influenza A virus. More importantly, the findings in this research demonstrate that host proteins can regulate the replication of influenza A virus by interacting with NP.
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Affiliation(s)
- Cheng-Kai Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Jene Chen
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
- Research Center for Emerging Viruses, China Medical University Hospital, Taichung, Taiwan
| | - Chih-Ching Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Shiau-Wen Chen
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Shin-Ru Shih
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Clinical Virology Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
- * E-mail: (SRS); (RLK)
| | - Rei-Lin Kuo
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
- * E-mail: (SRS); (RLK)
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25
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Meyerson NR, Zhou L, Guo YR, Zhao C, Tao YJ, Krug RM, Sawyer SL. Nuclear TRIM25 Specifically Targets Influenza Virus Ribonucleoproteins to Block the Onset of RNA Chain Elongation. Cell Host Microbe 2017; 22:627-638.e7. [PMID: 29107643 PMCID: PMC6309188 DOI: 10.1016/j.chom.2017.10.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 07/21/2017] [Accepted: 09/26/2017] [Indexed: 11/20/2022]
Abstract
TRIM25 is an E3 ubiquitin ligase that activates RIG-I to promote the antiviral interferon response. The NS1 protein from all strains of influenza A virus binds TRIM25, although not all virus strains block the interferon response, suggesting alternative mechanisms for TRIM25 action. Here we present a nuclear role for TRIM25 in specifically restricting influenza A virus replication. TRIM25 inhibits viral RNA synthesis through a direct mechanism that is independent of its ubiquitin ligase activity and the interferon pathway. This activity can be inhibited by the viral NS1 protein. TRIM25 inhibition of viral RNA synthesis results from its binding to viral ribonucleoproteins (vRNPs), the structures containing individual viral RNA segments, the viral polymerase, and multiple viral nucleoproteins. TRIM25 binding does not inhibit initiation of capped-RNA-primed viral mRNA synthesis by the viral polymerase. Rather, the onset of RNA chain elongation is inhibited because TRIM25 prohibits the movement of RNA into the polymerase complex.
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Affiliation(s)
- Nicholas R Meyerson
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Ligang Zhou
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA
| | - Yusong R Guo
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Chen Zhao
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA
| | - Yizhi J Tao
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Robert M Krug
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA.
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA.
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26
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Tsai CF, Lin HY, Hsu WL, Tsai CH. The novel mitochondria localization of influenza A virus NS1 visualized by FlAsH labeling. FEBS Open Bio 2017; 7:1960-1971. [PMID: 29226082 PMCID: PMC5715299 DOI: 10.1002/2211-5463.12336] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 12/11/2022] Open
Abstract
The nonstructural protein 1 (NS1) of the influenza A virus (IAV) is a multifunctional protein that counteracts host cell antiviral responses and inhibits host cell pre‐mRNA processing. NS1 contains two nuclear localization signals that facilitate NS1 shuttling between cytoplasm and nucleus. In this study, we initially observed the novel mitochondria localization of NS1 in a subset of transfected cells. We then further monitored the localization dynamics of the NS1 protein in live cells infected with IAV expressing NS1 with insertion of a tetracysteine‐tag. The resulting mutant virus showed similar levels of infectivity and expression pattern of NS1 to those of wild‐type IAV. Pulse labeling using a biarsenical compound (fluorescein arsenical hairpin binder) allowed us to visualize the dynamic subcellular distribution of NS1 real time. We detected NS1 in mitochondria at a very early infection time point [1.5 h postinfection (hpi)] and observed the formation of a granular structure pattern in the nucleus at 4 hpi. This is the first identification of the novel mitochondria localization of NS1. The possible role of NS1 at an early infection time point is discussed.
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Affiliation(s)
- Chuan-Fu Tsai
- Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan
| | - Hsin-Yi Lin
- Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health National Chung Hsing University Taichung Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan
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27
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Yi C, Zhao Z, Wang S, Sun X, Zhang D, Sun X, Zhang A, Jin M. Influenza A Virus PA Antagonizes Interferon-β by Interacting with Interferon Regulatory Factor 3. Front Immunol 2017; 8:1051. [PMID: 28955326 PMCID: PMC5600993 DOI: 10.3389/fimmu.2017.01051] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 08/14/2017] [Indexed: 01/07/2023] Open
Abstract
The influenza A virus (IAV) can be recognized by retinoic acid-inducible gene I (RIG-I) to activate the type I interferon response and induce antiviral effects. The virus has evolved several strategies to evade the innate immune response, including non-structural protein 1 (NS1) and its polymerase subunits. The mechanism by which NS1 inhibits interferon-β (IFN-β) is well understood, whereas the mechanism by which polymerase acid protein (PA) inhibits IFN-β remains to be elucidated. In this study, we observed that the IAV PA protein could inhibit the production of IFN-β and interferon-stimulated genes induced by Sendai virus through interferon regulatory factor 3 (IRF3), but not through nuclear factor-kappaB (NF-kappaB). In addition, PA inhibited IFN-β induction by RIG-I, melanoma differentiation-associated gene 5, mitochondria antiviral signaling protein, TANK-binding kinase 1, inhibitor of nuclear factor kappa-B kinase-ε (IKKε), and IRF3 overexpression. Furthermore, PA interacted with IRF3 to block its activation. The N-terminal endonuclease activity of PA was responsible for its interaction with IRF3 and inhibition of the IFN-β signaling pathway. In summary, our data reveal the mechanism by which IAV PA inhibits the IFN-β signaling pathway, providing a new mechanism by which the virus antagonizes the antiviral signaling pathway.
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Affiliation(s)
- Chenyang Yi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Zongzheng Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Shengyu Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xin Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Dan Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xiaomei Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Anding Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
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28
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Qian W, Wei X, Guo K, Li Y, Lin X, Zou Z, Zhou H, Jin M. The C-Terminal Effector Domain of Non-Structural Protein 1 of Influenza A Virus Blocks IFN-β Production by Targeting TNF Receptor-Associated Factor 3. Front Immunol 2017; 8:779. [PMID: 28717359 PMCID: PMC5494602 DOI: 10.3389/fimmu.2017.00779] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/19/2017] [Indexed: 12/21/2022] Open
Abstract
Influenza A virus non-structural protein 1 (NS1) antagonizes interferon response through diverse strategies, particularly by inhibiting the activation of interferon regulatory factor 3 (IRF3) and IFN-β transcription. However, the underlying mechanisms used by the NS1 C-terminal effector domain (ED) to inhibit the activation of IFN-β pathway are not well understood. In this study, we used influenza virus subtype of H5N1 to demonstrate that the NS1 C-terminal ED but not the N-terminal RNA-binding domain, binds TNF receptor-associated factor 3 (TRAF3). This results in an attenuation of the type I IFN signaling pathway. We found that the NS1 C-terminal ED (named NS1/126-225) inhibits the active caspase activation and recruitment domain-containing form of RIG-I [RIG-I(N)]-induced IFN-β reporter activity, the phosphorylation of IRF3, and the induction of IFN-β. Further analysis showed that NS1/126-225 binds to TRAF3 through the TRAF domain, subsequently decreasing TRAF3 K63-linked ubiquitination. NS1/126-225 binding also disrupted the formation of the mitochondrial antiviral signaling (MAVS)–TRAF3 complex, increasing the recruitment of IKKε to MAVS; ultimately shutting down the RIG-I(N)-mediated signal transduction and cellular antiviral responses. This attenuation of cellular antiviral responses leads to evasion of the innate immune response. Taken together, our findings offer an important insight into the interplay between the influenza virus and host innate immunity.
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Affiliation(s)
- Wei Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaoqin Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, China.,College of Agricultural and Animal Husbandry, Tibet University, Linzhi, China
| | - Kelei Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yongtao Li
- College of Animal Husbandry & Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Xian Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhong Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hongbo Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, China
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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29
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Nacken W, Wixler V, Ehrhardt C, Ludwig S. Influenza A virus NS1 protein-induced JNK activation and apoptosis are not functionally linked. Cell Microbiol 2017; 19. [DOI: 10.1111/cmi.12721] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/03/2017] [Accepted: 01/03/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Wolfgang Nacken
- Institute of Virology (IVM), University Hospital Münster; WWU; Germany
| | - Viktor Wixler
- Institute of Virology (IVM), University Hospital Münster; WWU; Germany
| | - Christina Ehrhardt
- Institute of Virology (IVM), University Hospital Münster; WWU; Germany
- Cluster of Excellence “Cells in Motion”; University of Muenster; Germany
- Interdisciplinary Center of Clinical Research (IZKF), UKM; WWU; Germany
| | - Stephan Ludwig
- Institute of Virology (IVM), University Hospital Münster; WWU; Germany
- Cluster of Excellence “Cells in Motion”; University of Muenster; Germany
- Interdisciplinary Center of Clinical Research (IZKF), UKM; WWU; Germany
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30
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Amarelle L, Lecuona E, Sznajder JI. Anti-Influenza Treatment: Drugs Currently Used and Under Development. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.arbr.2016.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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31
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Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH. Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Res 2016; 45:D466-D474. [PMID: 27679478 PMCID: PMC5210613 DOI: 10.1093/nar/gkw857] [Citation(s) in RCA: 233] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/12/2016] [Accepted: 09/16/2016] [Indexed: 12/26/2022] Open
Abstract
The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org.
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Affiliation(s)
- Yun Zhang
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - David F Burke
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Gwenaelle Dauphin
- Animal Health Service, Food and Agriculture Organization of the United Nations, Rome 00153, Italy
| | - Zhiping Gu
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Sherry He
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Sanjeev Kumar
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | | | | | - Xiaomei Li
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Catherine Macken
- Bioinformatics Institute, University of Auckland, Auckland 1010, New Zealand
| | - Colin Mahaffey
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | | | | | - Thomas Smith
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Lucy Stewart
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Guangyu Sun
- Vecna Technologies, Greenbelt, MD 20770, USA
| | - Lei Tong
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - Bryan Walters
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Sam Zaremba
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Hongtao Zhao
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Liwei Zhou
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | | | - Edward B Klem
- Northrop Grumman Health Solutions, Rockville, MD 20850, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA .,Department of Pathology, University of California, San Diego, CA 92093, USA.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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32
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Amarelle L, Lecuona E, Sznajder JI. Anti-Influenza Treatment: Drugs Currently Used and Under Development. Arch Bronconeumol 2016; 53:19-26. [PMID: 27519544 PMCID: PMC6889083 DOI: 10.1016/j.arbres.2016.07.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/24/2016] [Accepted: 07/10/2016] [Indexed: 02/06/2023]
Abstract
La gripe es una enfermedad contagiosa altamente prevalente y con significativa morbimortalidad. El tratamiento disponible con fármacos antivirales, de ser administrado de forma precoz, puede reducir el riesgo de complicaciones severas; sin embargo, muchos tipos de virus desarrollan resistencia a estos fármacos, reduciendo notablemente su efectividad. Ha habido un gran interés en el desarrollo de nuevas opciones terapéuticas para combatir la enfermedad. Una gran variedad de fármacos han demostrado tener actividad antiinfluenza, pero aún no están disponibles para su uso en la clínica. Muchos de ellos tienen como objetivo componentes del virus, mientras que otros son dirigidos a elementos de la célula huésped que participan en el ciclo viral. Modular los componentes del huésped es una estrategia que minimiza el desarrollo de cepas resistentes, dado que estos no están sujetos a la variabilidad genética que tiene el virus. Por otro lado, la principal desventaja es que existe un mayor riesgo de efectos secundarios asociados al tratamiento. El objetivo de la presente revisión es describir los principales agentes farmacológicos disponibles en la actualidad, así como los nuevos fármacos en estudio con potencial beneficio en el tratamiento de la gripe.
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Affiliation(s)
- Luciano Amarelle
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, Estados Unidos de América; Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Emilia Lecuona
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, Estados Unidos de América
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, Estados Unidos de América.
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