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Dugied G, Douche T, Dos Santos M, Giai Gianetto Q Q, Cassonnet C, Vuillier F, Cassonnet P, Jacob Y, van der Werf S, Komarova A, Matondo M, Karim M, Demeret C. Profiling Cullin4-E3 ligases interactomes and their rewiring in influenza A virus infection. Mol Cell Proteomics 2024:100856. [PMID: 39383947 DOI: 10.1016/j.mcpro.2024.100856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 09/11/2024] [Accepted: 10/06/2024] [Indexed: 10/11/2024] Open
Abstract
Understanding the integrated regulation of cellular processes during viral infection is crucial for developing host-targeted approaches. We have previously reported that an optimal in vitro infection by influenza A (IAV) requires three components of Cullin 4-RING E3 ubiquitin ligases (CRL4) complexes, namely the DDB1 adaptor and two Substrate Recognition Factors (SRF), DCAF11 and DCAF12L1, which mediate non-degradative poly-ubiquitination of the PB2 subunit of the viral polymerase. However, the impact of IAV infection on the CRL4 interactome remains elusive. Here, using Affinity Purification coupled with Mass Spectrometry (AP-MS) approaches, we identified cellular proteins interacting with these CRL4 components in IAV-infected and non-infected contexts. IAV infection induces significant modulations in protein interactions, resulting in a global loss of DDB1 and DCAF11 interactions, and an increase in DCAF12L1-associated proteins. The distinct rewiring of CRL4's associations upon infection impacted cellular proteins involved in protein folding, ubiquitination, translation, splicing, and stress responses. Using a split-nanoluciferase-based assay, we identified direct partners of CRL4 components and via siRNA-mediated silencing validated their role in IAV infection, representing potential substrates or regulators of CRL4 complexes. Our findings unravel the dynamic remodeling of the proteomic landscape of CRL4's E3 ubiquitin ligases during IAV infection, likely involved in shaping a cellular environment conducive to viral replication and offer potential for the exploration of future host-targeted antiviral therapeutic strategies.
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Affiliation(s)
- Guillaume Dugied
- Unit of Molecular Genetics of RNA Viruses, Institut Pasteur, Paris, France; Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France
| | - Thibaut Douche
- Institut Pasteur, Proteomics Core Facility, MSBio UtechS, UAR CNRS 2024, Université Paris Cité, Paris, France
| | - Melanie Dos Santos
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France
| | - Quentin Giai Gianetto Q
- Institut Pasteur, Proteomics Core Facility, MSBio UtechS, UAR CNRS 2024, Université Paris Cité, Paris, France; Institut Pasteur, Bioinformatics and Biostatistics Hub, Université Paris Cité, Paris
| | - Camille Cassonnet
- Unit of Molecular Genetics of RNA Viruses, Institut Pasteur, Paris, France
| | - Françoise Vuillier
- Unit of Molecular Genetics of RNA Viruses, Institut Pasteur, Paris, France
| | - Patricia Cassonnet
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France
| | - Yves Jacob
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France
| | - Sylvie van der Werf
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France
| | - Anastassia Komarova
- Unit of Molecular Genetics of RNA Viruses, Institut Pasteur, Paris, France; Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France
| | - Mariette Matondo
- Institut Pasteur, Proteomics Core Facility, MSBio UtechS, UAR CNRS 2024, Université Paris Cité, Paris, France
| | - Marwah Karim
- Unit of Molecular Genetics of RNA Viruses, Institut Pasteur, Paris, France.
| | - Caroline Demeret
- Unit of Molecular Genetics of RNA Viruses, Institut Pasteur, Paris, France; Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France.
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2
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Huang Y, Urban C, Hubel P, Stukalov A, Pichlmair A. Protein turnover regulation is critical for influenza A virus infection. Cell Syst 2024:S2405-4712(24)00268-0. [PMID: 39368468 DOI: 10.1016/j.cels.2024.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 08/16/2024] [Accepted: 09/13/2024] [Indexed: 10/07/2024]
Abstract
The abundance of a protein is defined by its continuous synthesis and degradation, a process known as protein turnover. Here, we systematically profiled the turnover of proteins in influenza A virus (IAV)-infected cells using a pulse-chase stable isotope labeling by amino acids in cell culture (SILAC)-based approach combined with downstream statistical modeling. We identified 1,798 virus-affected proteins with turnover changes (tVAPs) out of 7,739 detected proteins (data available at pulsechase.innatelab.org). In particular, the affected proteins were involved in RNA transcription, splicing and nuclear transport, protein translation and stability, and energy metabolism. Many tVAPs appeared to be known IAV-interacting proteins that regulate virus propagation, such as KPNA6, PPP6C, and POLR2A. Notably, our analysis identified additional IAV host and restriction factors, such as the splicing factor GPKOW, that exhibit significant turnover rate changes while their total abundance is minimally affected. Overall, we show that protein turnover is a critical factor both for virus replication and antiviral defense.
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Affiliation(s)
- Yiqi Huang
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Christian Urban
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Philipp Hubel
- Core Facility Hohenheim, Universität Hohenheim, Stuttgart, Germany
| | - Alexey Stukalov
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany; Institute of Virology, Helmholtz Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site, Munich, Germany.
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3
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Drobik-Czwarno W, Wolc A, Petal CR, Miedzinska K, Dekkers J, Fulton JE, Smith J. Candidate Genes Associated with Survival Following Highly Pathogenic Avian Influenza Infection in Chickens. Int J Mol Sci 2024; 25:10056. [PMID: 39337540 PMCID: PMC11432379 DOI: 10.3390/ijms251810056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/09/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
Highly pathogenic strains of avian influenza (HPAI) devastate poultry flocks and result in significant economic losses for farmers due to high mortality, reduced egg production, and mandated euthanization of infected flocks. Within recent years, HPAI outbreaks have affected egg production flocks across the world. The H5N2 outbreak in the US in 2015 resulted in over 99% mortality. Here, we analyze sequence data from chickens that survived (42 cases) along with uninfected controls (28 samples) to find genomic regions that differ between these two groups and that, therefore, may encompass prime candidates that are resistant to HPAI. Blood samples were obtained from survivors of the 2015 HPAI outbreak plus age and genetics-matched non-affected controls. A whole-genome sequence was obtained, and genetic variants were characterized and used in a genome-wide association study to identify regions showing significant association with survival. Regions associated with HPAI resistance were observed on chromosomes 1, 2, 5, 8, 10, 11, 15, 20, and 28, with a number of candidate genes identified. We did not detect a specific locus which could fully explain the difference between survivors and controls. Influenza virus replication depends on multiple components of the host cellular machinery, with many genes involved in the host response.
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Affiliation(s)
- Wioleta Drobik-Czwarno
- Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, 02-787 Warsaw, Poland;
| | - Anna Wolc
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (A.W.); (J.D.)
- Hy-Line International, P.O. Box 310, 2583 240th St., Dallas Center, IA 50063, USA;
| | - Callie R. Petal
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (C.R.P.); (K.M.)
| | - Katarzyna Miedzinska
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (C.R.P.); (K.M.)
| | - Jack Dekkers
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (A.W.); (J.D.)
| | - Janet E. Fulton
- Hy-Line International, P.O. Box 310, 2583 240th St., Dallas Center, IA 50063, USA;
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; (C.R.P.); (K.M.)
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4
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Farazuddin M, Acker G, Zourob J, O’Konek JJ, Wong PT, Morris S, Rasky AJ, Kim CH, Lukacs NW, Baker JR. Inhibiting retinoic acid signaling in dendritic cells suppresses respiratory syncytial virus infection through enhanced antiviral immunity. iScience 2024; 27:110103. [PMID: 39045100 PMCID: PMC11263793 DOI: 10.1016/j.isci.2024.110103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/21/2023] [Accepted: 05/21/2024] [Indexed: 07/25/2024] Open
Abstract
Retinoic acid (RA), controls the immunoregulatory functions of many immune cells, including dendritic cells (DCs), and is important for mucosal immunity. In DCs, RA regulates the expression of pattern recognition receptors and stimulates interferon production. Here, we investigated the role of RA in DCs in mounting immunity to respiratory syncytial virus (RSV). To abolish RA signaling in DCs, we used mice expressing a dominant negative form of retinoic acid receptor-α (RARα) under the CD11c promoter (CD11c-dnRARα). Paradoxically, upon RSV challenge, these animals had lower viral burden, reduced pathology, and greater Th1 polarized immunity than wild-type (WT) mice. Moreover, CD11c-dnRARα DCs infected with RSV showed enhancement in innate and adaptive immunity genes, while genes associated with viral replication were downregulated. These findings suggest that the absence of RA signaling in DCs enhances innate immunity against RSV infection leading to decreased viral load and reduced pathogenicity.
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Affiliation(s)
- Mohammad Farazuddin
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Grant Acker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joseph Zourob
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jessica J. O’Konek
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Pamela T. Wong
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Susan Morris
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Andrew J. Rasky
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chang H. Kim
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicholas W. Lukacs
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James R. Baker
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
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Dupont M, Krischuns T, Gianetto QG, Paisant S, Bonazza S, Brault JB, Douché T, Arragain B, Florez-Prada A, Perez-Perri J, Hentze M, Cusack S, Matondo M, Isel C, Courtney D, Naffakh N. The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication. Nucleic Acids Res 2024; 52:7188-7210. [PMID: 38686810 PMCID: PMC11229366 DOI: 10.1093/nar/gkae291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/22/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Genome-wide approaches have significantly advanced our knowledge of the repertoire of RNA-binding proteins (RBPs) that associate with cellular polyadenylated mRNAs within eukaryotic cells. Recent studies focusing on the RBP interactomes of viral mRNAs, notably SARS-Cov-2, have revealed both similarities and differences between the RBP profiles of viral and cellular mRNAs. However, the RBPome of influenza virus mRNAs remains unexplored. Herein, we identify RBPs that associate with the viral mRNA encoding the nucleoprotein (NP) of an influenza A virus. Focusing on TDP-43, we show that it binds several influenza mRNAs beyond the NP-mRNA, and that its depletion results in lower levels of viral mRNAs and proteins within infected cells, and a decreased yield of infectious viral particles. We provide evidence that the viral polymerase recruits TDP-43 onto viral mRNAs through a direct interaction with the disordered C-terminal domain of TDP-43. Notably, other RBPs found to be associated with influenza virus mRNAs also interact with the viral polymerase, which points to a role of the polymerase in orchestrating the assembly of viral messenger ribonucleoproteins.
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Affiliation(s)
- Maud Dupont
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
| | - Sylvain Paisant
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Stefano Bonazza
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Jean-Baptiste Brault
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Benoît Arragain
- European Molecular Biology Laboratory, 38042Grenoble, France
| | | | | | | | - Stephen Cusack
- European Molecular Biology Laboratory, 38042Grenoble, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Catherine Isel
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - David G Courtney
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
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6
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Ni Z, Wang J, Yu X, Wang Y, Wang J, He X, Li C, Deng G, Shi J, Kong H, Jiang Y, Chen P, Zeng X, Tian G, Chen H, Bu Z. Influenza virus uses mGluR2 as an endocytic receptor to enter cells. Nat Microbiol 2024; 9:1764-1777. [PMID: 38849624 PMCID: PMC11222159 DOI: 10.1038/s41564-024-01713-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Influenza virus infection is initiated by the attachment of the viral haemagglutinin (HA) protein to sialic acid receptors on the host cell surface. Most virus particles enter cells through clathrin-mediated endocytosis (CME). However, it is unclear how viral binding signals are transmitted through the plasma membrane triggering CME. Here we found that metabotropic glutamate receptor subtype 2 (mGluR2) and potassium calcium-activated channel subfamily M alpha 1 (KCa1.1) are involved in the initiation and completion of CME of influenza virus using an siRNA screen approach. Influenza virus HA directly interacted with mGluR2 and used it as an endocytic receptor to initiate CME. mGluR2 interacted and activated KCa1.1, leading to polymerization of F-actin, maturation of clathrin-coated pits and completion of the CME of influenza virus. Importantly, mGluR2-knockout mice were significantly more resistant to different influenza subtypes than the wild type. Therefore, blocking HA and mGluR2 interaction could be a promising host-directed antiviral strategy.
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Affiliation(s)
- Zixin Ni
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Jinliang Wang
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Xiaofei Yu
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Yifan Wang
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Jingfei Wang
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Xijun He
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Chengjun Li
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Guohua Deng
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Jianzhong Shi
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Huihui Kong
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Yongping Jiang
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Pucheng Chen
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Xianying Zeng
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Guobin Tian
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Hualan Chen
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China.
| | - Zhigao Bu
- State Key Laboratory for Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China.
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Khanna M, Sharma K, Saxena SK, Sharma JG, Rajput R, Kumar B. Unravelling the interaction between Influenza virus and the nuclear pore complex: insights into viral replication and host immune response. Virusdisease 2024; 35:231-242. [PMID: 39071870 PMCID: PMC11269558 DOI: 10.1007/s13337-024-00879-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024] Open
Abstract
Influenza viruses are known to cause severe respiratory infections in humans, often associated with significant morbidity and mortality rates. Virus replication relies on various host factors and pathways, which also determine the virus's infectious potential. Nonetheless, achieving a comprehensive understanding of how the virus interacts with host cellular components is essential for developing effective therapeutic strategies. One of the key components among host factors, the nuclear pore complex (NPC), profoundly affects both the Influenza virus life cycle and the host's antiviral defenses. Serving as the sole gateway connecting the cytoplasm and nucleoplasm, the NPC plays a vital role as a mediator in nucleocytoplasmic trafficking. Upon infection, the virus hijacks and alters the nuclear pore complex and the nuclear receptors. This enables the virus to infiltrate the nucleus and promotes the movement of viral components between the nucleus and cytoplasm. While the nucleus and cytoplasm play pivotal roles in cellular functions, the nuclear pore complex serves as a crucial component in the host's innate immune system, acting as a defense mechanism against virus infection. This review provides a comprehensive overview of the intricate relationship between the Influenza virus and the nuclear pore complex. Furthermore, we emphasize their mutual influence on viral replication and the host's immune responses.
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Affiliation(s)
- Madhu Khanna
- Department of Virology, V.P Chest Institute, University of Delhi, Delhi, India
| | - Kajal Sharma
- Department of Virology, V.P Chest Institute, University of Delhi, Delhi, India
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Shailendra K. Saxena
- Centre for Advanced Research (CFAR), Faculty of Medicine, King George’s Medical University (KGMU), Lucknow, India
| | - Jai Gopal Sharma
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Roopali Rajput
- Department of Virology, V.P Chest Institute, University of Delhi, Delhi, India
| | - Binod Kumar
- Department of Antiviral Research, Institute of Advanced Virology, Thiruvananthapuram, Kerala India
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8
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Ressel S, Kumar S, Bermúdez-Barrientos JR, Gordon K, Lane J, Wu J, Abreu-Goodger C, Schwarze J, Buck A. RNA-RNA interactions between respiratory syncytial virus and miR-26 and miR-27 are associated with regulation of cell cycle and antiviral immunity. Nucleic Acids Res 2024; 52:4872-4888. [PMID: 38412296 PMCID: PMC11109944 DOI: 10.1093/nar/gkae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 02/01/2024] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
microRNAs (miRNAs) regulate nearly all physiological processes but our understanding of exactly how they function remains incomplete, particularly in the context of viral infections. Here, we adapt a biochemical method (CLEAR-CLIP) and analysis pipeline to identify targets of miRNAs in lung cells infected with Respiratory syncytial virus (RSV). We show that RSV binds directly to miR-26 and miR-27 through seed pairing and demonstrate that these miRNAs target distinct gene networks associated with cell cycle and metabolism (miR-27) and antiviral immunity (miR-26). Many of the targets are de-repressed upon infection and we show that the miR-27 targets most sensitive to miRNA inhibition are those associated with cell cycle. Finally, we demonstrate that high confidence chimeras map to long noncoding RNAs (lncRNAs) and pseudogenes in transcriptional regulatory regions. We validate that a proportion of miR-27 and Argonaute 2 (AGO2) is nuclear and identify a long non-coding RNA (lncRNA) as a miR-27 target that is linked to transcriptional regulation of nearby genes. This work expands the target networks of miR-26 and miR-27 to include direct interactions with RSV and lncRNAs and implicate these miRNAs in regulation of key genes that impact the viral life cycle associated with cell cycle, metabolism, and antiviral immunity.
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Affiliation(s)
- Sarah Ressel
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sujai Kumar
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | | | - Katrina Gordon
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Julia Lane
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jin Wu
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jürgen Schwarze
- Child Life and Health, Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Amy H Buck
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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9
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Maes A, Botzki A, Mathys J, Impens F, Saelens X. Systematic review and meta-analysis of genome-wide pooled CRISPR screens to identify host factors involved in influenza A virus infection. J Virol 2024; 98:e0185723. [PMID: 38567969 PMCID: PMC11257101 DOI: 10.1128/jvi.01857-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/14/2024] [Indexed: 05/15/2024] Open
Abstract
The host-virus interactome is increasingly recognized as an important research field to discover new therapeutic targets to treat influenza. Multiple pooled genome-wide CRISPR-Cas screens have been reported to identify new pro- and antiviral host factors of the influenza A virus. However, at present, a comprehensive summary of the results is lacking. We performed a systematic review of all reported CRISPR studies in this field in combination with a meta-analysis using the algorithm of meta-analysis by information content (MAIC). Two ranked gene lists were generated based on evidence in 15 proviral and 4 antiviral screens. Enriched pathways in the proviral MAIC results were compared to those of a prior array-based RNA interference (RNAi) meta-analysis. The top 50 proviral MAIC list contained genes whose role requires further elucidation, such as the endosomal ion channel TPCN1 and the kinase WEE1. Moreover, MAIC indicated that ALYREF, a component of the transcription export complex, has antiviral properties, whereas former knockdown experiments attributed a proviral role to this host factor. CRISPR-Cas-pooled screens displayed a bias toward early-replication events, whereas the prior RNAi meta-analysis covered early and late-stage events. RNAi screens led to the identification of a larger fraction of essential genes than CRISPR screens. In summary, the MAIC algorithm points toward the importance of several less well-known pathways in host-influenza virus interactions that merit further investigation. The results from this meta-analysis of CRISPR screens in influenza A virus infection may help guide future research efforts to develop host-directed anti-influenza drugs. IMPORTANCE Viruses rely on host factors for their replication, whereas the host cell has evolved virus restriction factors. These factors represent potential targets for host-oriented antiviral therapies. Multiple pooled genome-wide CRISPR-Cas screens have been reported to identify pro- and antiviral host factors in the context of influenza virus infection. We performed a comprehensive analysis of the outcome of these screens based on the publicly available gene lists, using the recently developed algorithm meta-analysis by information content (MAIC). MAIC allows the systematic integration of ranked and unranked gene lists into a final ranked gene list. This approach highlighted poorly characterized host factors and pathways with evidence from multiple screens, such as the vesicle docking and lipid metabolism pathways, which merit further exploration.
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Affiliation(s)
- Annabel Maes
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Janssen Pharmaceutica NV, Beerse, Belgium
| | | | | | - Francis Impens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Xavier Saelens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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10
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Wang M, Yao X, Tong X, Qi D, Ye X. Lnc-RPS6P3 Inhibits Influenza A Virus Replication and Attenuates the Inhibitory Effect of NS1 on Innate Immune Response. Microorganisms 2024; 12:654. [PMID: 38674599 PMCID: PMC11052439 DOI: 10.3390/microorganisms12040654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Host factors play important roles in influenza A virus (IAV) replication. In order to identify novel host factors involved in IAV replication, we compared the differentially expressed genes in A549 cells after IAV infection. We found that lncRNA lnc-RPS6P3 was up-regulated upon viral infection and poly(I:C) and IFN-β treatment, indicating it was an interferon-stimulated gene. Functional analysis demonstrated that overexpression of lnc-RPS6P3 inhibited IAV replication while knockdown of lnc-RPS6P3 promoted viral infection in A549 cells. Lnc-RPS6P3 inhibited both transcription and replication of IAV. Further study showed that lnc-RPS6P3 interacted with viral NP and interfered with NP self-oligomerization and, consequently, inhibited vRNP activity. In addition, lnc-RPS6P3 interacted with viral NS1 and reduced the interaction of NS1 and RIG-I; it also attenuated the inhibitory effect of NS1 on IFN-β stimulation. In conclusion, we revealed that lnc-RPS6P3 is an interferon-stimulated gene that inhibits IAV replication and attenuates the inhibitory effect of NS1 on innate immune response.
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Affiliation(s)
- Mingge Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China;
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
| | - Xinli Yao
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomei Tong
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
| | - Dandan Qi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
| | - Xin Ye
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (X.Y.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Wang L, Yukselten Y, Nuwagaba J, Sutton RE. JAK/STAT signaling pathway affects CCR5 expression in human CD4 + T cells. SCIENCE ADVANCES 2024; 10:eadl0368. [PMID: 38507500 PMCID: PMC10954213 DOI: 10.1126/sciadv.adl0368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
CCR5 serves as R5-tropic HIV co-receptor. Knocking out CCR5 in HIV patients, which has occurred <10 times, is believed important for cure. JAK/STAT inhibitors tofacitinib and ruxolitinib inhibit CCR5 expression in HIV+ viremic patients. We investigated the association of JAK/STAT signaling pathway with CCR5/CCR2 expression in human primary CD4+ T cells and confirmed its importance. Six of nine JAK/STAT inhibitors that reduced CCR5/CCR2 expression were identified. Inhibitor-treated CD4+ T cells were relatively resistant, specifically to R5-tropic HIV infection. Furthermore, single JAK2, STAT3, STAT5A, and STAT5B knockout and different combinations of JAK/STAT knockout significantly reduced CCR2/CCR5 expression of both RNA and protein levels, indicating that CCR5/CCR2 expression was positively regulated by JAK-STAT pathway in CD4+ T cells. Serum and glucocorticoid-regulated kinase 1 (SGK1) knockout affected CCR2/CCR5 gene expression, suggesting that SGK1 is involved in CCR2/CCR5 regulation. If cell surface CCR5 levels can be specifically and markedly down-regulated without adverse effects, that may have a major impact on the HIV cure agenda.
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Affiliation(s)
- Lingyun Wang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Yunus Yukselten
- Section of Infectious Diseases, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Julius Nuwagaba
- Section of Infectious Diseases, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Richard E. Sutton
- Section of Infectious Diseases, Department of Internal Medicine, Yale University, New Haven, CT, USA
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12
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Su R, Li X, Xiao J, Xu J, Tian J, Liu T, Hu Y. UiO-66 nanoparticles combat influenza A virus in mice by activating the RIG-I-like receptor signaling pathway. J Nanobiotechnology 2024; 22:99. [PMID: 38461229 PMCID: PMC10925002 DOI: 10.1186/s12951-024-02358-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/20/2024] [Indexed: 03/11/2024] Open
Abstract
The Influenza A virus (IAV) is a zoonotic pathogen that infects humans and various animal species. Infection with IAV can cause fever, anorexia, and dyspnea and is often accompanied by pneumonia characterized by an excessive release of cytokines (i.e., cytokine storm). Nanodrug delivery systems and nanoparticles are a novel approach to address IAV infections. Herein, UiO-66 nanoparticles (NPs) are synthesized using a high-temperature melting reaction. The in vitro and in vivo optimal concentrations of UiO-66 NPs for antiviral activity are 200 μg mL-1 and 60 mg kg-1, respectively. Transcriptome analysis revealed that UiO-66 NPs can activate the RIG-I-like receptor signaling pathway, thereby enhancing the downstream type I interferon antiviral effect. These NPs suppress inflammation-related pathways, including the FOXO, HIF, and AMPK signaling pathways. The inhibitory effect of UiO-66 NPs on the adsorption and entry of IAV into A549 cells is significant. This study presents novel findings that demonstrate the effective inhibition of IAV adsorption and entry into cells via UiO-66 NPs and highlights their ability to activate the cellular RIG-I-like receptor signaling pathway, thereby exerting an anti-IAV effect in vitro or in mice. These results provide valuable insights into the mechanism of action of UiO-66 NPs against IAV and substantial data for advancing innovative antiviral nanomedicine.
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Affiliation(s)
- Ruijing Su
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xinsen Li
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jin Xiao
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Zhongmu Institutes of China Animal Husbandry Industry Co., Ltd, Beijing, People's Republic of China
| | - Jiawei Xu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jijing Tian
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Tianlong Liu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Yanxin Hu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
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13
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Hu Y, Jiang L, Wang G, Song Y, Shan Z, Wang X, Deng G, Shi J, Tian G, Zeng X, Liu L, Chen H, Li C. M6PR interacts with the HA2 subunit of influenza A virus to facilitate the fusion of viral and endosomal membranes. SCIENCE CHINA. LIFE SCIENCES 2024; 67:579-595. [PMID: 38038885 DOI: 10.1007/s11427-023-2471-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
Influenza A virus (IAV) commandeers numerous host cellular factors for successful replication. However, very few host factors have been revealed to be involved in the fusion of viral envelope and late endosomal membranes. In this study, we identified cation-dependent mannose-6-phosphate receptor (M6PR) as a crucial host factor for the replication of IAV. We found that siRNA knockdown of M6PR expression significantly reduced the growth titers of different subtypes of IAV, and that the inhibitory effect of M6PR siRNA treatment on IAV growth was overcome by the complement of exogenously expressed M6PR. When A549 cells were treated with siRNA targeting M6PR, the nuclear accumulation of viral nucleoprotein (NP) was dramatically inhibited at early timepoints post-infection, indicating that M6PR engages in the early stage of the IAV replication cycle. By investigating the role of M6PR in the individual entry and post-entry steps of IAV replication, we found that the downregulation of M6PR expression had no effect on attachment, internalization, early endosome trafficking, or late endosome acidification. However, we found that M6PR expression was critical for the fusion of viral envelope and late endosomal membranes. Of note, M6PR interacted with the hemagglutinin (HA) protein of IAV, and further studies showed that the lumenal domain of M6PR and the ectodomain of HA2 mediated the interaction and directly promoted the fusion of the viral and late endosomal membranes, thereby facilitating IAV replication. Together, our findings highlight the importance of the M6PR-HA interaction in the fusion of viral and late endosomal membranes during IAV replication.
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Affiliation(s)
- Yuzhen Hu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Li Jiang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Guangwen Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Yangming Song
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Zhibo Shan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xuyuan Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Guohua Deng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Jianzhong Shi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Guobin Tian
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xianying Zeng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Liling Liu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Hualan Chen
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Chengjun Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
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14
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Rashid MU, Coombs KM. Chloride Intracellular Channel Protein 1 (CLIC1) Is a Critical Host Cellular Factor for Influenza A Virus Replication. Viruses 2024; 16:129. [PMID: 38257829 PMCID: PMC10819074 DOI: 10.3390/v16010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
(1) Background: Influenza A Virus (IAV) uses host cellular proteins during replication in host cells. IAV infection causes elevated expression of chloride intracellular channel protein 1 (CLIC1) in lung epithelial cells, but the importance of this protein in IAV replication is unknown. (2) In this study, we determined the role of CLIC1 in IAV replication by investigating the effects of CLIC1 knockdown (KD) on IAV viral protein translation, genomic RNA transcription, and host cellular proteome dysregulation. (3) Results: CLIC1 KD in A549 human lung epithelial cells resulted in a significant decrease in progeny supernatant IAV, but virus protein expression was unaffected. However, a significantly larger number of viral RNAs accumulated in CLIC1 KD cells. Treatment with a CLIC1 inhibitor also caused a significant reduction in IAV replication, suggesting that CLIC1 is an important host factor in IAV replication. SomaScan®, which measures 1322 proteins, identified IAV-induced dysregulated proteins in wild-type cells and in CLIC1 KD cells. The expression of 116 and 149 proteins was significantly altered in wild-type and in CLIC1 KD cells, respectively. A large number of the dysregulated proteins in CLIC1 KD cells were associated with cellular transcription and predicted to be inhibited during IAV replication. (4) Conclusions: This study suggests that CLIC1 is involved in later stages of IAV replication. Further investigation should clarify mechanism(s) for the development of anti-IAV drugs targeting CLIC1 protein.
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Affiliation(s)
- Mahamud-ur Rashid
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Room 543 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg, MB R3E OJ9, Canada
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Room 543 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg, MB R3E OJ9, Canada
- Manitoba Centre for Proteomics and Systems Biology, Room 799, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, Room 513, John Buhler Research Centre, 715 McDermot Avenue, Winnipeg, MB R3E 3P4, Canada
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15
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Wuchty S, White AK, Olthof AM, Drake K, Hume AJ, Olejnik J, Aguiar-Pulido V, Mühlberger E, Kanadia RN. Minor intron-containing genes as an ancient backbone for viral infection? PNAS NEXUS 2024; 3:pgad479. [PMID: 38274120 PMCID: PMC10810330 DOI: 10.1093/pnasnexus/pgad479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
Minor intron-containing genes (MIGs) account for <2% of all human protein-coding genes and are uniquely dependent on the minor spliceosome for proper excision. Despite their low numbers, we surprisingly found a significant enrichment of MIG-encoded proteins (MIG-Ps) in protein-protein interactomes and host factors of positive-sense RNA viruses, including SARS-CoV-1, SARS-CoV-2, MERS coronavirus, and Zika virus. Similarly, we observed a significant enrichment of MIG-Ps in the interactomes and sets of host factors of negative-sense RNA viruses such as Ebola virus, influenza A virus, and the retrovirus HIV-1. We also found an enrichment of MIG-Ps in double-stranded DNA viruses such as Epstein-Barr virus, human papillomavirus, and herpes simplex viruses. In general, MIG-Ps were highly connected and placed in central positions in a network of human-host protein interactions. Moreover, MIG-Ps that interact with viral proteins were enriched with essential genes. We also provide evidence that viral proteins interact with ancestral MIGs that date back to unicellular organisms and are mainly involved in basic cellular functions such as cell cycle, cell division, and signal transduction. Our results suggest that MIG-Ps form a stable, evolutionarily conserved backbone that viruses putatively tap to invade and propagate in human host cells.
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Affiliation(s)
- Stefan Wuchty
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
- Institute of Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33134, USA
| | - Alisa K White
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Kyle Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Adam J Hume
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
- Center for Emerging Infectious Diseases Policy and Research, Boston University, Boston, MA 02118, USA
| | - Judith Olejnik
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | | | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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16
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Martinez-Gzegozewska Y, Rasmussen L, McKellip S, Manuvakhova A, Nebane NM, Reece AJ, Ruiz P, Sosa M, Bostwick R, Vinson P. High-Throughput cell-based immunofluorescence assays against influenza. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:66-76. [PMID: 37925159 DOI: 10.1016/j.slasd.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
A rapid drug discovery response to influenza outbreaks with the potential to reach pandemic status could help minimize the virus's impact by reducing the time to identify anti-influenza drugs. Although several anti-influenza strategies have been considered in the search for new drugs, only a few therapeutic agents are approved for clinical use. The cytopathic effect induced by the influenza virus in Madin Darby canine kidney (MDCK) cells has been widely used for high-throughput anti-influenza drug screening, but the fact that the MDCK cells are not human cells constitutes a disadvantage when searching for new therapeutic agents for human use. We have developed a highly sensitive cell-based imaging assay for the identification of inhibitors of influenza A and B virus that is high-throughput compatible using the A549 human cell line. The assay has also been optimized for the assessment of the neutralizing effect of anti-influenza antibodies in the absence of trypsin, which allows testing of purified antibodies and serum samples. This assay platform can be applied to full high-throughput screening campaigns or later stages requiring quantitative potency determinations for structure-activity relationships.
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Affiliation(s)
- Yohanka Martinez-Gzegozewska
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States.
| | - Lynn Rasmussen
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Sara McKellip
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Anna Manuvakhova
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - N Miranda Nebane
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Andrew J Reece
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Pedro Ruiz
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Melinda Sosa
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Robert Bostwick
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Paige Vinson
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
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17
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Yao X, Jing T, Geng Q, Pang M, Zhao X, Li S, Chen D, Ma W. Dual analysis of wild-type and attenuated Orf virus and host cell transcriptomes revealed novel virus-host cell interactions. mSphere 2023; 8:e0039823. [PMID: 37982609 PMCID: PMC10732022 DOI: 10.1128/msphere.00398-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Currently, the only available commercial vaccines for Orf virus (ORFV) are live attenuated vaccines, which present a potential risk of reversion to virulence. Therefore, understanding the pathogenic mechanisms of different virulent strains of ORFV and host immune responses triggered by these viruses is crucial for developing new vaccines and interventions. In this study, we found that the attenuated strain downregulates the host innate immune response and antiviral activity. In addition, we noted that the wild-type strain can induce the immune response pattern centered on interferon-stimulated genes and interferon regulatory factor gene family. We predicted that STAT1 and STAT2 are the main transcription factors upstream of target gene promoters through gene regulatory networks and exert significant regulatory effects on co-expressed genes. Our study elucidated the complex interaction between ORFV strains and host cell immune responses, providing new insights into vaccine research for ORFV.
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Affiliation(s)
- Xiaoting Yao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Tian Jing
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingru Geng
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ming Pang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuanduo Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Shaofei Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Dekun Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Wentao Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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18
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Ren C, Chen T, Zhang S, Gao Q, Zou J, Li P, Wang B, Zhao Y, OuYang A, Suolang S, Zhou H. PLK3 facilitates replication of swine influenza virus by phosphorylating viral NP protein. Emerg Microbes Infect 2023; 12:2275606. [PMID: 37874309 PMCID: PMC10768867 DOI: 10.1080/22221751.2023.2275606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Swine H1N1/2009 influenza is a highly infectious respiratory disease in pigs, which poses a great threat to pig production and human health. In this study, we investigated the global expression profiling of swine-encoded genes in response to swine H1N1/2009 influenza A virus (SIV-H1N1/2009) in newborn pig trachea (NPTr) cells. In total, 166 genes were found to be differentially expressed (DE) according to the gene microarray. After analyzing the DE genes which might affect the SIV-H1N1/2009 replication, we focused on polo-like kinase 3 (PLK3). PLK3 is a member of the PLK family, which is a highly conserved serine/threonine kinase in eukaryotes and well known for its role in the regulation of cell cycle and cell division. We validated that the expression of PLK3 was upregulated after SIV-H1N1/2009 infection. Additionally, PLK3 was found to interact with viral nucleoprotein (NP), significantly increased NP phosphorylation and oligomerization, and promoted viral ribonucleoprotein assembly and replication. Furthermore, we identified serine 482 (S482) as the phosphorylated residue on NP by PLK3. The phosphorylation of S482 regulated NP oligomerization, viral polymerase activity and growth. Our findings provide further insights for understanding the replication of influenza A virus.
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Affiliation(s)
- Caiyue Ren
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Tong Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Shishuo Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Qingxia Gao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Jiahui Zou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Peng Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Biaoxiong Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yaxin Zhao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Aotian OuYang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Sizhu Suolang
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, People’s Republic of China
| | - Hongbo Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Hubei Hongshan Laboratory, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People’s Republic of China
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19
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Shi W, Shan Z, Jiang L, Wang G, Wang X, Chang Y, Hu Y, Wang B, Li Q, Wang Y, Deng G, Shi J, Jiang Y, Zeng X, Tian G, Chen H, Li C. ABTB1 facilitates the replication of influenza A virus by counteracting TRIM4-mediated degradation of viral NP protein. Emerg Microbes Infect 2023; 12:2270073. [PMID: 37823597 PMCID: PMC10623896 DOI: 10.1080/22221751.2023.2270073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Influenza A viruses (IAVs) continue to cause tremendous economic losses to the global animal industry and respiratory diseases and deaths among humans. The nuclear import of the vRNP complex, composed of polymerase basic protein 1 (PB1), polymerase basic protein 2 (PB2), polymerase acidic protein (PA), nucleoprotein (NP), and viral RNA, is essential for the efficient replication of IAV. Host factors involved in this process can be targeted for the development of countermeasures against IAV infection. Here, we found that Ankyrin Repeat and BTB Domain Containing 1 (ABTB1) promotes the replication of IAV, and positively regulates the nuclear import of the vRNP complex. ABTB1 did not interact directly with NP, indicating that ABTB1 plays an indirect role in facilitating the nuclear import of the vRNP complex. Immunoprecipitation and mass spectrometry revealed that Tripartite Motif Containing 4 (TRIM4) interacts with ABTB1. We found that TRIM4 relies on its E3 ubiquitin ligase activity to inhibit the replication of IAV by targeting and degrading NP within the incoming vRNP complex as well as the newly synthesized NP. ABTB1 interacted with TRIM4, leading to TRIM4 degradation through the proteasome system. Notably, ABTB1-mediated degradation of TRIM4 blocked the effect of TRIM4 on NP stability, and largely counteracted the inhibitory effect of TRIM4 on IAV replication. Our findings define a novel role for ABTB1 in aiding the nuclear import of the vRNP complex of IAV by counteracting the destabilizing effect of TRIM4 on the viral NP protein.
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Affiliation(s)
- Wenjun Shi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Zhibo Shan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Li Jiang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Guangwen Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Xuyuan Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Yu Chang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Yuzhen Hu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Bo Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Qibing Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Yihan Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Guohua Deng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Jianzhong Shi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Yongping Jiang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Xianying Zeng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Guobin Tian
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Hualan Chen
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Chengjun Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
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20
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Sheppard CM, Goldhill DH, Swann OC, Staller E, Penn R, Platt OK, Sukhova K, Baillon L, Frise R, Peacock TP, Fodor E, Barclay WS. An Influenza A virus can evolve to use human ANP32E through altering polymerase dimerization. Nat Commun 2023; 14:6135. [PMID: 37816726 PMCID: PMC10564888 DOI: 10.1038/s41467-023-41308-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/09/2023] [Indexed: 10/12/2023] Open
Abstract
Human ANP32A and ANP32B are essential but redundant host factors for influenza virus genome replication. While most influenza viruses cannot replicate in edited human cells lacking both ANP32A and ANP32B, some strains exhibit limited growth. Here, we experimentally evolve such an influenza A virus in these edited cells and unexpectedly, after 2 passages, we observe robust viral growth. We find two mutations in different subunits of the influenza polymerase that enable the mutant virus to use a novel host factor, ANP32E, an alternative family member, which is unable to support the wild type polymerase. Both mutations reside in the symmetric dimer interface between two polymerase complexes and reduce polymerase dimerization. These mutations have previously been identified as adapting influenza viruses to mice. Indeed, the evolved virus gains the ability to use suboptimal mouse ANP32 proteins and becomes more virulent in mice. We identify further mutations in the symmetric dimer interface which we predict allow influenza to adapt to use suboptimal ANP32 proteins through a similar mechanism. Overall, our results suggest a balance between asymmetric and symmetric dimers of influenza virus polymerase that is influenced by the interaction between polymerase and ANP32 host proteins.
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Affiliation(s)
- Carol M Sheppard
- Department of Infectious Disease, Imperial College London, London, UK.
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Olivia C Swann
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ecco Staller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rebecca Penn
- Department of Infectious Disease, Imperial College London, London, UK
| | - Olivia K Platt
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, London, UK
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK.
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21
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Hamele CE, Spurrier MA, Leonard RA, Heaton NS. Segmented, Negative-Sense RNA Viruses of Humans: Genetic Systems and Experimental Uses of Reporter Strains. Annu Rev Virol 2023; 10:261-282. [PMID: 37774125 PMCID: PMC10795101 DOI: 10.1146/annurev-virology-111821-120445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Negative-stranded RNA viruses are a large group of viruses that encode their genomes in RNA across multiple segments in an orientation antisense to messenger RNA. Their members infect broad ranges of hosts, and there are a number of notable human pathogens. Here, we examine the development of reverse genetic systems as applied to these virus families, emphasizing conserved approaches illustrated by some of the prominent members that cause significant human disease. We also describe the utility of their genetic systems in the development of reporter strains of the viruses and some biological insights made possible by their use. To conclude the review, we highlight some possible future uses of reporter viruses that not only will increase our basic understanding of how these viruses replicate and cause disease but also could inform the development of new approaches to therapeutically intervene.
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Affiliation(s)
- Cait E Hamele
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA;
| | - M Ariel Spurrier
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca A Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA;
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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22
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Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun 2023; 14:6030. [PMID: 37758692 PMCID: PMC10533562 DOI: 10.1038/s41467-023-41442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT.
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Affiliation(s)
- Kelsey M Haas
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Michael J McGregor
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Thong T Nguyen
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Heejin Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Michael A P Williams
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, 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
| | - Veronica V Rezelj
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Alexandra Hardy
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Andrea Fossati
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Erica J Stevenson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Ellie Sukerman
- Division of Infectious Diseases, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Tiffany Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sudhir Penugonda
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Elena Moreno
- Department of Microbiology, 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
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal and IRYCIS, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Yuan Zhou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Giorgi Metreveli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bhavya Harjai
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Tia A Tummino
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - James E Melnyk
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Jyoti Batra
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Laura Martin-Sancho
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Infectious Disease, Imperial College London, London, SW7 2BX, UK
| | - Jared Carlson-Stevermer
- Synthego Corporation, Redwood City, CA, 94063, USA
- Serotiny Inc., South San Francisco, CA, 94080, USA
| | - Alexander S Jureka
- Molecular Virology and Vaccine Team, Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization & Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, 30333, USA
- General Dynamics Information Technology, Federal Civilian Division, Atlanta, GA, 30329, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Brian K Shoichet
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63105, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Jeffrey R Johnson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medical Biosciences, University of the Western Cape, Bellville, 7535, Western Cape, South Africa
| | - Sumit K Chanda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Tonia C Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Maureen E Smith
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, 53706, USA
| | - Randy A Albrecht
- Department of Microbiology, 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
| | - Marco Vignuzzi
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Lorena Zuliani-Alvarez
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kris M White
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, 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
| | - Judd F Hultquist
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
| | - Robyn M Kaake
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
| | - Adolfo García-Sastre
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Department of Microbiology, 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.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular and Cell-Based Medicine, 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.
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
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23
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Melano I, Cheng WC, Kuo LL, Liu YM, Chou YC, Hung MC, Lai MMC, Sher YP, Su WC. A disintegrin and metalloproteinase domain 9 facilitates SARS-CoV-2 entry into cells with low ACE2 expression. Microbiol Spectr 2023; 11:e0385422. [PMID: 37713503 PMCID: PMC10581035 DOI: 10.1128/spectrum.03854-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 07/18/2023] [Indexed: 09/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the Coronavirus disease-19 (COVID-19) pandemic, utilizes angiotensin-converting enzyme 2 (ACE2) as a receptor for virus infection. However, the expression pattern of ACE2 does not coincide with the tissue tropism of SARS-CoV-2, hinting that other host proteins might be involved in facilitating SARS-CoV-2 entry. To explore potential host factors for SARS-CoV-2 entry, we performed an arrayed shRNA screen in H1650 and HEK293T cells. Here, we identified a disintegrin and a metalloproteinase domain 9 (ADAM9) protein as an important host factor for SARS-CoV-2 entry. Our data showed that silencing ADAM9 reduced virus entry, while its overexpression promoted infection. The knockdown of ADAM9 decreased the infectivity of the variants of concern tested-B.1.1.7 (alpha), B.1.617.2 (delta), and B.1.1.529 (omicron). Furthermore, mechanistic studies indicated that ADAM9 is involved in the binding and endocytosis stages of SARS-CoV-2 entry. Through immunoprecipitation experiments, we demonstrated that ADAM9 binds to the S1 subunit of the SARS-CoV-2 Spike. Additionally, ADAM9 can interact with ACE2, and co-expression of both proteins markedly enhances virus infection. Moreover, the enzymatic activity of ADAM9 facilitates virus entry. Our study reveals an insight into the mechanism of SARS-CoV-2 virus entry and elucidates the role of ADAM9 in virus infection. IMPORTANCE COVID-19, an infectious respiratory disease caused by SARS-CoV-2, has greatly impacted global public health and the economy. Extensive vaccination efforts have been launched worldwide over the last couple of years. However, several variants of concern that reduce the efficacy of vaccines have kept emerging. Thereby, further understanding of the mechanism of SARS-CoV-2 entry is indispensable, which will allow the development of an effective antiviral strategy. Here, we identify a disintegrin and metalloproteinase domain 9 (ADAM9) protein as a co-factor of ACE2 important for SARS-CoV-2 entry, even for the variants of concern, and show that ADAM9 interacts with Spike to aid virus entry. This virus-host interaction could be exploited to develop novel therapeutics against COVID-19.
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Affiliation(s)
- Ivonne Melano
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Wei-Chung Cheng
- Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taipei, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Li-Lan Kuo
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Yuag-Meng Liu
- Department of Internal Medicine, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Infectious Diseases, Changhua Christian Medical Foundation, Changhua Christian Hospital, Changhua, Taiwan
| | - Yu Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Biotechnology, Asia University, Taichung, Taiwan
| | - Michael M. C. Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yuh-Pyng Sher
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taipei, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- International Master’s Program of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- International Master’s Program of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Drug Development Center, China Medical University, Taichung, Taiwan
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King CR, Liu Y, Amato KA, Schaack GA, Mickelson C, Sanders AE, Hu T, Gupta S, Langlois RA, Smith JA, Mehle A. Pathogen-driven CRISPR screens identify TREX1 as a regulator of DNA self-sensing during influenza virus infection. Cell Host Microbe 2023; 31:1552-1567.e8. [PMID: 37652009 PMCID: PMC10528757 DOI: 10.1016/j.chom.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
Host:pathogen interactions dictate the outcome of infection, yet the limitations of current approaches leave large regions of this interface unexplored. Here, we develop a novel fitness-based screen that queries factors important during the middle to late stages of infection. This is achieved by engineering influenza virus to direct the screen by programming dCas9 to modulate host gene expression. Our genome-wide screen for pro-viral factors identifies the cytoplasmic DNA exonuclease TREX1. TREX1 degrades cytoplasmic DNA to prevent inappropriate innate immune activation by self-DNA. We reveal that this same process aids influenza virus replication. Infection triggers release of mitochondrial DNA into the cytoplasm, activating antiviral signaling via cGAS and STING. TREX1 metabolizes the DNA, preventing its sensing. Collectively, these data show that self-DNA is deployed to amplify innate immunity, a process tempered by TREX1. Moreover, they demonstrate the power and generality of pathogen-driven fitness-based screens to pinpoint key host regulators of infection.
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Affiliation(s)
- Cason R King
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yiping Liu
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine A Amato
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Grace A Schaack
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Clayton Mickelson
- Department of Microbiology and Immunology and the Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Autumn E Sanders
- Department of Microbiology and Immunology and the Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Tony Hu
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Srishti Gupta
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ryan A Langlois
- Department of Microbiology and Immunology and the Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Judith A Smith
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew Mehle
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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25
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Xie E, Ahmad S, Smyth RP, Sieben C. Advanced fluorescence microscopy in respiratory virus cell biology. Adv Virus Res 2023; 116:123-172. [PMID: 37524480 DOI: 10.1016/bs.aivir.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Respiratory viruses are a major public health burden across all age groups around the globe, and are associated with high morbidity and mortality rates. They can be transmitted by multiple routes, including physical contact or droplets and aerosols, resulting in efficient spreading within the human population. Investigations of the cell biology of virus replication are thus of utmost importance to gain a better understanding of virus-induced pathogenicity and the development of antiviral countermeasures. Light and fluorescence microscopy techniques have revolutionized investigations of the cell biology of virus infection by allowing the study of the localization and dynamics of viral or cellular components directly in infected cells. Advanced microscopy including high- and super-resolution microscopy techniques available today can visualize biological processes at the single-virus and even single-molecule level, thus opening a unique view on virus infection. We will highlight how fluorescence microscopy has supported investigations on virus cell biology by focusing on three major respiratory viruses: respiratory syncytial virus (RSV), Influenza A virus (IAV) and SARS-CoV-2. We will review our current knowledge of virus replication and highlight how fluorescence microscopy has helped to improve our state of understanding. We will start by introducing major imaging and labeling modalities and conclude the chapter with a perspective discussion on remaining challenges and potential opportunities.
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Affiliation(s)
- Enyu Xie
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Shazeb Ahmad
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany; Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Christian Sieben
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany.
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26
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Cui Z, Weng B, Yao Y, Shao H, Ye J, Qin A, Qian K. Chicken Glycogen Synthase Kinase 3β Suppresses Innate Immune Responses and Enhances Avian Leukosis Virus Replication in DF-1 Cells. Microbiol Spectr 2023; 11:e0523522. [PMID: 36995259 PMCID: PMC10269865 DOI: 10.1128/spectrum.05235-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/04/2023] [Indexed: 03/31/2023] Open
Abstract
Glycogen synthase kinase 3β (GSK3β) is a widely distributed multifunctional serine/threonine kinase. In mammals, GSK3β regulates important life activities such as proinflammatory response, anti-inflammatory response, immunity, and cancer development. However, the biological functions of chicken GSK3β (chGSK3β) are still unknown. In the present study, the full-length cDNA of chGSK3β was first cloned and analyzed. Absolute quantification of chicken chGSK3β in 1-day-old specific-pathogen-free birds has shown that it is widely expressed in all tissues, with the highest level in brain and the lowest level in pancreas. Overexpression of chGSK3β in DF-1 cells significantly decreased the gene expression levels of interferon beta (IFN-β), IFN regulatory factor 7 (IRF7), Toll-like receptor 3 (TLR3), melanoma differentiation-associated protein 5 (MDA5), MX-1, protein kinase R (PKR), and oligoadenylate synthase-like (OASL), while promoting the replication of avian leukosis virus subgroup J (ALV-J). Conversely, levels of most of the genes detected in this study were increased when chGSK3β expression was knocked down using small interfering RNA (siRNA), which also inhibited the replication of ALV-J. These results suggest that chGSK3β plays an important role in the antiviral innate immune response in DF-1 cells, and it will be valuable to carry out further studies on the biological functions of chGSK3β. IMPORTANCE GSK3β regulates many life activities in mammals. Recent studies revealed that chGSK3β was involved in regulating antiviral innate immunity in DF-1 cells and also could positively regulate ALV-J replication. These results provide new insights into the biofunction of chGSK3β and the virus-host interactions of ALV-J. In addition, this study provides a basis for further research on the function of GSK3 in poultry.
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Affiliation(s)
- Zhouhao Cui
- Ministry of Education Key Laboratory for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Jiangsu Key Laboratory of Preventive Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Bei Weng
- Ministry of Education Key Laboratory for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Jiangsu Key Laboratory of Preventive Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Yongxiu Yao
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Surrey, United Kingdom
| | - Hongxia Shao
- Ministry of Education Key Laboratory for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Jiangsu Key Laboratory of Preventive Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Jianqiang Ye
- Ministry of Education Key Laboratory for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Jiangsu Key Laboratory of Preventive Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Aijian Qin
- Ministry of Education Key Laboratory for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Jiangsu Key Laboratory of Preventive Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
| | - Kun Qian
- Ministry of Education Key Laboratory for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Jiangsu Key Laboratory of Preventive Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, People’s Republic of China
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27
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Zhou A, Zhang W, Wang B. Host factor TNK2 is required for influenza virus infection. Genes Genomics 2023; 45:771-781. [PMID: 37133719 DOI: 10.1007/s13258-023-01384-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 04/03/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND Host factors are required for Influenza virus infection and have great potential to become antiviral target. OBJECTIVE Here we demonstrate the role of TNK2 in influenza virus infection. CRISPR/Cas9 induced TNK2 deletion in A549 cells. METHODS CRISPR/Cas9-mediated deletion of TNK2. Western blotting and qPCR was used to measure the expression of TNK2 and other proteins. RESULTS CRISPR/Cas9-mediated deletion of TNK2 decreased the replication of influenza virus and significantly inhibited the ex-pression of viral proteins and TNK2 inhibitors (XMD8-87 and AIM-100) reduced the expression of influenza M2, while over-expression of TNK2 weakened the resistance of TNK2-knockout cells to influenza virus infection. Furthermore, a decrease of nuclear import of IAV in the infected TNK2 mutant cells was observed in 3 h post-infection. Interestingly, TNK2 deletion enhanced the colocalization of LC3 with autophagic receptor p62 and led to the attenuation of influenza virus-caused accumulation of autophagosomes in TNK2 mutant cells. Further, confocal microscopy visualization result showed that influenza viral matrix 2 (M2) was colocalized with Lamp1 in the infected TNK2 mutant cells in early infection, while almost no colocalization between M2 and Lamp1 was observed in IAV-infected wild-type cells. Moreover, TNK2 depletion also affected the trafficking of early endosome and the movement of influenza viral NP and M2. CONCLUSION Our results identified TNK2 as a critical host factor for influenza viral M2 protein trafficking, suggesting that TNK2 will be an attractive target for the development of antivirals therapeutics.
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Affiliation(s)
- Ao Zhou
- School of Animal Science and Nutritional Engineering, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Wuhan Polytechnic University, Wuhan, 430023, Hubei, China.
- Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Hubei Wuhan, Hubei, 430023, China.
| | - Wenhua Zhang
- School of Animal Science and Nutritional Engineering, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Wuhan Polytechnic University, Wuhan, 430023, Hubei, China
- Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Hubei Wuhan, Hubei, 430023, China
| | - Baoxin Wang
- School of Animal Science and Nutritional Engineering, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Wuhan Polytechnic University, Wuhan, 430023, Hubei, China
- Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Hubei Wuhan, Hubei, 430023, China
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28
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Shum D, Bhinder B, Mahida J, Radu C, Calder PA, Djaballah H. A Genome-Wide RNAi Screen Reveals Common Host-Virus Gene Signatures: Implication for Dengue Antiviral Drug Discovery. GEN BIOTECHNOLOGY 2023; 2:133-148. [PMID: 37928776 PMCID: PMC10623629 DOI: 10.1089/genbio.2023.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/02/2023] [Indexed: 11/07/2023]
Abstract
Dengue is the most common mosquito-borne viral disease that in recent years has become a major international public health concern. Dengue is a tropical neglected disease with increasing global incidences, affecting millions of people worldwide, and without the availability of specific treatments to combat it. The identification of host-target genes essential for the virus life cycle, for which effective modulators may already exist, would provide an alternative path to a rapid drug development of the much needed antidengue agents. For this purpose, we performed the first genome-wide RNAi screen, combining two high-content readouts for dengue virus infection (DENV E infection intensity) and host cell toxicity (host cell stained nuclei), against an arrayed lentiviral-based short hairpin RNA library covering 16,000 genes with a redundancy of at least 5 hairpins per gene. The screen identified 1924 gene candidates in total; of which, 1730 gene candidates abrogated dengue infection, whereas 194 gene candidates were found to enhance its infectivity in HEK293 cells. A first pass clustering analysis of hits revealed a well-orchestrated gene-network dependency on host cell homeostasis and physiology triggering distinct cellular pathways for infectivity, replication, trafficking, and egress; a second analysis revealed a comprehensive gene signature of 331 genes common to hits identified in 28 published RNAi host-viral interaction screens. Taken together, our findings provide novel antiviral molecular targets with the potential for drug discovery and development.
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Affiliation(s)
- David Shum
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, USA; Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Bhavneet Bhinder
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, USA; Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jeni Mahida
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, USA; Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Constantin Radu
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, USA; Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Paul A. Calder
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, USA; Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hakim Djaballah
- HTS Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York, USA; Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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29
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Soni S, Mebratu YA. B-cell lymphoma-2 family proteins-activated proteases as potential therapeutic targets for influenza A virus and severe acute respiratory syndrome coronavirus-2: Killing two birds with one stone? Rev Med Virol 2023; 33:e2411. [PMID: 36451345 PMCID: PMC9877712 DOI: 10.1002/rmv.2411] [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: 09/22/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led to a global health emergency. There are many similarities between SARS-CoV-2 and influenza A virus (IAV); both are single-stranded RNA viruses infecting airway epithelial cells and have similar modes of replication and transmission. Like IAVs, SARS-CoV-2 infections poses serious challenges due to the lack of effective therapeutic interventions, frequent appearances of new strains of the virus, and development of drug resistance. New approaches to control these infectious agents may stem from cellular factors or pathways that directly or indirectly interact with viral proteins to enhance or inhibit virus replication. One of the emerging concepts is that host cellular factors and pathways are required for maintaining viral genome integrity, which is essential for viral replication. Although IAVs have been studied for several years and many cellular proteins involved in their replication and pathogenesis have been identified, very little is known about how SARS-CoV-2 hijacks host cellular proteins to promote their replication. IAV induces apoptotic cell death, mediated by the B-cell lymphoma-2 (Bcl-2) family proteins in infected epithelia, and the pro-apoptotic members of this family promotes viral replication by activating host cell proteases. This review compares the life cycle and mode of replication of IAV and SARS-CoV-2 and examines the potential roles of host cellular proteins, belonging to the Bcl-2 family, in SARS-CoV-2 replication to provide future research directions.
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Affiliation(s)
- Sourabh Soni
- Division of Pulmonary, Critical Care, and Sleep MedicineDepartment of Internal MedicineThe Ohio State University Wexner Medical CenterColumbusOhioUSA
| | - Yohannes A. Mebratu
- Division of Pulmonary, Critical Care, and Sleep MedicineDepartment of Internal MedicineThe Ohio State University Wexner Medical CenterColumbusOhioUSA
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30
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ElHady AK, El-Gamil DS, Abadi AH, Abdel-Halim M, Engel M. An overview of cdc2-like kinase 1 (Clk1) inhibitors and their therapeutic indications. Med Res Rev 2023; 43:343-398. [PMID: 36262046 DOI: 10.1002/med.21928] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/07/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Over the past decade, Clk1 has been identified as a promising target for the treatment of various diseases, in which deregulated alternative splicing plays a role. First small molecules targeting Clk1 are in clinical trials for the treatment of solid cancer, where variants of oncogenic proteins derived from alternative splicing promote tumor progression. Since many infectious pathogens hi-jack the host cell's splicing machinery to ensure efficient replication, further indications in this area are under investigation, such as Influenza A, HIV-1 virus, and Trypanosoma infections, and more will likely be discovered in the future. In addition, Clk1 was found to contribute to the progression of Alzheimer's disease through causing an imbalance of tau splicing products. Interestingly, homozygous Clk1 knockout mice showed a rather mild phenotype, opposed to what might be expected in view of the profound role of Clk1 in alternative splicing. A major drawback of most Clk1 inhibitors is their insufficient selectivity; in particular, Dyrk kinases and haspin were frequently identified as off-targets, besides the other Clk isoforms. Only few inhibitors were shown to be selective over Dyrk1A and haspin, whereas no Clk1 inhibitor so far achieved selectivity over the Clk4 isoform. In this review, we carefully compiled all Clk1 inhibitors from the scientific literature and summarized their structure-activity relationships (SAR). In addition, we critically discuss the available selectivity data and describe the inhibitor's efficacy in cellular models, if reported. Thus, we provide a comprehensive overview on the current state of Clk1 drug discovery and highlight the most promising chemotypes.
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Affiliation(s)
- Ahmed K ElHady
- Department of Organic and Pharmaceutical Chemistry, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Dalia S El-Gamil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt.,Department of Chemistry, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Matthias Engel
- Department of Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
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31
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Yang ML, Chen YC, Wang CT, Chong HE, Chung NH, Leu CH, Liu FT, Lai MMC, Ling P, Wu CL, Shiau AL. Upregulation of galectin-3 in influenza A virus infection promotes viral RNA synthesis through its association with viral PA protein. J Biomed Sci 2023; 30:14. [PMID: 36823664 PMCID: PMC9948428 DOI: 10.1186/s12929-023-00901-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/11/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Influenza is one of the most important viral infections globally. Viral RNA-dependent RNA polymerase (RdRp) consists of the PA, PB1, and PB2 subunits, and the amino acid residues of each subunit are highly conserved among influenza A virus (IAV) strains. Due to the high mutation rate and emergence of drug resistance, new antiviral strategies are needed. Host cell factors are involved in the transcription and replication of influenza virus. Here, we investigated the role of galectin-3, a member of the β-galactoside-binding animal lectin family, in the life cycle of IAV infection in vitro and in mice. METHODS We used galectin-3 knockout and wild-type mice and cells to study the intracellular role of galectin-3 in influenza pathogenesis. Body weight and survival time of IAV-infected mice were analyzed, and viral production in mouse macrophages and lung fibroblasts was examined. Overexpression and knockdown of galectin-3 in A549 human lung epithelial cells were exploited to assess viral entry, viral ribonucleoprotein (vRNP) import/export, transcription, replication, virion production, as well as interactions between galectin-3 and viral proteins by immunoblotting, immunofluorescence, co-immunoprecipitation, RT-qPCR, minireplicon, and plaque assays. We also employed recombinant galectin-3 proteins to identify specific step(s) of the viral life cycle that was affected by exogenously added galectin-3 in A549 cells. RESULTS Galectin-3 levels were increased in the bronchoalveolar lavage fluid and lungs of IAV-infected mice. There was a positive correlation between galectin-3 levels and viral loads. Notably, galectin-3 knockout mice were resistant to IAV infection. Knockdown of galectin-3 significantly reduced the production of viral proteins and virions in A549 cells. While intracellular galectin-3 did not affect viral entry, it increased vRNP nuclear import, RdRp activity, and viral transcription and replication, which were associated with the interaction of galectin-3 with viral PA subunit. Galectin-3 enhanced the interaction between viral PA and PB1 proteins. Moreover, exogenously added recombinant galectin-3 proteins also enhanced viral adsorption and promoted IAV infection in A549 cells. CONCLUSION We demonstrate that galectin-3 enhances viral infection through increases in vRNP nuclear import and RdRp activity, thereby facilitating viral transcription and replication. Our findings also identify galectin-3 as a potential therapeutic target for influenza.
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Affiliation(s)
- Mei-Lin Yang
- grid.64523.360000 0004 0532 3255Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, 1, University Road, Tainan, 701401 Taiwan ,grid.413878.10000 0004 0572 9327Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Yi-Cheng Chen
- grid.64523.360000 0004 0532 3255Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, 1, University Road, Tainan, 701401 Taiwan
| | - Chung-Teng Wang
- grid.64523.360000 0004 0532 3255Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, 1, University Road, Tainan, 701401 Taiwan
| | - Hao-Earn Chong
- grid.64523.360000 0004 0532 3255Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, 1, University Road, Tainan, 701401 Taiwan
| | - Nai-Hui Chung
- grid.64523.360000 0004 0532 3255Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, 1, University Road, Tainan, 701401 Taiwan
| | - Chia-Hsing Leu
- grid.64523.360000 0004 0532 3255Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, 1, University Road, Tainan, 701401 Taiwan
| | - Fu-Tong Liu
- grid.28665.3f0000 0001 2287 1366Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Michael M. C. Lai
- grid.254145.30000 0001 0083 6092Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan ,grid.28665.3f0000 0001 2287 1366Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Pin Ling
- grid.64523.360000 0004 0532 3255Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, 1, University Road, Tainan, 701401 Taiwan
| | - Chao-Liang Wu
- Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan. .,Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, 1, University Road, Tainan, 701401, Taiwan.
| | - Ai-Li Shiau
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, 1, University Road, Tainan, 701401, Taiwan. .,Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan.
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King CR, Liu Y, Amato KA, Schaack GA, Hu T, Smith JA, Mehle A. Pathogen-driven CRISPR screens identify TREX1 as a regulator of DNA self-sensing during influenza virus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527556. [PMID: 36798235 PMCID: PMC9934597 DOI: 10.1101/2023.02.07.527556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Intracellular pathogens interact with host factors, exploiting those that enhance replication while countering those that suppress it. Genetic screens have begun to define the host:pathogen interface and establish a mechanistic basis for host-directed therapies. Yet, limitations of current approaches leave large regions of this interface unexplored. To uncover host factors with pro-pathogen functions, we developed a novel fitness-based screen that queries factors important during the middle-to-late stages of infection. This was achieved by engineering influenza virus to direct the screen by programing dCas9 to modulate host gene expression. A genome-wide screen identified the cytoplasmic DNA exonuclease TREX1 as a potent pro-viral factor. TREX1 normally degrades cytoplasmic DNA to prevent inappropriate innate immune activation by self DNA. Our mechanistic studies revealed that this same process functions during influenza virus infection to enhance replication. Infection triggered release of mitochondrial DNA into the cytoplasm, activating antiviral signaling via cGAS and STING. TREX1 metabolized the mitochondrial DNA preventing its sensing. Collectively, these data show that self-DNA is deployed to amplify host innate sensing during RNA virus infection, a process tempered by TREX1. Moreover, they demonstrate the power and generality of pathogen driven fitness-based screens to pinpoint key host regulators of intracellular pathogens.
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Affiliation(s)
- Cason R. King
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yiping Liu
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine A. Amato
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Grace A. Schaack
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tony Hu
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith A Smith
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew Mehle
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Teulière J, Bernard C, Bonnefous H, Martens J, Lopez P, Bapteste E. Interactomics: Dozens of Viruses, Co-evolving With Humans, Including the Influenza A Virus, may Actively Distort Human Aging. Mol Biol Evol 2023; 40:msad012. [PMID: 36649176 PMCID: PMC9897028 DOI: 10.1093/molbev/msad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/07/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Some viruses (e.g., human immunodeficiency virus 1 and severe acute respiratory syndrome coronavirus 2) have been experimentally proposed to accelerate features of human aging and of cellular senescence. These observations, along with evolutionary considerations on viral fitness, raised the more general puzzling hypothesis that, beyond documented sources in human genetics, aging in our species may also depend on virally encoded interactions distorting our aging to the benefits of diverse viruses. Accordingly, we designed systematic network-based analyses of the human and viral protein interactomes, which unraveled dozens of viruses encoding proteins experimentally demonstrated to interact with proteins from pathways associated with human aging, including cellular senescence. We further corroborated our predictions that specific viruses interfere with human aging using published experimental evidence and transcriptomic data; identifying influenza A virus (subtype H1N1) as a major candidate age distorter, notably through manipulation of cellular senescence. By providing original evidence that viruses may convergently contribute to the evolution of numerous age-associated pathways through co-evolution, our network-based and bipartite network-based methodologies support an ecosystemic study of aging, also searching for genetic causes of aging outside a focal aging species. Our findings, predicting age distorters and targets for anti-aging therapies among human viruses, could have fundamental and practical implications for evolutionary biology, aging study, virology, medicine, and demography.
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Affiliation(s)
- Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Charles Bernard
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Hugo Bonnefous
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Johannes Martens
- Sciences, Normes, Démocratie (SND), Sorbonne Université, CNRS, Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
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Lv C, Li Y, Wang T, Zhang Q, Qi J, Sima M, Li E, Qin T, Shi Z, Li F, Wang X, Sun W, Feng N, Yang S, Xia X, Jin N, Zhou Y, Gao Y. Taurolidine improved protection against highly pathogenetic avian influenza H5N1 virus lethal-infection in mouse model by regulating the NF-κB signaling pathway. Virol Sin 2023; 38:119-127. [PMID: 36450323 PMCID: PMC10006309 DOI: 10.1016/j.virs.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Taurolidine (TRD), a derivative of taurine, has anti-bacterial and anti-tumor effects by chemically reacting with cell-walls, endotoxins and exotoxins to inhibit the adhesion of microorganisms. However, its application in antiviral therapy is seldom reported. Here, we reported that TRD significantly inhibited the replication of influenza virus H5N1 in MDCK cells with the half-maximal inhibitory concentration (EC50) of 34.45 μg/mL. Furthermore, the drug inhibited the amplification of the cytokine storm effect and improved the survival rate of mice lethal challenged with H5N1 (protection rate was 86%). Moreover, TRD attenuated virus-induced lung damage and reduced virus titers in mice lungs. Administration of TRD reduced the number of neutrophils and increased the number of lymphocytes in the blood of H5N1 virus-infected mice. Importantly, the drug regulated the NF-κB signaling pathway by inhibiting the separation of NF-κB and IκBa, thereby reducing the expression of inflammatory factors. In conclusion, our findings suggested that TRD could act as a potential anti-influenza drug candidate in further clinical studies.
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Affiliation(s)
- Chaoxiang Lv
- College of Life Sciences, Northeast Normal University, Changchun, Jilin, 130021, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Yuanguo Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China; College of Animal Medicine, Jilin University, Changchun, 130000, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Qiqi Zhang
- College of Life Sciences, Northeast Normal University, Changchun, Jilin, 130021, China
| | - Jing Qi
- College of Life Sciences, Northeast Normal University, Changchun, Jilin, 130021, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Mingwei Sima
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China; College of Basic Medicine, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Tian Qin
- College of Life Sciences, Northeast Normal University, Changchun, Jilin, 130021, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Zhuangzhuang Shi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130033, China
| | - Fangxu Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China; College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Xuefeng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Weiyang Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Songtao Yang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China
| | - Ningyi Jin
- College of Life Sciences, Northeast Normal University, Changchun, Jilin, 130021, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China; College of Basic Medicine, Changchun University of Chinese Medicine, Changchun, 130117, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130033, China.
| | - Yifa Zhou
- College of Life Sciences, Northeast Normal University, Changchun, Jilin, 130021, China.
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Changchun, 130122, China; College of Basic Medicine, Changchun University of Chinese Medicine, Changchun, 130117, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130033, China; College of Life Sciences, Shandong Normal University, Jinan, 250014, China.
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35
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Chen J, Liu J, Chen Z, Feng D, Zhu C, Fan J, Zhang S, Zhang X, Xu J. Nonmuscle myosin IIA promotes the internalization of influenza A virus and regulates viral polymerase activity through interacting with nucleoprotein in human pulmonary cells. Virol Sin 2023; 38:128-141. [PMID: 36509386 PMCID: PMC10006312 DOI: 10.1016/j.virs.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Influenza A virus (IAV), responsible for seasonal epidemics and recurring pandemics, represents a global threat to public health. Given the risk of a potential IAV pandemic, it is increasingly important to better understand virus-host interactions and develop new anti-viral strategies. Here, we reported nonmuscle myosin IIA (MYH9)-mediated regulation of IAV infection. MYH9 depletion caused a profound inhibition of IAV infection by reducing viral attachment and internalization in human lung epithelial cells. Surprisingly, overexpression of MYH9 also led to a significant reduction in viral productive infection. Interestingly, overexpression of MYH9 retained viral attachment, internalization, or uncoating, but suppressed the viral ribonucleoprotein (vRNP) activity in a minigenome system. Further analyses found that excess MYH9 might interrupt the formation of vRNP by interacting with the viral nucleoprotein (NP) and result in the reduction of the completed vRNP in the nucleus, thereby inhibiting subsequent viral RNA transcription and replication. Together, we discovered that MYH9 can interact with IAV NP protein and engage in the regulation of vRNP complexes, thereby involving viral replication. These findings enlighten new mechanistic insights into the complicated interface of host-IAV interactions, ultimately making it an attractive target for the generation of antiviral drugs.
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Affiliation(s)
- Jian Chen
- Clinical Center for Bio-Therapy, Zhongshan Hospital, Fudan University (Xiamen Branch), Shanghai, 200032, China; Center for Infectious Disease Research, Science of Life Sciences, Westlake University, Hangzhou, 310024, China; Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Jian Liu
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Zhilu Chen
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Daobin Feng
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Cuisong Zhu
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Jun Fan
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Shuye Zhang
- Clinical Center for Bio-Therapy, Zhongshan Hospital, Fudan University (Xiamen Branch), Shanghai, 200032, China; Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.
| | - Xiaoyan Zhang
- Clinical Center for Bio-Therapy, Zhongshan Hospital, Fudan University (Xiamen Branch), Shanghai, 200032, China; Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.
| | - Jianqing Xu
- Clinical Center for Bio-Therapy, Zhongshan Hospital, Fudan University (Xiamen Branch), Shanghai, 200032, China; Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China. ORCID%
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36
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Harwood MC, Woo TT, Takeo Y, DiMaio D, Tsai B. HPV is a cargo for the COPI sorting complex during virus entry. SCIENCE ADVANCES 2023; 9:eadc9830. [PMID: 36662862 PMCID: PMC9858521 DOI: 10.1126/sciadv.adc9830] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/20/2022] [Indexed: 05/30/2023]
Abstract
During entry, human papillomavirus (HPV) traffics from the cell surface to the endosome and then to the trans-Golgi network (TGN) and Golgi apparatus. HPV must transit across the TGN/Golgi and exit these compartments to reach the nucleus to cause infection, although how these steps are accomplished is unclear. Combining cellular fractionation, unbiased proteomics, and gene knockdown strategies, we identified the coat protein complex I (COPI), a highly conserved protein complex that facilitates retrograde trafficking of cellular cargos, as a host factor required for HPV infection. Upon TGN/Golgi arrival, the cytoplasmic segment of HPV L2 binds directly to COPI. COPI depletion causes the accumulation of HPV in the TGN/Golgi, resembling the fate of a COPI binding-defective L2 mutant. We propose that the L2-COPI interaction drives HPV trafficking through the TGN and Golgi stacks during virus entry. This shows that an incoming virus is a cargo of the COPI complex.
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Affiliation(s)
- Mara C. Harwood
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tai-Ting Woo
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Yuka Takeo
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
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37
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Othumpangat S, Noti JD. β-Defensin-1 Regulates Influenza Virus Infection in Human Bronchial Epithelial Cells through the STAT3 Signaling Pathway. Pathogens 2023; 12:pathogens12010123. [PMID: 36678471 PMCID: PMC9865356 DOI: 10.3390/pathogens12010123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Understanding the host response to influenza A virus (IAV) infection is vital for developing intervention strategies. The primary barriers for invading respiratory pathogens are the respiratory tract epithelial cells and antimicrobial proteins generated by these cells. The antimicrobial peptide, β-defensin-1, has antiviral activity against both enveloped and non-enveloped viruses. Significant downregulation of β-defensin1 gene (DEFB1) expression was observed when human bronchial epithelial cells (HBEpCs) were exposed to IAV. HBEpCs overexpressing DEFB1 caused a significant reduction in IAV, that was confirmed by IAV matrix gene analysis, plaque assay, and confocal microscopy. DEFB1 expression after transfection with two micro RNAs (miRNAs), hsa-miR-186-5p and hsa-miR-340-5p, provided evidence that DEFB1 expression could be modulated by these miRNAs and hsa-miR-186-5p had a higher binding efficiency with DEFB1. Overexpression of DEFB1 in IAV-infected HBEpCs led to increased NF-κB expression. In a PCR array analysis of 84 transcription factors, either overexpressing DEFB1 or siRNA silencing of DEFB1 expression significantly modulated the expression of signal transducer and activator of transcription 3 (STAT3). In addition, Ingenuity Pathway Analysis (IPA) integrated with PCR array data showed that the JAK1/STAT3 pathway was significantly altered in cells overexpressing DEFB1, suggesting this to be one of the pathways by which defensin regulates IAV replication in HBEpCs. In conclusion, the reduction in IAV copy number in DEFB1 overexpressing cells suggests that β-defensin-1 plays a key role in regulating IAV survival through STAT3 and is a potential target for antiviral drug development.
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38
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Miyake Y, Hara Y, Umeda M, Banerjee I. Influenza A Virus: Cellular Entry. Subcell Biochem 2023; 106:387-401. [PMID: 38159235 DOI: 10.1007/978-3-031-40086-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The frequent emergence of pathogenic viruses with pandemic potential has posed a significant threat to human health and economy, despite enormous advances in our understanding of infection mechanisms and devising countermeasures through developing various prophylactic and therapeutic strategies. The recent coronavirus disease (COVID-19) pandemic has re-emphasised the importance of rigorous research on virus infection mechanisms and highlighted the need for our preparedness for potential pandemics. Although viruses cannot self-replicate, they tap into host cell factors and processes for their entry, propagation and dissemination. Upon entering the host cells, viruses ingeniously utilise the innate biological functions of the host cell to replicate themselves and maintain their existence in the hosts. Influenza A virus (IAV), which has a negative-sense, single-stranded RNA as its genome, is no exception. IAVs are enveloped viruses with a lipid bilayer derived from the host cell membrane and have a surface covered with the spike glycoprotein haemagglutinin (HA) and neuraminidase (NA). Viral genome is surrounded by an M1 shell, forming a "capsid" in the virus particle. IAV particles use HA to recognise sialic acids on the cell surface of lung epithelial cells for their attachment. After attachment to the cell surface, IAV particles are endocytosed and sorted into the early endosomes. Subsequently, as the early endosomes mature into late endosomes, the endosomal lumen becomes acidified, and the low pH of the late endosomes induces conformational reaggangements in the HA to initiate fusion between the endosomal and viral membranes. Upon fusion, the viral capsid disintegrates and the viral ribonucleoprotein (vRNP) complexes containing the viral genome are released into the cytosol. The process of viral capsid disintegration is called "uncoating". After successful uncoating, the vRNPs are imported into the nucleus by importin α/β (IMP α/β), where viral replication and transcription take place and the new vRNPs are assembled. Recently, we have biochemically elucidated the molecular mechanisms of the processes of viral capsid uncoating subsequent viral genome dissociation. In this chapter, we present the molecular details of the viral uncoating process.
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Affiliation(s)
- Yasuyuki Miyake
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Institute for Advanced Research (IAR), Nagoya University, Nagoya, Japan.
| | - Yuya Hara
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miki Umeda
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Indranil Banerjee
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali (IISER Mohali), Mohali, India.
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Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus. PLoS Biol 2022; 20:e3001934. [PMID: 36542656 PMCID: PMC9815647 DOI: 10.1371/journal.pbio.3001934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Viruses must balance their reliance on host cell machinery for replication while avoiding host defense. Influenza A viruses are zoonotic agents that frequently switch hosts, causing localized outbreaks with the potential for larger pandemics. The host range of influenza virus is limited by the need for successful interactions between the virus and cellular partners. Here we used immunocompetitive capture-mass spectrometry to identify cellular proteins that interact with human- and avian-style viral polymerases. We focused on the proviral activity of heterogenous nuclear ribonuclear protein U-like 1 (hnRNP UL1) and the antiviral activity of mitochondrial enoyl CoA-reductase (MECR). MECR is localized to mitochondria where it functions in mitochondrial fatty acid synthesis (mtFAS). While a small fraction of the polymerase subunit PB2 localizes to the mitochondria, PB2 did not interact with full-length MECR. By contrast, a minor splice variant produces cytoplasmic MECR (cMECR). Ectopic expression of cMECR shows that it binds the viral polymerase and suppresses viral replication by blocking assembly of viral ribonucleoprotein complexes (RNPs). MECR ablation through genome editing or drug treatment is detrimental for cell health, creating a generic block to virus replication. Using the yeast homolog Etr1 to supply the metabolic functions of MECR in MECR-null cells, we showed that specific antiviral activity is independent of mtFAS and is reconstituted by expressing cMECR. Thus, we propose a strategy where alternative splicing produces a cryptic antiviral protein that is embedded within a key metabolic enzyme.
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40
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Russell T, Gangotia D, Barry G. Assessing the potential of repurposing ion channel inhibitors to treat emerging viral diseases and the role of this host factor in virus replication. Biomed Pharmacother 2022; 156:113850. [DOI: 10.1016/j.biopha.2022.113850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/25/2022] [Accepted: 10/06/2022] [Indexed: 12/03/2022] Open
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41
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Dolinski AC, Homola JJ, Jankowski MD, Robinson JD, Owen JC. Host gene expression is associated with viral shedding magnitude in blue-winged teals (Spatula discors) infected with low-path avian influenza virus. Comp Immunol Microbiol Infect Dis 2022; 90-91:101909. [PMID: 36410069 PMCID: PMC10500253 DOI: 10.1016/j.cimid.2022.101909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Intraspecific variation in host infectiousness affects disease transmission dynamics in human, domestic animal, and many wildlife host-pathogen systems including avian influenza virus (AIV); therefore, identifying host factors related to host infectiousness is important for understanding, controlling, and preventing future outbreaks. Toward this goal, we used RNA-seq data collected from low pathogenicity avian influenza virus (LPAIV)-infected blue-winged teal (Spatula discors) to determine the association between host gene expression and intraspecific variation in cloacal viral shedding magnitude, the transmissible fraction of virus. We found that host genes were differentially expressed between LPAIV-infected and uninfected birds early in the infection, host genes were differentially expressed between shed level groups at one-, three-, and five-days post-infection, host gene expression was associated with LPAIV infection patterns over time, and genes of the innate immune system had a positive linear relationship with cloacal viral shedding. This study provides important insights into host gene expression patterns associated with intraspecific LPAIV shedding variation and can serve as a foundation for future studies focused on the identification of host factors that drive or permit the emergence of high viral shedding individuals.
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Affiliation(s)
- Amanda C Dolinski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jared J Homola
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Mark D Jankowski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; US Environmental Protection Agency, Region 10, Seattle, WA 98101, USA
| | - John D Robinson
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jennifer C Owen
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; Michigan State University, Department of Large Animal Clinical Sciences, 736 Wilson Road, East Lansing, MI 48824, USA.
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Gao P, Ji M, Liu X, Chen X, Liu H, Li S, Jia B, Li C, Ren L, Zhao X, Wang Q, Bi Y, Tan X, Hou B, Zhou X, Tan W, Deng T, Wang J, Gao GF, Zhang F. Apolipoprotein E mediates cell resistance to influenza virus infection. SCIENCE ADVANCES 2022; 8:eabm6668. [PMID: 36129973 PMCID: PMC9491715 DOI: 10.1126/sciadv.abm6668] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Viruses exploit host cell machinery to support their replication. Defining the cellular proteins and processes required for a virus during infection is crucial to understanding the mechanisms of virally induced disease and designing host-directed therapeutics. Here, we perform a genome-wide CRISPR-Cas9-based screening in lung epithelial cells infected with the PR/8/NS1-GFP virus and use GFPhi cell as a unique screening marker to identify host factors that inhibit influenza A virus (IAV) infection. We discovered that APOE affects influenza virus infection both in vitro and in vivo. Cell deficiency in APOE conferred substantially increased susceptibility to IAV; mice deficient in APOE manifested more severe lung pathology, increased virus load, and decreased survival rate. Mechanistically, lack of cell-produced APOE results in impaired cell cholesterol homeostasis, enhancing influenza virus attachment. Thus, we identified a previously unrecognized role of APOE in restraining IAV infection.
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Affiliation(s)
- Ping Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Miao Ji
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyuan Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaotong Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Hongtao Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihua Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Baoqian Jia
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Chao Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Ren
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Xu Tan
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Baidong Hou
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Wenjie Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Tao Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Fuping Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
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TREX (transcription/export)-NP complex exerts a dual effect on regulating polymerase activity and replication of influenza A virus. PLoS Pathog 2022; 18:e1010835. [PMID: 36084138 PMCID: PMC9491529 DOI: 10.1371/journal.ppat.1010835] [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: 05/08/2022] [Revised: 09/21/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
Influenza A viruses effectively hijack the intracellular "resources" to complete transcription and replication, which involve extensive interactions between the viral and host proteins. Herein, we screened the host factors, which belong to DExD/H-box protein family members, RNA-binding proteins or mitochondrial anchoring proteins, to investigate their effects on polymerase activity. We observed DDX39B and DDX39A, DEAD-box RNA-Helicases, exert a dual effect on regulating polymerase activity and replication of influenza A viruses. We further revealed that DDX39B and DDX39A interact with viral NP and NS1 proteins. Interestingly, the viral NP proteins could reverse the inhibitory effect of excess DDX39B or DDX39A on polymerase activity. Mechanistically, the TREX complex subunits, THOC1, THOC4 and CIP29, were recruited to DDX39B-DDX39A-NP complex in an ATP-dependent manner, via the interaction with DDX39B or DDX39A, followed by excess TREX-NP complexes interfere with the normal oligomerization state of NP depending on the ratio between the viral and host proteins. On the other hand, the TREX complex, an evolutionarily conserved protein complex, is responsible for the integration of several mRNA processing steps to export viral mRNA. Knockdown of TREX complex subunits significantly down-regulated viral titers and protein levels, accompanied by retention of viral mRNA in the nucleus. Taken together, screening the host factors that regulate the replication of influenza virus advances our understanding of viral pathogenesis and our findings point out a previously unclear mechanism of TREX complex function. In this study, we investigated the regulation of polymerase activity by host factors associated with vRNPs (PB2627E, PB2627K, PB2627 domain del, PB2627 CON) and provided novel insights into regulatory mechanisms of DDX39B and DDX39A during viral replication. Our results demonstrated that DDX39B and its paralog DDX39A inhibited polymerase activity via forming TREX-NP complex with concomitant effects on the oligomeric state of NP proteins. Moreover, TREX complex is necessary for expression of viral proteins. Our findings provided potential therapeutic targets for dealing with IAV infection.
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Xu M, Xia S, Wang M, Liu X, Li X, Chen W, Wang Y, Li H, Xia C, Chen J, Wu J. Enzymatic independent role of sphingosine kinase 2 in regulating the expression of type I interferon during influenza A virus infection. PLoS Pathog 2022; 18:e1010794. [PMID: 36070294 PMCID: PMC9451060 DOI: 10.1371/journal.ppat.1010794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Influenza virus has the ability to circumvent host innate immune system through regulating certain host factors for its effective propagation. However, the detailed mechanism is still not fully understood. Here, we report that a host sphingolipid metabolism-related factor, sphingosine kinase 2 (SPHK2), upregulated during influenza A virus (IAV) infection, promotes IAV infection in an enzymatic independent manner. The enhancement of the virus replication is not abolished in the catalytic-incompetent SPHK2 (G212E) overexpressing cells. Intriguingly, the sphingosine-1-phosphate (S1P) related factor HDAC1 also plays a crucial role in SPHK2-mediated IAV infection. We found that SPHK2 cannot facilitate IAV infection in HDAC1 deficient cells. More importantly, SPHK2 overexpression diminishes the IFN-β promoter activity upon IAV infection, resulting in the suppression of type I IFN signaling. Furthermore, ChIP-qPCR assay revealed that SPHK2 interacts with IFN-β promoter through the binding of demethylase TET3, but not with the other promoters regulated by TET3, such as TGF-β1 and IL6 promoters. The specific regulation of SPHK2 on IFN-β promoter through TET3 can in turn recruit HDAC1 to the IFN-β promoter, enhancing the deacetylation of IFN-β promoter, therefore leading to the inhibition of IFN-β transcription. These findings reveal an enzymatic independent mechanism on host SPHK2, which associates with TET3 and HDAC1 to negatively regulate type I IFN expression and thus facilitates IAV propagation.
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Affiliation(s)
- Mengqiong Xu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Sisi Xia
- Department of Biological Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Mei Wang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Xiaolian Liu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Xin Li
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Weijie Chen
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Yaohao Wang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Hongjian Li
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (HL); (CX); (JC); (JW)
| | - Chuan Xia
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, China
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
- * E-mail: (HL); (CX); (JC); (JW)
| | - Jun Chen
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Foshan Institute of Medical Microbiology, Foshan, Guangdong, China
- * E-mail: (HL); (CX); (JC); (JW)
| | - Jianguo Wu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Foshan Institute of Medical Microbiology, Foshan, Guangdong, China
- * E-mail: (HL); (CX); (JC); (JW)
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Günther SC, Martínez-Romero C, Sempere Borau M, Pham CTN, García-Sastre A, Stertz S. Proteomic Identification of Potential Target Proteins of Cathepsin W for Its Development as a Drug Target for Influenza. Microbiol Spectr 2022; 10:e0092122. [PMID: 35867415 PMCID: PMC9431242 DOI: 10.1128/spectrum.00921-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Influenza A virus (IAV) coopts numerous host factors for efficient replication. The cysteine protease cathepsin W (CTSW) has been identified as one host factor required for IAV entry, specifically for the escape of IAVs from late endosomes. However, the substrate specificity of CTSW and the proviral mechanism are thus far unknown. Here, we show that intracellular but not secreted CTSW promotes viral entry. We reveal 79 potential direct and 31 potential indirect cellular target proteins of CTSW using the high-throughput proteomic approach terminal amine isotopic labeling of substrates (TAILS) and determine the cleavage motif shared by the substrates of CTSW. Subsequent integration with data from RNA interference (RNAi) screens for IAV host factors uncovers first insights into the proviral function of CTSW. Notably, CTSW-deficient mice display a 25% increase in survival and a delay in mortality compared to wild-type mice upon IAV infection. Altogether, these findings support the development of drugs targeting CTSW as novel host-directed antiviral therapies. IMPORTANCE Influenza viruses are respiratory pathogens and pose a constant threat to human health. Although antiviral drugs are available for influenza, the emergence and spread of drug-resistant viruses is cause for concern. Therefore, the development of new antivirals with lower chances of their target viruses acquiring resistance is urgently needed to reduce the high morbidity and mortality caused by influenza. Promising alternatives to drugs targeting viral proteins are those directed against host factors required for viral replication. The cysteine protease cathepsin W (CTSW) is an important host factor for IAV replication, and its proteolytic activity is required for fusion of viral and endosomal membranes. In this work, we identify a number of hitherto unknown CTSW substrates, providing new insights into virus-host interactions, and reveal that CTSW might also play a proviral role in an in vivo model. These results support the development of CTSW as a drug target for next-generation antivirals against influenza.
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Affiliation(s)
- Sira C. Günther
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Carles Martínez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Milagros Sempere Borau
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Christine T. N. Pham
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Jheng JR, Hsieh CF, Chang YH, Ho JY, Tang WF, Chen ZY, Liu CJ, Lin TJ, Huang LY, Chern JH, Horng JT. Rosmarinic acid interferes with influenza virus A entry and replication by decreasing GSK3β and phosphorylated AKT expression levels. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:598-610. [PMID: 35650006 DOI: 10.1016/j.jmii.2022.04.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/20/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The purpose of this study was to examine the in vivo activity of rosmarinic acid (RA) - a phytochemical with antioxidant, anti-inflammatory, and antiviral properties - against influenza virus (IAV). An antibody-based kinase array and different in vitro functional assays were also applied to identify the mechanistic underpinnings by which RA may exert its anti-IAV activity. METHODS We initially examined the potential efficacy of RA using an in vivo mouse model. A time-of-addition assay and an antibody-based kinase array were subsequently applied to investigate mechanism-of-action targets for RA. The hemagglutination inhibition assay, neuraminidase inhibition assay, and cellular entry assay were also performed. RESULTS RA increased survival and prevented body weight loss in IAV-infected mice. In vitro experiments revealed that RA inhibited different IAV viruses - including oseltamivir-resistant strains. From a mechanistic point of view, RA downregulated the GSK3β and Akt signaling pathways - which are known to facilitate IAV entry and replication into host cells. CONCLUSIONS RA has promising preclinical efficacy against IAV, primarily by interfering with the GSK3β and Akt signaling pathways.
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Affiliation(s)
- Jia-Rong Jheng
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333, Taiwan; Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chung-Fan Hsieh
- Research Center for Emerging Viral Infections, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Yu-Hsiu Chang
- National Defense Medical Center, Institute of Preventive Medicine, Taipei 104, Taiwan
| | - Jin-Yuan Ho
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Wen-Fang Tang
- Research Center for Emerging Viral Infections, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Zi-Yi Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Chien-Jou Liu
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Ta-Jen Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Li-Yu Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Jyh-Haur Chern
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan
| | - Jim-Tong Horng
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333, Taiwan; Research Center for Emerging Viral Infections, Chang Gung University, Kweishan, Taoyuan 333, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 333, Taiwan; Research Center for Food and Cosmetic Safety, Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan.
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Fénéant L, Leske A, Günther K, Groseth A. Generation of Reporter-Expressing New World Arenaviruses: A Systematic Comparison. Viruses 2022; 14:v14071563. [PMID: 35891543 PMCID: PMC9317149 DOI: 10.3390/v14071563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 02/01/2023] Open
Abstract
Replication-competent reporter-expressing viruses are crucial tools in molecular virology with applications that range from antiviral screening to live-cell imaging of protein spatiotemporal dynamics. However, there is currently little information available regarding viable strategies to develop reporter-expressing arenaviruses. To address this, we used Tacaribe virus (TCRV), an apathogenic BSL2 arenavirus, to assess the feasibility of different reporter expression approaches. We first generated trisegmented TCRV viruses with either the glycoprotein (GP) or nucleoprotein (NP) replaced by a reporter (GFP, mCherry, or nanoluciferase). These viruses were all viable, but showed marked differences in brightness and attenuation. Next, we generated terminal fusions with each of the TCRV proteins (i.e., NP, GP, polymerase (L), matrix protein (Z)) either with or without a T2A self-cleavage site. We tested both the function of the reporter-fused proteins alone, and the viability of corresponding recombinant TCRVs. We successfully rescued viruses with both direct and cleavable reporter fusions at the C-terminus of Z, as well as cleavable N-terminal fusions with NP. These viruses all displayed detectable reporter activity, but were also moderately attenuated. Finally, reporter proteins were inserted into a flexible hinge region within L. These viruses were also viable and showed moderate attenuation; however, reporter expression was only detectable for the luminescent virus. These strategies provide an exciting range of new tools for research into the molecular biology of TCRV that can likely also be adapted to other arenaviruses.
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Liu M, Huang LZX, Smits AA, Büll C, Narimatsu Y, van Kuppeveld FJM, Clausen H, de Haan CAM, de Vries E. Human-type sialic acid receptors contribute to avian influenza A virus binding and entry by hetero-multivalent interactions. Nat Commun 2022; 13:4054. [PMID: 35831293 PMCID: PMC9279479 DOI: 10.1038/s41467-022-31840-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
Establishment of zoonotic viruses, causing pandemics like the Spanish flu and Covid-19, requires adaptation to human receptors. Pandemic influenza A viruses (IAV) that crossed the avian-human species barrier switched from binding avian-type α2-3-linked sialic acid (2-3Sia) to human-type 2-6Sia receptors. Here, we show that this specificity switch is however less dichotomous as generally assumed. Binding and entry specificity were compared using mixed synthetic glycan gradients of 2-3Sia and 2-6Sia and by employing a genetically remodeled Sia repertoire on the surface of a Sia-free cell line and on a sialoglycoprotein secreted from these cells. Expression of a range of (mixed) 2-3Sia and 2-6Sia densities shows that non-binding human-type receptors efficiently enhanced avian IAV binding and entry provided the presence of a low density of high affinity avian-type receptors, and vice versa. Considering the heterogeneity of sialoglycan receptors encountered in vivo, hetero-multivalent binding is physiologically relevant and will impact evolutionary pathways leading to host adaptation. It is believed that human Influenza HA glycoprotein attaches to alpha2-6 linked sialic acids (SA) on cells, while avian viruses bind to alpha2-3 linked sialic acids, therewith contributing to host tropism. Here, Liu et al. show that mixing low-affinity alpha2-3 SA with low amounts of high-affinity alpha2-6 SA increases binding and entry of human viruses and the converse for avian virus. This shows that receptor recognition is not as strict as currently assumed and provides evidence that heteromultivalent interactions between human/avian HA and SA contributes to host adaptation.
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Affiliation(s)
- Mengying Liu
- Virology group, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Liane Z X Huang
- Virology group, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Anthony A Smits
- Virology group, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Christian Büll
- Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.,Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Yoshiki Narimatsu
- Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Frank J M van Kuppeveld
- Virology group, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Henrik Clausen
- Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Cornelis A M de Haan
- Virology group, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Erik de Vries
- Virology group, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Zhao L, Zhao Y, Liu Q, Huang J, Lu Y, Ping J. DDX5/METTL3-METTL14/YTHDF2 Axis Regulates Replication of Influenza A Virus. Microbiol Spectr 2022; 10:e0109822. [PMID: 35583334 PMCID: PMC9241928 DOI: 10.1128/spectrum.01098-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022] Open
Abstract
DEAD-box helicase 5 (DDX5), a member of the DEAD/H-box helicases, is known to participate in all aspects of RNA metabolism. However, its regulatory effect in antiviral innate immunity during replication of influenza virus remains unclear. Herein, we found that human DDX5 promotes replication of influenza virus in A549 cells. Moreover, our results further revealed that DDX5 relies on its N terminus to interact with the nucleoprotein (NP) of influenza virus, which is independent of RNA. Of course, we also observed colocalization of DDX5 with NP in the context of transfection or infection. However, influenza virus infection had no significant effect on the protein expression and nucleocytoplasmic distribution of DDX5. Importantly, we found that DDX5 suppresses antiviral innate immunity induced by influenza virus infection. Mechanistically, DDX5 downregulated the mRNA levels of interferon beta (IFN-β), interleukin 6 (IL-6), and DHX58 via the METTL3-METTL14/YTHDF2 axis. We revealed that DDX5 bound antiviral transcripts and regulated immune responses through YTHDF2-dependent mRNA decay. Taken together, our data demonstrate that the DDX5/METTL3-METTL14/YTHDF2 axis regulates the replication of influenza A virus. IMPORTANCE The replication and transcription of influenza virus depends on the participation of many host factors in cells. Exploring the relationship between viruses and host factors will help us fully understand the characteristics and pathogenic mechanisms of influenza viruses. In this study, we showed that DDX5 interacted with the NP of influenza virus. We demonstrated that DDX5 downregulated the expression of IFN-β and IL-6 and the transcription of antiviral genes downstream from IFN-β in influenza virus-infected A549 cells. Additionally, DDX5 downregulated the mRNA levels of antiviral transcripts via the METTL3-METTL14/YTHDF2 axis. Our findings provide a novel perspective to understand the mechanism by which DDX5 regulates antiviral immunity.
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Affiliation(s)
- Lingcai Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yongzhen Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qingzheng Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jingjin Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yuanlu Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jihui Ping
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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50
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Puerta-Guardo H, Biering SB, de Sousa FTG, Shu J, Glasner DR, Li J, Blanc SF, Beatty PR, Harris E. Flavivirus NS1 Triggers Tissue-Specific Disassembly of Intercellular Junctions Leading to Barrier Dysfunction and Vascular Leak in a GSK-3β-Dependent Manner. Pathogens 2022; 11:615. [PMID: 35745469 PMCID: PMC9228372 DOI: 10.3390/pathogens11060615] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 02/05/2023] Open
Abstract
The flavivirus nonstructural protein 1 (NS1) is secreted from infected cells and contributes to endothelial barrier dysfunction and vascular leak in a tissue-dependent manner. This phenomenon occurs in part via disruption of the endothelial glycocalyx layer (EGL) lining the endothelium. Additionally, we and others have shown that soluble DENV NS1 induces disassembly of intercellular junctions (IJCs), a group of cellular proteins critical for maintaining endothelial homeostasis and regulating vascular permeability; however, the specific mechanisms by which NS1 mediates IJC disruption remain unclear. Here, we investigated the relative contribution of five flavivirus NS1 proteins, from dengue (DENV), Zika (ZIKV), West Nile (WNV), Japanese encephalitis (JEV), and yellow fever (YFV) viruses, to the expression and localization of the intercellular junction proteins β-catenin and VE-cadherin in endothelial cells from human umbilical vein and brain tissues. We found that flavivirus NS1 induced the mislocalization of β-catenin and VE-cadherin in a tissue-dependent manner, reflecting flavivirus disease tropism. Mechanistically, we observed that NS1 treatment of cells triggered internalization of VE-cadherin, likely via clathrin-mediated endocytosis, and phosphorylation of β-catenin, part of a canonical IJC remodeling pathway during breakdown of endothelial barriers that activates glycogen synthase kinase-3β (GSK-3β). Supporting this model, we found that a chemical inhibitor of GSK-3β reduced both NS1-induced permeability of human umbilical vein and brain microvascular endothelial cell monolayers in vitro and vascular leakage in a mouse dorsal intradermal model. These findings provide insight into the molecular mechanisms regulating NS1-mediated endothelial dysfunction and identify GSK-3β as a potential therapeutic target for treatment of vascular leakage during severe dengue disease.
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Affiliation(s)
- Henry Puerta-Guardo
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720-3370, USA; (S.B.B.); (F.T.G.d.S.); (J.S.); (D.R.G.); (J.L.); (S.F.B.); (P.R.B.)
- Laboratorio de Virologia, CIR-Biomedicas y Unidad Colaborativa de Bioensayos Entomologicos (UCBE), Universidad Autonoma de Yucatan, Merida 97000, Mexico
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720-3370, USA; (S.B.B.); (F.T.G.d.S.); (J.S.); (D.R.G.); (J.L.); (S.F.B.); (P.R.B.)
| | - Francielle Tramontini Gomes de Sousa
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720-3370, USA; (S.B.B.); (F.T.G.d.S.); (J.S.); (D.R.G.); (J.L.); (S.F.B.); (P.R.B.)
| | - Jeffrey Shu
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720-3370, USA; (S.B.B.); (F.T.G.d.S.); (J.S.); (D.R.G.); (J.L.); (S.F.B.); (P.R.B.)
| | - Dustin R. Glasner
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720-3370, USA; (S.B.B.); (F.T.G.d.S.); (J.S.); (D.R.G.); (J.L.); (S.F.B.); (P.R.B.)
| | - Jeffrey Li
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720-3370, USA; (S.B.B.); (F.T.G.d.S.); (J.S.); (D.R.G.); (J.L.); (S.F.B.); (P.R.B.)
| | - Sophie F. Blanc
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720-3370, USA; (S.B.B.); (F.T.G.d.S.); (J.S.); (D.R.G.); (J.L.); (S.F.B.); (P.R.B.)
| | - P. Robert Beatty
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720-3370, USA; (S.B.B.); (F.T.G.d.S.); (J.S.); (D.R.G.); (J.L.); (S.F.B.); (P.R.B.)
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720-3370, USA; (S.B.B.); (F.T.G.d.S.); (J.S.); (D.R.G.); (J.L.); (S.F.B.); (P.R.B.)
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