101
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Zhao X, Chen D, Li X, Griffith L, Chang J, An P, Guo JT. Interferon Control of Human Coronavirus Infection and Viral Evasion: Mechanistic Insights and Implications for Antiviral Drug and Vaccine Development. J Mol Biol 2022; 434:167438. [PMID: 34990653 PMCID: PMC8721920 DOI: 10.1016/j.jmb.2021.167438] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 12/16/2022]
Abstract
Recognition of viral infections by various pattern recognition receptors (PRRs) activates an inflammatory cytokine response that inhibits viral replication and orchestrates the activation of adaptive immune responses to control the viral infection. The broadly active innate immune response puts a strong selective pressure on viruses and drives the selection of variants with increased capabilities to subvert the induction and function of antiviral cytokines. This revolutionary process dynamically shapes the host ranges, cell tropism and pathogenesis of viruses. Recent studies on the innate immune responses to the infection of human coronaviruses (HCoV), particularly SARS-CoV-2, revealed that HCoV infections can be sensed by endosomal toll-like receptors and/or cytoplasmic RIG-I-like receptors in various cell types. However, the profiles of inflammatory cytokines and transcriptome response induced by a specific HCoV are usually cell type specific and determined by the virus-specific mechanisms of subverting the induction and function of interferons and inflammatory cytokines as well as the genetic trait of the host genes of innate immune pathways. We review herein the recent literatures on the innate immune responses and their roles in the pathogenesis of HCoV infections with emphasis on the pathobiological roles and therapeutic effects of type I interferons in HCoV infections and their antiviral mechanisms. The knowledge on the mechanism of innate immune control of HCoV infections and viral evasions should facilitate the development of therapeutics for induction of immune resolution of HCoV infections and vaccines for efficient control of COVID-19 pandemics and other HCoV infections.
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Affiliation(s)
- Xuesen Zhao
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.
| | - Danying Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xinglin Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Lauren Griffith
- Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Jinhong Chang
- Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Ping An
- Basic Research Laboratory, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA.
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102
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Jung C, Kmiec D, Koepke L, Zech F, Jacob T, Sparrer KMJ, Kirchhoff F. Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning? J Virol 2022; 96:e0207721. [PMID: 35225672 PMCID: PMC8941872 DOI: 10.1128/jvi.02077-21] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/27/2022] [Indexed: 11/20/2022] Open
Abstract
Emerging strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, that show increased transmission fitness and/or immune evasion are classified as "variants of concern" (VOCs). Recently, a SARS-CoV-2 variant first identified in November 2021 in South Africa has been recognized as a fifth VOC, termed "Omicron." What makes this VOC so alarming is the high number of changes, especially in the viral Spike protein, and accumulating evidence for increased transmission efficiency and escape from neutralizing antibodies. In an amazingly short time, the Omicron VOC has outcompeted the previously dominating Delta VOC. However, it seems that the Omicron VOC is overall less pathogenic than other SARS-CoV-2 VOCs. Here, we provide an overview of the mutations in the Omicron genome and the resulting changes in viral proteins compared to other SARS-CoV-2 strains and discuss their potential functional consequences.
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Affiliation(s)
- Christoph Jung
- Institute of Electrochemistry, Ulm University, Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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103
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Singh AK, Wang R, Lombardo KA, Praharaj M, Bullen CK, Um P, Davis S, Komm O, Illei PB, Ordonez AA, Bahr M, Huang J, Gupta A, Psoter KJ, Jain SK, Bivalacqua TJ, Yegnasubramanian S, Bishai WR. Dynamic single-cell RNA sequencing reveals BCG vaccination curtails SARS-CoV-2 induced disease severity and lung inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.15.484018. [PMID: 35313583 PMCID: PMC8936112 DOI: 10.1101/2022.03.15.484018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
COVID-19 continues to exact a toll on human health despite the availability of several vaccines. Bacillus Calmette Guérin (BCG) has been shown to confer heterologous immune protection against viral infections including COVID-19 and has been proposed as vaccine against SARS-CoV-2 (SCV2). Here we tested intravenous BCG vaccination against COVID-19 using the golden Syrian hamster model together with immune profiling and single cell RNA sequencing (scRNAseq). We observed that BCG reduced both lung SCV2 viral load and bronchopneumonia. This was accompanied by an increase in lung alveolar macrophages, a reversal of SCV2-mediated T cell lymphopenia, and reduced lung granulocytes. Single cell transcriptome profiling showed that BCG uniquely recruits immunoglobulin-producing plasma cells to the lung suggesting accelerated antibody production. BCG vaccination also recruited elevated levels of Th1, Th17, Treg, CTLs, and Tmem cells, and differentially expressed gene (DEG) analysis showed a transcriptional shift away from exhaustion markers and towards antigen presentation and repair. Similarly, BCG enhanced lung recruitment of alveolar macrophages and reduced key interstitial macrophage subsets, with both cell-types also showing reduced IFN-associated gene expression. Our observations indicate that BCG vaccination protects against SCV2 immunopathology by promoting early lung immunoglobulin production and immunotolerizing transcriptional patterns among key myeloid and lymphoid populations.
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Affiliation(s)
- Alok K. Singh
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Rulin Wang
- Sydney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Kara A. Lombardo
- Johns Hopkins University, School of Medicine, Department of Urology, Baltimore, MD, USA
| | - Monali Praharaj
- Bloomberg~Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD, USA
| | - C. Korin Bullen
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Peter Um
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Stephanie Davis
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Oliver Komm
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Peter B. Illei
- Johns Hopkins University, School of Medicine, Department of Pathology, Baltimore, MD, USA
| | - Alvaro A. Ordonez
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore MD, USA
| | - Melissa Bahr
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore MD, USA
| | - Joy Huang
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
| | - Anuj Gupta
- Sydney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Kevin J. Psoter
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of General Pediatrics, Baltimore, MD, USA
| | - Sanjay K. Jain
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore MD, USA
| | - Trinity J. Bivalacqua
- Perelman School of Medicine at the University of Pennsylvania, Division of Urology, Department of Surgery, Philadelphia, PA, USA
| | | | - William R. Bishai
- Johns Hopkins University, School of Medicine, Department of Medicine, Center for Tuberculosis Research, Baltimore, MD, USA
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104
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Kim J, Koo BK, Clevers H. Organoid Studies in COVID-19 Research. Int J Stem Cells 2022; 15:3-13. [PMID: 35220288 PMCID: PMC8889327 DOI: 10.15283/ijsc21251] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/15/2022] [Indexed: 01/08/2023] Open
Affiliation(s)
- Jihoon Kim
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, Korea
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Korea
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands
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105
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Feng Z, Xu L, Xie Z. Receptors for Respiratory Syncytial Virus Infection and Host Factors Regulating the Life Cycle of Respiratory Syncytial Virus. Front Cell Infect Microbiol 2022; 12:858629. [PMID: 35281439 PMCID: PMC8913501 DOI: 10.3389/fcimb.2022.858629] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 12/02/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a common cause of lower respiratory tract infections and responsible for a large proportion of mortality in children and the elderly. There are no licensed vaccines available to date. Prophylaxis and therapeutic RSV-specific antibodies are limited to populations at high risk owing to high cost and uncertain clinical value. Receptors and host factors are two determinants important for virus entry and establishment of infection in vivo. The identification and understanding of viral receptors and host factors can help us to gain insight into the pathogenesis of RSV infection. Herein, we reviewed receptors and host factors that have been reported thus far. RSV could bind to CX3C chemokine receptor 1 and heparan sulfate proteoglycans via the G protein, and to nucleolin, insulin-like growth factor-1 receptor, epidermal growth factor, and intercellular adhesion molecule-1 via the F protein. Seven host restriction factors and 13 host factors essential for RSV infection were reviewed. We characterized the functions and their roles in the life cycle of RSV, trying to provide an update on the information of RSV-related receptors and host factors.
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Affiliation(s)
- Ziheng Feng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Lili Xu,
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, China
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106
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Zhang Y, Almazi JG, Ong HX, Johansen MD, Ledger S, Traini D, Hansbro PM, Kelleher AD, Ahlenstiel CL. Nanoparticle Delivery Platforms for RNAi Therapeutics Targeting COVID-19 Disease in the Respiratory Tract. Int J Mol Sci 2022; 23:2408. [PMID: 35269550 PMCID: PMC8909959 DOI: 10.3390/ijms23052408] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Since December 2019, a pandemic of COVID-19 disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread across the globe. At present, the Food and Drug Administration (FDA) has issued emergency approval for the use of some antiviral drugs. However, these drugs still have limitations in the specific treatment of COVID-19, and as such, new treatment strategies urgently need to be developed. RNA-interference-based gene therapy provides a tractable target for antiviral treatment. Ensuring cell-specific targeted delivery is important to the success of gene therapy. The use of nanoparticles (NPs) as carriers for the delivery of small interfering RNA (siRNAs) to specific tissues or organs of the human body could play a crucial role in the specific therapy of severe respiratory infections, such as COVID-19. In this review, we describe a variety of novel nanocarriers, such as lipid NPs, star polymer NPs, and glycogen NPs, and summarize the pre-clinical/clinical progress of these nanoparticle platforms in siRNA delivery. We also discuss the application of various NP-capsulated siRNA as therapeutics for SARS-CoV-2 infection, the challenges with targeting these therapeutics to local delivery in the lung, and various inhalation devices used for therapeutic administration. We also discuss currently available animal models that are used for preclinical assessment of RNA-interference-based gene therapy. Advances in this field have the potential for antiviral treatments of COVID-19 disease and could be adapted to treat a range of respiratory diseases.
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Affiliation(s)
- Yuan Zhang
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
| | - Juhura G. Almazi
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Hui Xin Ong
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW 2050, Australia; (M.D.J.); (P.M.H.)
| | - Scott Ledger
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
| | - Daniela Traini
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW 2050, Australia; (M.D.J.); (P.M.H.)
| | - Anthony D. Kelleher
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
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107
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Rahmani W, Chung H, Sinha S, Bui-Marinos MP, Arora R, Jaffer A, Corcoran JA, Biernaskie J, Chun J. Attenuation of SARS-CoV-2 infection by losartan in human kidney organoids. iScience 2022; 25:103818. [PMID: 35106453 PMCID: PMC8795780 DOI: 10.1016/j.isci.2022.103818] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 11/04/2021] [Accepted: 01/21/2022] [Indexed: 12/27/2022] Open
Abstract
COVID-19-associated acute kidney injury (COVID-AKI) is a common complication of SARS-CoV-2 infection in hospitalized patients. The susceptibility of human kidneys to direct SARS-CoV-2 infection and modulation of the renin-angiotensin II signaling (RAS) pathway by viral infection remain poorly characterized. Using induced pluripotent stem cell-derived kidney organoids, SARS-CoV-1, SARS-CoV-2, and MERS-CoV tropism, defined by the paired expression of a host receptor (ACE2, NRP1 or DPP4) and protease (TMPRSS2, TMPRSS4, FURIN, CTSB or CTSL), was identified primarily among proximal tubule cells. Losartan, an angiotensin II receptor blocker being tested in patients with COVID-19, inhibited angiotensin II-mediated internalization of ACE2, upregulated interferon-stimulated genes (IFITM1 and BST2) known to restrict viral entry, and attenuated the infection of proximal tubule cells by SARS-CoV-2. Our work highlights the susceptibility of proximal tubule cells to SARS-CoV-2 and reveals a putative protective role for RAS inhibitors during SARS-CoV-2 infection. SARS-CoV-2 kidney organoid tropism is primarily among proximal tubule cells Losartan attenuates angiotensin II-mediated ACE2 internalization Losartan upregulates viral restrictive genes IFITM1 and BST2 SARS-CoV-2 infection is enhanced by angiotensin II and attenuated by losartan
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Affiliation(s)
- Waleed Rahmani
- Department of Medicine, Health Research Innovation Centre 4A12, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada.,Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Hyunjae Chung
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sarthak Sinha
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Heritage Medical Research Building, Room 402, 3300 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Maxwell P Bui-Marinos
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Microbiology, Immunology and Infectious Diseases Department and Charbonneau Cancer Research Institute, University of Calgary, Calgary, AB, Canada
| | - Rohit Arora
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Heritage Medical Research Building, Room 402, 3300 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Arzina Jaffer
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Heritage Medical Research Building, Room 402, 3300 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Jennifer A Corcoran
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Microbiology, Immunology and Infectious Diseases Department and Charbonneau Cancer Research Institute, University of Calgary, Calgary, AB, Canada
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Heritage Medical Research Building, Room 402, 3300 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Justin Chun
- Department of Medicine, Health Research Innovation Centre 4A12, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada.,Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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108
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Sahajpal NS, Jill Lai CY, Hastie A, Mondal AK, Dehkordi SR, van der Made CI, Fedrigo O, Al-Ajli F, Jalnapurkar S, Byrska-Bishop M, Kanagal-Shamanna R, Levy B, Schieck M, Illig T, Bacanu SA, Chou JS, Randolph AG, Rojiani AM, Zody MC, Brownstein CA, Beggs AH, Bafna V, Jarvis ED, Hoischen A, Chaubey A, Kolhe R. Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19. iScience 2022; 25:103760. [PMID: 35036860 PMCID: PMC8744399 DOI: 10.1016/j.isci.2022.103760] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/04/2021] [Accepted: 01/07/2022] [Indexed: 12/16/2022] Open
Abstract
Impressive global efforts have identified both rare and common gene variants associated with severe COVID-19 using sequencing technologies. However, these studies lack the sensitivity to accurately detect several classes of variants, especially large structural variants (SVs), which account for a substantial proportion of genetic diversity including clinically relevant variation. We performed optical genome mapping on 52 severely ill COVID-19 patients to identify rare/unique SVs as decisive predisposition factors associated with COVID-19. We identified 7 SVs involving genes implicated in two key host-viral interaction pathways: innate immunity and inflammatory response, and viral replication and spread in nine patients, of which SVs in STK26 and DPP4 genes are the most intriguing candidates. This study is the first to systematically assess the potential role of SVs in the pathogenesis of COVID-19 severity and highlights the need to evaluate SVs along with sequencing variants to comprehensively associate genomic information with interindividual variability in COVID-19 phenotypes.
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Affiliation(s)
- Nikhil Shri Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA
| | | | - Alex Hastie
- Bionano Genomics, Inc., San Diego, CA 92121, USA
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA
| | - Siavash Raeisi Dehkordi
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA 92093, USA
| | - Caspar I. van der Made
- Department of Human Genetics, Radboud University Medical Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, and Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
| | - Farooq Al-Ajli
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
| | - Sawan Jalnapurkar
- Department of Medicine, Medical College of Georgia, Augusta University, GA 30912, USA
| | | | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York 10032, USA
| | - Maximilian Schieck
- Department of Human Genetics, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover 30625, Germany
| | - Thomas Illig
- Department of Human Genetics, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover 30625, Germany
- Hannover Unified Biobank (HUB), Hannover 30625, Germany
| | - Silviu-Alin Bacanu
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Janet S. Chou
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Adrienne G. Randolph
- Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Departments of Anesthesia and Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Amyn M. Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA
| | | | - Catherine A. Brownstein
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alan H. Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA 92093, USA
| | - Erich D. Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, and Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Alka Chaubey
- Department of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA
- Bionano Genomics, Inc., San Diego, CA 92121, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA
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109
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Abstract
Virus entry, consisting of attachment to and penetration into the host target cell, is the first step of the virus life cycle and is a critical 'do or die' event that governs virus emergence in host populations. Most antiviral vaccines induce neutralizing antibodies that prevent virus entry into cells. However, while the prevention of virus invasion by humoral immunity is well appreciated, considerably less is known about the immune defences present within cells (known as intrinsic immunity) that interfere with virus entry. The interferon-induced transmembrane (IFITM) proteins, known for inhibiting fusion between viral and cellular membranes, were once the only factors known to restrict virus entry. However, the progressive development of genetic and pharmacological screening platforms and the onset of the COVID-19 pandemic have galvanized interest in how viruses infiltrate cells and how cells defend against it. Several host factors with antiviral potential are now implicated in the regulation of virus entry, including cholesterol 25-hydroxylase (CH25H), lymphocyte antigen 6E (LY6E), nuclear receptor co-activator protein 7 (NCOA7), interferon-γ-inducible lysosomal thiol reductase (GILT), CD74 and ARFGAP with dual pleckstrin homology domain-containing protein 2 (ADAP2). This Review summarizes what is known and what remains to be understood about the intrinsic factors that form the first line of defence against virus infection.
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110
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Das T, Yang X, Lee H, Garst E, Valencia E, Chandran K, Im W, Hang H. S-palmitoylation and sterol interactions mediate antiviral specificity of IFITM isoforms. RESEARCH SQUARE 2021:rs.3.rs-1179000. [PMID: 34981045 PMCID: PMC8722608 DOI: 10.21203/rs.3.rs-1179000/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Interferon-induced transmembrane proteins (IFITM1, 2 and 3) are important antiviral proteins that are active against many viruses, including influenza A virus (IAV), dengue virus (DENV), Ebola virus (EBOV), Zika virus (ZIKV) and severe acute respiratory syndrome coronavirus (SARS-CoV). IFITMs exhibit isoform-specific activity, but their distinct mechanisms of action and regulation are unclear. Since S -palmitoylation and cholesterol homeostasis are crucial for viral infections, we investigated IFITM interactions with cholesterol by molecular dynamic stimulations, nuclear magnetic resonance analysis in vitro and photoaffinity crosslinking in mammalian cells. These studies suggest that cholesterol can alter the conformation of IFITMs in membrane bilayers and directly interact with S -palmitoylated IFITMs in cells. Notably, we discovered that the S -palmitoylation levels regulate differential IFITM isoform interactions with cholesterol in mammalian cells and specificity of antiviral activity towards IAV, SARS-CoV-2 and EBOV. Our studies suggest that modulation of IFITM S -palmitoylation levels and cholesterol interaction may influence host susceptibility to different viruses.
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Affiliation(s)
| | | | | | | | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
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111
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Cioccarelli C, Sánchez-Rodríguez R, Angioni R, Venegas FC, Bertoldi N, Munari F, Cattelan A, Molon B, Viola A. IL1β Promotes TMPRSS2 Expression and SARS-CoV-2 Cell Entry Through the p38 MAPK-GATA2 Axis. Front Immunol 2021; 12:781352. [PMID: 34950146 PMCID: PMC8691651 DOI: 10.3389/fimmu.2021.781352] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/16/2021] [Indexed: 01/14/2023] Open
Abstract
After the outburst of the SARS-CoV-2 pandemic, a worldwide research effort has led to the uncovering of many aspects of the COVID-19, among which we can count the outstanding role played by inflammatory cytokine milieu in the disease progression. Despite that, molecular mechanisms that regulate SARS-CoV-2 pathogenesis are still almost unidentified. In this study, we investigated whether the pro-inflammatory milieu of the host affects the susceptibility of SARS-CoV-2 infection by modulating ACE2 and TMPRSS2 expression. Our results indicated that the host inflammatory milieu favors SARS-CoV-2 infection by directly increasing TMPRSS2 expression. We unveiled the molecular mechanism that regulates this process and that can be therapeutically advantageously targeted.
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Affiliation(s)
- Chiara Cioccarelli
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica (IRP), Fondazione Città della Speranza, Padova, Italy
| | - Ricardo Sánchez-Rodríguez
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica (IRP), Fondazione Città della Speranza, Padova, Italy
| | - Roberta Angioni
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica (IRP), Fondazione Città della Speranza, Padova, Italy
| | - Francisca C Venegas
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica (IRP), Fondazione Città della Speranza, Padova, Italy
| | - Nicole Bertoldi
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica (IRP), Fondazione Città della Speranza, Padova, Italy
| | - Fabio Munari
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica (IRP), Fondazione Città della Speranza, Padova, Italy
| | | | - Barbara Molon
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica (IRP), Fondazione Città della Speranza, Padova, Italy
| | - Antonella Viola
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatrica (IRP), Fondazione Città della Speranza, Padova, Italy
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112
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Zani A, Kenney AD, Kawahara J, Eddy AC, Wang XL, Kc M, Lu M, Hemann EA, Li J, Peeples ME, Hall-Stoodley L, Forero A, Cai C, Ma J, Yount JS. Interferon-induced transmembrane protein 3 (IFITM3) limits lethality of SARS-CoV-2 in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.22.473914. [PMID: 34981061 PMCID: PMC8722598 DOI: 10.1101/2021.12.22.473914] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Interferon-induced transmembrane protein 3 (IFITM3) is a host antiviral protein that alters cell membranes to block fusion of viruses. Published reports have identified conflicting pro- and antiviral effects of IFITM3 on SARS-CoV-2 in cultured cells, and its impact on viral pathogenesis in vivo remains unclear. Here, we show that IFITM3 knockout (KO) mice infected with mouse-adapted SARS-CoV-2 experienced extreme weight loss and lethality, while wild type (WT) mice lost minimal weight and recovered. KO mice had higher lung viral titers and increases in lung inflammatory cytokine levels, CD45-positive immune cell infiltration, and histopathology, compared to WT mice. Mechanistically, we observed disseminated viral antigen staining throughout the lung tissue and pulmonary vasculature in KO mice, while staining was observed in confined regions in WT lungs. Global transcriptomic analysis of infected lungs identified upregulation of gene signatures associated with interferons, inflammation, and angiogenesis in KO versus WT animals, highlighting changes in lung gene expression programs that precede severe lung pathology and fatality. Corroborating the protective effect of IFITM3 in vivo , K18-hACE2/IFITM3 KO mice infected with non-adapted SARS-CoV-2 showed enhanced, rapid weight loss and early death compared to control mice. Increased heart infection was observed in both mouse models in the absence of IFITM3, indicating that IFITM3 constrains extrapulmonary dissemination of SARS-CoV-2. Our results establish IFITM3 KO mice as a new animal model for studying severe SARS-CoV-2 infection of the lung and cardiovascular system, and overall demonstrate that IFITM3 is protective in SARS-CoV-2 infections of mice.
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113
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Hossain MG, Tang YD, Akter S, Zheng C. Roles of the polybasic furin cleavage site of spike protein in SARS-CoV-2 replication, pathogenesis, and host immune responses and vaccination. J Med Virol 2021; 94:1815-1820. [PMID: 34936124 DOI: 10.1002/jmv.27539] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/11/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
Abstract
The polybasic furin cleavage site insertion with four amino acid motifs (PRRA) in spike protein's S1/S2 junction site is important in determining viral infectivity, transmission, and host range. However, there is no review so far explaining the effect of the furin cleavage site of the spike protein on SARS-CoV-2 replication and pathogenesis in the host and immune responses and vaccination. Therefore, here we specifically focused on genomic evolution and properties of the cleavage site of spike protein in the context of SARS-CoV-2 followed by its effect on viral entry, replication, and pathogenesis. We also explored whether the spike protein furin cleavage site affected the host immune responses and SARS-CoV-2 vaccination. This review will help to provide novel insights into the effects of polybasic furin cleavage site on the current COVID-19 pandemic.
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Affiliation(s)
- Md Golzar Hossain
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Yan-Dong Tang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Sharmin Akter
- Department of Physiology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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114
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Interferon-Induced Transmembrane Proteins Inhibit Infection by the Kaposi's Sarcoma-Associated Herpesvirus and the Related Rhesus Monkey Rhadinovirus in a Cell-Specific Manner. mBio 2021; 12:e0211321. [PMID: 34933450 PMCID: PMC8689460 DOI: 10.1128/mbio.02113-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The interferon-induced transmembrane proteins (IFITMs) are broad-spectrum antiviral proteins that inhibit the entry of enveloped viruses. We analyzed the effect of IFITMs on the gamma-2 herpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV) and the closely related rhesus monkey rhadinovirus (RRV). We used CRISPR/Cas9-mediated gene knockout to generate A549 cells, human foreskin fibroblasts (HFF), and human umbilical vein endothelial cells (HUVEC) with combined IFITM1/2/3 knockout and identified IFITMs as cell-dependent inhibitors of KSHV and RRV infection in A549 cells and HFF but not HUVEC. IFITM overexpression revealed IFITM1 as the relevant IFITM that inhibits KSHV and RRV infection. Fluorescent KSHV particles did not pronouncedly colocalize with IFITM-positive compartments. However, we found that KSHV and RRV glycoprotein-mediated cell-cell fusion is enhanced upon IFITM1/2/3 knockout. Taken together, we identified IFITM1 as a cell-dependent restriction factor of KSHV and RRV that acts at the level of membrane fusion. Of note, our results indicate that recombinant IFITM overexpression may lead to results that are not representative for the situation at endogenous levels. Strikingly, we observed that the endotheliotropic KSHV circumvents IFITM-mediated restriction in HUVEC despite high IFITM expression, while influenza A virus (IAV) glycoprotein-driven entry into HUVEC is potently restricted by IFITMs even in the absence of interferon. Mechanistically, we found that KSHV colocalizes less with IFITM1 and IFITM2 in HUVEC than in A549 cells immediately after attachment, potentially contributing to the observed difference in restriction. IMPORTANCE IFITM proteins are the first line of defense against infection by many pathogens and may also have therapeutic importance, as they, among other effectors, mediate the antiviral effect of interferons. Neither their function against herpesviruses nor their mechanism of action is well understood. We report here that in some cells but not in, for example, primary umbilical vein endothelial cells, IFITM1 restricts KSHV and RRV and that, mechanistically, this is likely effected by reducing the fusogenicity of the cell membrane. Further, we demonstrate potent inhibition of IAV glycoprotein-driven infection of cells of extrapulmonary origin by high constitutive IFITM expression.
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115
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Cuesta-Llavona E, Albaiceta GM, García-Clemente M, Duarte-Herrera ID, Amado-Rodríguez L, Hermida-Valverde T, Enríquez-Rodriguez AI, Hernández-González C, Melón S, Alvarez-Argüelles ME, Boga JA, Rojo-Alba S, Vázquez-Coto D, Gómez J, Coto E. Association between the interferon-induced transmembrane protein 3 gene ( IFITM3) rs34481144 / rs12252 haplotypes and COVID-19. CURRENT RESEARCH IN VIROLOGICAL SCIENCE 2021; 2:100016. [PMID: 34870250 PMCID: PMC8629514 DOI: 10.1016/j.crviro.2021.100016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/26/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022]
Abstract
The interferon induced transmembrane-protein 3 (IFITM3) plays an important role in the defence against viral infection. IFITM3 gene variants have been linked to differences in expression and associated with the risk of severe influenza by some authors. More recently, these variants have been associated with the risk of COVID-19 after SARS-CoV-2 infection. We determined the effect of two common IFITM3 polymorphisms (rs34481144 C/T and rs12252 A/G) on the risk of hospitalization due to COVID-19 by comparing 484 patients (152 required support in thr intensive care unit, ICU) and 182 age and sex matched controls (no disease symptoms). We found significantly higher frequencies of rs34481144 T and rs12252 G carriers among the patients (OR = 2.02 and OR = 1.51, respectively). None of the two variants were associated with ICU-admission or death. We found a significantly higher frequency of rs34481144 CC + rs12252 AA genotype carriers among the controls, suggesting a protective effect (p = 0.001, OR = 0.56, 95%CI = 0.40–0.80). Moreover, haplotype rs34481144 C - rs12252 A was significantly increased in the controls (p = 0.008, OR = 0.71, 95%CI = 0.55–0.91). Our results showed a significant effect of the IFITM3 variants in the risk for hospitalization after SARS-CoV-2 infection.
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Affiliation(s)
- Elías Cuesta-Llavona
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - Guillermo M Albaiceta
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain.,Universidad de Oviedo, Oviedo, Spain.,CIBER-Enfermedades Respiratorias. Instituto de Salud Carlos III. Madrid, Spain.,Instituto Universitario de Oncología del Principado de Asturias. Oviedo, Spain
| | - Marta García-Clemente
- Neumología, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | | | - Laura Amado-Rodríguez
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain.,Universidad de Oviedo, Oviedo, Spain.,CIBER-Enfermedades Respiratorias. Instituto de Salud Carlos III. Madrid, Spain.,Instituto Universitario de Oncología del Principado de Asturias. Oviedo, Spain
| | - Tamara Hermida-Valverde
- Neumología, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - Ana I Enríquez-Rodriguez
- Neumología, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - Cristina Hernández-González
- Neumología, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - Santiago Melón
- Microbiologia, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - Marta E Alvarez-Argüelles
- Microbiologia, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - José A Boga
- Microbiologia, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - Susana Rojo-Alba
- Microbiologia, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | | | - Juan Gómez
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - Eliecer Coto
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain.,Universidad de Oviedo, Oviedo, Spain
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116
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Hatton CF, Botting RA, Dueñas ME, Haq IJ, Verdon B, Thompson BJ, Spegarova JS, Gothe F, Stephenson E, Gardner AI, Murphy S, Scott J, Garnett JP, Carrie S, Powell J, Khan CMA, Huang L, Hussain R, Coxhead J, Davey T, Simpson AJ, Haniffa M, Hambleton S, Brodlie M, Ward C, Trost M, Reynolds G, Duncan CJA. Delayed induction of type I and III interferons mediates nasal epithelial cell permissiveness to SARS-CoV-2. Nat Commun 2021; 12:7092. [PMID: 34876592 PMCID: PMC8651658 DOI: 10.1038/s41467-021-27318-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
The nasal epithelium is a plausible entry point for SARS-CoV-2, a site of pathogenesis and transmission, and may initiate the host response to SARS-CoV-2. Antiviral interferon (IFN) responses are critical to outcome of SARS-CoV-2. Yet little is known about the interaction between SARS-CoV-2 and innate immunity in this tissue. Here we apply single-cell RNA sequencing and proteomics to a primary cell model of human nasal epithelium differentiated at air-liquid interface. SARS-CoV-2 demonstrates widespread tropism for nasal epithelial cell types. The host response is dominated by type I and III IFNs and interferon-stimulated gene products. This response is notably delayed in onset relative to viral gene expression and compared to other respiratory viruses. Nevertheless, once established, the paracrine IFN response begins to impact on SARS-CoV-2 replication. When provided prior to infection, recombinant IFNβ or IFNλ1 induces an efficient antiviral state that potently restricts SARS-CoV-2 viral replication, preserving epithelial barrier integrity. These data imply that the IFN-I/III response to SARS-CoV-2 initiates in the nasal airway and suggest nasal delivery of recombinant IFNs to be a potential chemoprophylactic strategy.
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Affiliation(s)
- Catherine F Hatton
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Iram J Haq
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Bernard Verdon
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Benjamin J Thompson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Jarmila Stremenova Spegarova
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Florian Gothe
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Aaron I Gardner
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sandra Murphy
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Scott
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - James P Garnett
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sean Carrie
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jason Powell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - C M Anjam Khan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lei Huang
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Rafiqul Hussain
- Genomics Core Facility, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Coxhead
- Genomics Core Facility, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tracey Davey
- Electron Microscopy Research Services, Newcastle University, Newcastle upon Tyne, UK
| | - A John Simpson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Department of Dermatology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Malcolm Brodlie
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Chris Ward
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthias Trost
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J A Duncan
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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117
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When good turns bad: how viruses exploit innate immunity factors. Curr Opin Virol 2021; 52:60-67. [PMID: 34872031 DOI: 10.1016/j.coviro.2021.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/11/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022]
Abstract
Humans evolved numerous cell-intrinsic restriction factors as a first line of defense against viral pathogens. Typically, they inhibit efficient viral replication and thus prevent viral zoonoses and pandemics. However, viruses show enormous adaptability and are well known for their ability to counteract antiviral mechanisms. Accumulating evidence shows that some viruses are even capable of exploiting antiviral factors for efficient infection. In addition, antiviral factors may exert enhancing effects under specific circumstances. While much progress has been made in understanding the antiviral mechanisms of restriction factors, their proviral effects are poorly defined. Here, we summarize current knowledge on how viral pathogens may exploit otherwise antiviral cellular factors for efficient infection and replication.
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118
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Mavrikaki M, Lee JD, Solomon IH, Slack FJ. Severe COVID-19 induces molecular signatures of aging in the human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.11.24.21266779. [PMID: 34845457 PMCID: PMC8629201 DOI: 10.1101/2021.11.24.21266779] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is predominantly an acute respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and remains a significant threat to public health. COVID-19 is accompanied by neurological symptoms and cognitive decline, but the molecular mechanisms underlying this effect remain unclear. As aging induces distinct molecular signatures in the brain associated with cognitive decline in healthy populations, we hypothesized that COVID-19 may induce molecular signatures of aging. Here, we performed whole transcriptomic analysis of human frontal cortex, a critical area for cognitive function, in 12 COVID-19 cases and age- and sex-matched uninfected controls. COVID-19 induces profound changes in gene expression, despite the absence of detectable virus in brain tissue. Pathway analysis shows downregulation of genes involved in synaptic function and cognition and upregulation of genes involved in immune processes. Comparison with five independent transcriptomic datasets of aging human frontal cortex reveals striking similarities between aged individuals and severe COVID-19 patients. Critically, individuals below 65 years of age exhibit profound transcriptomic changes not observed among older individuals in our patient cohort. Our data indicate that severe COVID-19 induces molecular signatures of aging in the human brain and emphasize the value of neurological follow-up in recovered individuals.
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Affiliation(s)
- Maria Mavrikaki
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally: Maria Mavrikaki and Jonathan D. Lee
- Correspondence to M.M. and F.J.S.: ;
| | - Jonathan D. Lee
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally: Maria Mavrikaki and Jonathan D. Lee
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Frank J. Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02215, USA
- Correspondence to M.M. and F.J.S.: ;
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119
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Regulation of Viral Restriction by Post-Translational Modifications. Viruses 2021; 13:v13112197. [PMID: 34835003 PMCID: PMC8618861 DOI: 10.3390/v13112197] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/17/2022] Open
Abstract
Intrinsic immunity is orchestrated by a wide range of host cellular proteins called restriction factors. They have the capacity to interfere with viral replication, and most of them are tightly regulated by interferons (IFNs). In addition, their regulation through post-translational modifications (PTMs) constitutes a major mechanism to shape their action positively or negatively. Following viral infection, restriction factor modification can be decisive. Palmitoylation of IFITM3, SUMOylation of MxA, SAMHD1 and TRIM5α or glycosylation of BST2 are some of those PTMs required for their antiviral activity. Nonetheless, for their benefit and by manipulating the PTMs machinery, viruses have evolved sophisticated mechanisms to counteract restriction factors. Indeed, many viral proteins evade restriction activity by inducing their ubiquitination and subsequent degradation. Studies on PTMs and their substrates are essential for the understanding of the antiviral defense mechanisms and provide a global vision of all possible regulations of the immune response at a given time and under specific infection conditions. Our aim was to provide an overview of current knowledge regarding the role of PTMs on restriction factors with an emphasis on their impact on viral replication.
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120
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Vavougios GD, Breza M, Mavridis T, Krogfelt KA. FYN, SARS-CoV-2, and IFITM3 in the neurobiology of Alzheimer's disease. BRAIN DISORDERS 2021. [DOI: 10.1016/j.dscb.2021.100022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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121
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Lv T, Meng F, Yu M, Huang H, Lin X, Zhao B. Defense of COVID-19 by Human Organoids. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:113-128. [PMID: 35233559 PMCID: PMC8277987 DOI: 10.1007/s43657-021-00015-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has created an immense menace to public health worldwide, exerting huge effects on global economic and political conditions. Understanding the biology and pathogenesis mechanisms of this novel virus, in large parts, relies on optimal physiological models that allow replication and propagation of SARS-CoV-2. Human organoids, derived from stem cells, are three-dimensional cell cultures that recapitulate the cellular organization, transcriptional and epigenetic signatures of their counterpart organs. Recent studies have indicated their great values as experimental virology platforms, making human organoid an ideal tool for investigating host-pathogen interactions. Here, we summarize research developments for SARS-CoV-2 infection of various human organoids involved in multiple systems, including lung, liver, brain, intestine, kidney and blood vessel organoids. These studies help us reveal the pathogenesis mechanism of COVID-19, and facilitate the development of effective vaccines and drugs as well as other therapeutic regimes.
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Affiliation(s)
- Ting Lv
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438 China
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 200040 China
| | - Fanlu Meng
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023 China
| | - Meng Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438 China
| | - Haihui Huang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 200040 China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438 China
| | - Bing Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438 China
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