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Demian WL, Cormier O, Mossman K. Immunological features of bats: resistance and tolerance to emerging viruses. Trends Immunol 2024; 45:198-210. [PMID: 38453576 DOI: 10.1016/j.it.2024.01.008] [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: 12/14/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 03/09/2024]
Abstract
Bats are among the most diverse mammalian species, representing over 20% of mammalian diversity. The past two decades have witnessed a disproportionate spillover of viruses from bats to humans compared with other mammalian hosts, attributed to the viral richness within bats, their phylogenetic likeness to humans, and increased human contact with wildlife. Unique evolutionary adaptations in bat genomes, particularly in antiviral protection and immune tolerance genes, enable bats to serve as reservoirs for pandemic-inducing viruses. Here, we discuss current limitations and advances made in understanding the role of bats as drivers of pandemic zoonoses. We also discuss novel technologies that have revealed spatial, dynamic, and physiological factors driving virus and host coevolution.
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Affiliation(s)
- Wael L Demian
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Olga Cormier
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
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2
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Edalat F, Khakpour N, Heli H, Letafati A, Ramezani A, Hosseini SY, Moattari A. Immunological mechanisms of the nucleocapsid protein in COVID-19. Sci Rep 2024; 14:3711. [PMID: 38355695 PMCID: PMC10867304 DOI: 10.1038/s41598-024-53906-3] [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: 09/24/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
The emergence of corona virus disease 2019 (COVID-19), resulting from Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has left an indelible mark on a global scale, causing countless infections and fatalities. This investigation delves into the role of the SARS-CoV-2 nucleocapsid (N) protein within the HEK293 cells, shedding light on its influence over apoptosis, interferon signaling, and cytokines production. The N gene was amplified, inserted into the pAdTrack-CMV vector, and then transfected to the HEK293 cells. Changes in the expression of IRF3, IRF7, IFN-β, BAK, BAX, and BCL-2 genes were evaluated. The levels of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α were also determined. The N protein exhibited an anti-apoptotic effect by modulating critical genes associated with apoptosis, including BAK, BAX, and BCL-2. This effect potentially prolonged the survival of infected cells. The N protein also played a role in immune evasion by suppressing the interferon pathway, evidenced by the downregulation of essential interferon regulatory factors of IRF3 and IRF7, and IFN-β expression. The N protein expression led to a substantial increase in the production of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α. The N protein emerged as a versatile factor and was exerted over apoptosis, interferon signaling, and cytokine production. These findings carry potential implications for the development of targeted therapies to combat COVID-19 and mitigate its global health impact.
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Affiliation(s)
- Fahime Edalat
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Heli
- Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Younes Hosseini
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran.
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Bhargava A, Szachnowski U, Chazal M, Foretek D, Caval V, Aicher SM, Pipoli da Fonseca J, Jeannin P, Beauclair G, Monot M, Morillon A, Jouvenet N. Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2. iScience 2023; 26:108449. [PMID: 38213785 PMCID: PMC10783605 DOI: 10.1016/j.isci.2023.108449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.
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Affiliation(s)
- Anvita Bhargava
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Ugo Szachnowski
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Dominika Foretek
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Vincent Caval
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Sophie-Marie Aicher
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | | | - Patricia Jeannin
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité Épidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Guillaume Beauclair
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Marc Monot
- Institut Pasteur, Université de Paris, Biomics Platform, C2RT, 75015 Paris, France
| | - Antonin Morillon
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
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Demian WL, Jacob RA, Cormier O, Nazli A, Melki M, Asavajaru A, Baid K, Zhang A, Miller MS, Kaushic C, Banerjee A, Mossman K. ASK1 inhibitors are potential pan-antiviral drugs, which dampen replication of diverse viruses including SARS-CoV2. Antiviral Res 2023; 220:105736. [PMID: 37863359 DOI: 10.1016/j.antiviral.2023.105736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Apoptosis signal-regulating kinase 1 (ASK1)/MAP3K5 is a stress response kinase that is activated by various stimuli. It is known as an upstream activator of p38- Mitogen-activated protein kinase (p38MAPK) and c-Jun N-terminal kinase (JNK) that are reactive oxygen species (ROS)-induced kinases. Accumulating evidence show that ROS accumulate in virus-infected cells. Here, we investigated the relationship between viruses and ASK1/p38MAPK or ASK1/JNK pathways. Our findings suggest that virus infection activates ASK1 related pathways. In parallel, ASK1 inhibition led to a remarkable reduction in the replication of a broad range of viruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), vaccinia virus (VV), vesicular stomatitis virus (VSV), Herpes Simplex Virus (HSV), and Human Immunodeficiency virus (HIV) in different human cell lines. Our work demonstrates the potential therapeutic use of Selonsertib, an ASK1 inhibitor, as a pan-antiviral drug in humans. Surprisingly, we observed differential effects of Selonsertib in in vitro and in vivo hamster models, suggesting caution in using rodent models to predict clinical and therapeutic outcomes in humans.
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Affiliation(s)
- Wael L Demian
- Department of Medicine, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Rajesh Abraham Jacob
- Department of Medicine, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Olga Cormier
- Department of Medicine, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Aisha Nazli
- Department of Medicine, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Matthew Melki
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Akarin Asavajaru
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
| | - Kaushal Baid
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada
| | - Ali Zhang
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Matthew S Miller
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Charu Kaushic
- Department of Medicine, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, S7N 5E3, Canada; Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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Potamias G, Gkoublia P, Kanterakis A. The two-stage molecular scenery of SARS-CoV-2 infection with implications to disease severity: An in-silico quest. Front Immunol 2023; 14:1251067. [PMID: 38077337 PMCID: PMC10699200 DOI: 10.3389/fimmu.2023.1251067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction The two-stage molecular profile of the progression of SARS-CoV-2 (SCOV2) infection is explored in terms of five key biological/clinical questions: (a) does SCOV2 exhibits a two-stage infection profile? (b) SARS-CoV-1 (SCOV1) vs. SCOV2: do they differ? (c) does and how SCOV2 differs from Influenza/INFL infection? (d) does low viral-load and (e) does COVID-19 early host response relate to the two-stage SCOV2 infection profile? We provide positive answers to the above questions by analyzing the time-series gene-expression profiles of preserved cell-lines infected with SCOV1/2 or, the gene-expression profiles of infected individuals with different viral-loads levels and different host-response phenotypes. Methods Our analytical methodology follows an in-silico quest organized around an elaborate multi-step analysis pipeline including: (a) utilization of fifteen gene-expression datasets from NCBI's gene expression omnibus/GEO repository; (b) thorough designation of SCOV1/2 and INFL progression stages and COVID-19 phenotypes; (c) identification of differentially expressed genes (DEGs) and enriched biological processes and pathways that contrast and differentiate between different infection stages and phenotypes; (d) employment of a graph-based clustering process for the induction of coherent groups of networked genes as the representative core molecular fingerprints that characterize the different SCOV2 progression stages and the different COVID-19 phenotypes. In addition, relying on a sensibly selected set of induced fingerprint genes and following a Machine Learning approach, we devised and assessed the performance of different classifier models for the differentiation of acute respiratory illness/ARI caused by SCOV2 or other infections (diagnostic classifiers), as well as for the prediction of COVID-19 disease severity (prognostic classifiers), with quite encouraging results. Results The central finding of our experiments demonstrates the down-regulation of type-I interferon genes (IFN-1), interferon induced genes (ISGs) and fundamental innate immune and defense biological processes and molecular pathways during the early SCOV2 infection stages, with the inverse to hold during the later ones. It is highlighted that upregulation of these genes and pathways early after infection may prove beneficial in preventing subsequent uncontrolled hyperinflammatory and potentially lethal events. Discussion The basic aim of our study was to utilize in an intuitive, efficient and productive way the most relevant and state-of-the-art bioinformatics methods to reveal the core molecular mechanisms which govern the progression of SCOV2 infection and the different COVID-19 phenotypes.
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Affiliation(s)
- George Potamias
- Computational Biomedicine Laboratory (CBML), Institute of Computer Science, Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Polymnia Gkoublia
- Computational Biomedicine Laboratory (CBML), Institute of Computer Science, Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
- Graduate Bioinformatics Program, School of Medicine, University of Crete, Heraklion, Greece
| | - Alexandros Kanterakis
- Computational Biomedicine Laboratory (CBML), Institute of Computer Science, Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
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Pereira EPV, da Silva Felipe SM, de Freitas RM, da Cruz Freire JE, Oliveira AER, Canabrava N, Soares PM, van Tilburg MF, Guedes MIF, Grueter CE, Ceccatto VM. Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways. Pathogens 2023; 12:1373. [PMID: 38003837 PMCID: PMC10674242 DOI: 10.3390/pathogens12111373] [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: 09/15/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The COVID-19 disease, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), emerged in late 2019 and rapidly spread worldwide, becoming a pandemic that infected millions of people and caused significant deaths. COVID-19 continues to be a major threat, and there is a need to deepen our understanding of the virus and its mechanisms of infection. To study the cellular responses to SARS-CoV-2 infection, we performed an RNA sequencing of infected vs. uninfected Calu-3 cells. Total RNA was extracted from infected (0.5 MOI) and control Calu-3 cells and converted to cDNA. Sequencing was performed, and the obtained reads were quality-analyzed and pre-processed. Differential expression was assessed with the EdgeR package, and functional enrichment was performed in EnrichR for Gene Ontology, KEGG pathways, and WikiPathways. A total of 1040 differentially expressed genes were found in infected vs. uninfected Calu-3 cells, of which 695 were up-regulated and 345 were down-regulated. Functional enrichment analyses revealed the predominant up-regulation of genes related to innate immune response, response to virus, inflammation, cell proliferation, and apoptosis. These transcriptional changes following SARS-CoV-2 infection may reflect a cellular response to the infection and help to elucidate COVID-19 pathogenesis, in addition to revealing potential biomarkers and drug targets.
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Affiliation(s)
- Eric Petterson Viana Pereira
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - Stela Mirla da Silva Felipe
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - Raquel Martins de Freitas
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - José Ednésio da Cruz Freire
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | | | - Natália Canabrava
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (N.C.); (M.F.v.T.); (M.I.F.G.)
| | - Paula Matias Soares
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - Mauricio Fraga van Tilburg
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (N.C.); (M.F.v.T.); (M.I.F.G.)
| | - Maria Izabel Florindo Guedes
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (N.C.); (M.F.v.T.); (M.I.F.G.)
| | - Chad Eric Grueter
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Vânia Marilande Ceccatto
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
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Schoen A, Hölzer M, Müller MA, Wallerang KB, Drosten C, Marz M, Lamp B, Weber F. Functional comparisons of the virus sensor RIG-I from humans, the microbat Myotis daubentonii, and the megabat Rousettus aegyptiacus, and their response to SARS-CoV-2 infection. J Virol 2023; 97:e0020523. [PMID: 37728614 PMCID: PMC10653997 DOI: 10.1128/jvi.00205-23] [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: 02/07/2023] [Accepted: 07/09/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE A common hypothesis holds that bats (order Chiroptera) are outstanding reservoirs for zoonotic viruses because of a special antiviral interferon (IFN) system. However, functional studies about key components of the bat IFN system are rare. RIG-I is a cellular sensor for viral RNA signatures that activates the antiviral signaling chain to induce IFN. We cloned and functionally characterized RIG-I genes from two species of the suborders Yangochiroptera and Yinpterochiroptera. The bat RIG-Is were conserved in their sequence and domain organization, and similar to human RIG-I in (i) mediating virus- and IFN-activated gene expression, (ii) antiviral signaling, (iii) temperature dependence, and (iv) recognition of RNA ligands. Moreover, RIG-I of Rousettus aegyptiacus (suborder Yinpterochiroptera) and of humans were found to recognize SARS-CoV-2 infection. Thus, members of both bat suborders encode RIG-Is that are comparable to their human counterpart. The ability of bats to harbor zoonotic viruses therefore seems due to other features.
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Affiliation(s)
- Andreas Schoen
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Martin Hölzer
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
- European Virus Bioinformatics Center, Jena, Germany
| | - Marcel A. Müller
- German Centre for Infection Research (DZIF), Partner Sites Giessen and Charité, Berlin, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Kai B. Wallerang
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Christian Drosten
- European Virus Bioinformatics Center, Jena, Germany
- German Centre for Infection Research (DZIF), Partner Sites Giessen and Charité, Berlin, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
- European Virus Bioinformatics Center, Jena, Germany
| | - Benjamin Lamp
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
- European Virus Bioinformatics Center, Jena, Germany
- German Centre for Infection Research (DZIF), Partner Sites Giessen and Charité, Berlin, Germany
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Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen L, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB. Regulation of human interferon signaling by transposon exonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557241. [PMID: 37745311 PMCID: PMC10515820 DOI: 10.1101/2023.09.11.557241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Innate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues, and functions as a decoy receptor that potently inhibits interferon signaling including in cells infected with SARS-CoV-2. Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.
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Affiliation(s)
- Giulia Irene Maria Pasquesi
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303
| | - Holly Allen
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Atma Ivancevic
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Olivia Joyner
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - David M. Simpson
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Keala Gapin
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Isabella Horton
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Lily Nguyen
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Qing Yang
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109
| | - Cody J. Warren
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- The Ohio State University College of Veterinary Medicine, Columbus, OH, 43210
| | - Liliana D. Florea
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
| | - Benjamin G. Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Sara L. Sawyer
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Edward B. Chuong
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303
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Lücke J, Heinrich F, Malsy J, Meins N, Schnell J, Böttcher M, Nawrocki M, Zhang T, Bertram F, Sabihi M, Kempski J, Blankenburg T, Duprée A, Reeh M, Wolter S, Mann O, Izbicki JR, Lohse AW, Gagliani N, Lütgehetmann M, Bunders MJ, Altfeld M, Sauter G, Giannou AD, Krasemann S, Ondruschka B, Huber S. Intestinal IL-1β Plays a Role in Protecting against SARS-CoV-2 Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1052-1061. [PMID: 37556130 PMCID: PMC10476162 DOI: 10.4049/jimmunol.2200844] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/11/2023] [Indexed: 08/10/2023]
Abstract
The intestine is constantly balancing the maintenance of a homeostatic microbiome and the protection of the host against pathogens such as viruses. Many cytokines mediate protective inflammatory responses in the intestine, among them IL-1β. IL-1β is a proinflammatory cytokine typically activated upon specific danger signals sensed by the inflammasome. SARS-CoV-2 is capable of infecting multiple organs, including the intestinal tract. Severe cases of COVID-19 were shown to be associated with a dysregulated immune response, and blocking of proinflammatory pathways was demonstrated to improve patient survival. Indeed, anakinra, an Ab against the receptor of IL-1β, has recently been approved to treat patients with severe COVID-19. However, the role of IL-1β during intestinal SARS-CoV-2 infection has not yet been investigated. Here, we analyzed postmortem intestinal and blood samples from patients who died of COVID-19. We demonstrated that high levels of intestinal IL-1β were associated with longer survival time and lower intestinal SARS-CoV-2 RNA loads. Concurrently, type I IFN expression positively correlated with IL-1β levels in the intestine. Using human intestinal organoids, we showed that autocrine IL-1β sustains RNA expression of IFN type I by the intestinal epithelial layer. These results outline a previously unrecognized key role of intestinal IL-1β during SARS-CoV-2 infection.
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Affiliation(s)
- Jöran Lücke
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Heinrich
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jakob Malsy
- I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
- German Center for Infection Research, Hamburg-Lubeck-Borstel-Riems, Germany
| | - Nicholas Meins
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Josa Schnell
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marius Böttcher
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mikolaj Nawrocki
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tao Zhang
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franziska Bertram
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Morsal Sabihi
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Kempski
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tom Blankenburg
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Duprée
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Reeh
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Wolter
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Oliver Mann
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jakob R. Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ansgar W. Lohse
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Gagliani
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Madeleine J. Bunders
- Leibniz Institute of Virology, Hamburg, Germany
- III Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anastasios D. Giannou
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Susanne Krasemann
- Institute for Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Ondruschka
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- Section of Molecular Immunology and Gastroenterology, I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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10
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Ramirez GA, Gerosa M, Bellocchi C, Arroyo-Sánchez D, Asperti C, Argolini LM, Gallina G, Cornalba M, Scotti I, Suardi I, Moroni L, Beretta L, Bozzolo EP, Caporali R, Dagna L. Efficacy and Safety of Anti-SARS-CoV-2 Antiviral Agents and Monoclonal Antibodies in Patients with SLE: A Case-Control Study. Biomolecules 2023; 13:1273. [PMID: 37759674 PMCID: PMC10527378 DOI: 10.3390/biom13091273] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/15/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related disease (COVID-19) has spread pandemically with high rates of morbidity and mortality. COVID-19 has also posed unprecedented challenges in terms of rapid development of pharmacological countermeasures to prevent or contrast SARS-CoV-2 pathogenicity. Anti-SARS-CoV-2 antiviral agents and monoclonal antibodies have been specifically designed to attenuate COVID-19 morbidity and prevent mortality in vulnerable subjects, such as patients with immune-mediated diseases, but evidence for the safe and effective use of these drugs in this latter population group is scarce. Therefore, we designed a retrospective, multicentre, observational, case-control study to analyse the impact of these treatments in COVID-19 patients with systemic lupus erythematosus (SLE), a paradigmatic, multi-organ autoimmune disease. We identified 21 subjects treated with antivirals and/or monoclonal antibodies who were matched with 42 untreated patients by age, sex, SLE extension and duration. Treated patients had higher baseline SLE disease activity index 2000 scores [SLEDAI-2K median (interquartile range) = 4 (1-5) vs. 0 (0-2); p = 0.009], higher prednisone doses [5 (0-10) mg vs. 0 (0-3) mg; p = 0.002], and more severe COVID-19 symptoms by a five-point World Health Organisation-endorsed analogue scale [1 (0-1) vs. 0 (0-1); p < 0.010] compared to untreated patients. There was no difference between groups in terms of COVID-19 outcomes and sequelae, nor in terms of post-COVID-19 SLE exacerbations. Three subjects reported mild adverse events (two with monoclonal antibodies, one with nirmatrelvir/ritonavir). These data suggest that anti-SARS-CoV-2 antivirals and monoclonal antibodies might be safely and effectively used in patients with SLE, especially with active disease and more severe COVID-19 symptoms at presentation.
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Affiliation(s)
- Giuseppe A. Ramirez
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy; (D.A.-S.); (C.A.); (G.G.); (L.M.); (E.P.B.); (L.D.)
- Faculty of Medicine, Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Maria Gerosa
- Department of Clinical Science of Community Health, Research Center for Adult and Pediatric Rheumatic Diseases, Università degli Studi di Milano, Via Festa del Perdono 7, 20122 Milan, Italy; (M.G.); (L.M.A.); (M.C.); (I.S.); (I.S.); (R.C.)
- Unit of Rheumatology, ASST Gaetano Pini-CTO, Piazza Cardinale Andrea Ferrari 1, 20122 Milan, Italy
| | - Chiara Bellocchi
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Via Francesco Sforza 35, 20122 Milan, Italy; (C.B.); (L.B.)
- Department of Clinical Science of Community Health, Section of Internal Medicine, Università degli Studi di Milano, Via Festa del Perdono 7, 20122 Milan, Italy
| | - Daniel Arroyo-Sánchez
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy; (D.A.-S.); (C.A.); (G.G.); (L.M.); (E.P.B.); (L.D.)
- Department of Immunology, Hospital Universitario 12 de Octubre, Av de Córdoba, 28041 Madrid, Spain
- Department of Immunology, Instituto de Investigación Biomédica, Hospital Universitario 12 de Octubre, Av de Córdoba, 28041 Madrid, Spain
| | - Chiara Asperti
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy; (D.A.-S.); (C.A.); (G.G.); (L.M.); (E.P.B.); (L.D.)
- Faculty of Medicine, Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Lorenza M. Argolini
- Department of Clinical Science of Community Health, Research Center for Adult and Pediatric Rheumatic Diseases, Università degli Studi di Milano, Via Festa del Perdono 7, 20122 Milan, Italy; (M.G.); (L.M.A.); (M.C.); (I.S.); (I.S.); (R.C.)
- Unit of Rheumatology, ASST Gaetano Pini-CTO, Piazza Cardinale Andrea Ferrari 1, 20122 Milan, Italy
| | - Gabriele Gallina
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy; (D.A.-S.); (C.A.); (G.G.); (L.M.); (E.P.B.); (L.D.)
- Faculty of Medicine, Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Martina Cornalba
- Department of Clinical Science of Community Health, Research Center for Adult and Pediatric Rheumatic Diseases, Università degli Studi di Milano, Via Festa del Perdono 7, 20122 Milan, Italy; (M.G.); (L.M.A.); (M.C.); (I.S.); (I.S.); (R.C.)
- Unit of Rheumatology, ASST Gaetano Pini-CTO, Piazza Cardinale Andrea Ferrari 1, 20122 Milan, Italy
| | - Isabella Scotti
- Department of Clinical Science of Community Health, Research Center for Adult and Pediatric Rheumatic Diseases, Università degli Studi di Milano, Via Festa del Perdono 7, 20122 Milan, Italy; (M.G.); (L.M.A.); (M.C.); (I.S.); (I.S.); (R.C.)
- Unit of Rheumatology, ASST Gaetano Pini-CTO, Piazza Cardinale Andrea Ferrari 1, 20122 Milan, Italy
| | - Ilaria Suardi
- Department of Clinical Science of Community Health, Research Center for Adult and Pediatric Rheumatic Diseases, Università degli Studi di Milano, Via Festa del Perdono 7, 20122 Milan, Italy; (M.G.); (L.M.A.); (M.C.); (I.S.); (I.S.); (R.C.)
- Unit of Rheumatology, ASST Gaetano Pini-CTO, Piazza Cardinale Andrea Ferrari 1, 20122 Milan, Italy
| | - Luca Moroni
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy; (D.A.-S.); (C.A.); (G.G.); (L.M.); (E.P.B.); (L.D.)
- Faculty of Medicine, Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Via Francesco Sforza 35, 20122 Milan, Italy; (C.B.); (L.B.)
- Department of Clinical Science of Community Health, Section of Internal Medicine, Università degli Studi di Milano, Via Festa del Perdono 7, 20122 Milan, Italy
| | - Enrica P. Bozzolo
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy; (D.A.-S.); (C.A.); (G.G.); (L.M.); (E.P.B.); (L.D.)
| | - Roberto Caporali
- Department of Clinical Science of Community Health, Research Center for Adult and Pediatric Rheumatic Diseases, Università degli Studi di Milano, Via Festa del Perdono 7, 20122 Milan, Italy; (M.G.); (L.M.A.); (M.C.); (I.S.); (I.S.); (R.C.)
- Unit of Rheumatology, ASST Gaetano Pini-CTO, Piazza Cardinale Andrea Ferrari 1, 20122 Milan, Italy
| | - Lorenzo Dagna
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy; (D.A.-S.); (C.A.); (G.G.); (L.M.); (E.P.B.); (L.D.)
- Faculty of Medicine, Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
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11
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Corleis B, Bastian M, Hoffmann D, Beer M, Dorhoi A. Animal models for COVID-19 and tuberculosis. Front Immunol 2023; 14:1223260. [PMID: 37638020 PMCID: PMC10451089 DOI: 10.3389/fimmu.2023.1223260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Respiratory infections cause tremendous morbidity and mortality worldwide. Amongst these diseases, tuberculosis (TB), a bacterial illness caused by Mycobacterium tuberculosis which often affects the lung, and coronavirus disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), stand out as major drivers of epidemics of global concern. Despite their unrelated etiology and distinct pathology, these infections affect the same vital organ and share immunopathogenesis traits and an imperative demand to model the diseases at their various progression stages and localizations. Due to the clinical spectrum and heterogeneity of both diseases experimental infections were pursued in a variety of animal models. We summarize mammalian models employed in TB and COVID-19 experimental investigations, highlighting the diversity of rodent models and species peculiarities for each infection. We discuss the utility of non-human primates for translational research and emphasize on the benefits of non-conventional experimental models such as livestock. We epitomize advances facilitated by animal models with regard to understanding disease pathophysiology and immune responses. Finally, we highlight research areas necessitating optimized models and advocate that research of pulmonary infectious diseases could benefit from cross-fertilization between studies of apparently unrelated diseases, such as TB and COVID-19.
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Affiliation(s)
- Björn Corleis
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Max Bastian
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Anca Dorhoi
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Faculty of Mathematics and Natural Sciences, University of Greifswald, Greifswald, Germany
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12
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Serrat J, Francés-Gómez C, Becerro-Recio D, González-Miguel J, Geller R, Siles-Lucas M. Antigens from the Helminth Fasciola hepatica Exert Antiviral Effects against SARS-CoV-2 In Vitro. Int J Mol Sci 2023; 24:11597. [PMID: 37511355 PMCID: PMC10380311 DOI: 10.3390/ijms241411597] [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: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
SARS-CoV-2, the causal agent of COVID-19, is a new coronavirus that has rapidly spread worldwide and significantly impacted human health by causing a severe acute respiratory syndrome boosted by a pulmonary hyperinflammatory response. Previous data from our lab showed that the newly excysted juveniles of the helminth parasite Fasciola hepatica (FhNEJ) modulate molecular routes within host cells related to vesicle-mediated transport and components of the innate immune response, which could potentially be relevant during viral infections. Therefore, the aim of the present study was to determine whether FhNEJ-derived molecules influence SARS-CoV-2 infection efficiency in Vero cells. Pre-treatment of Vero cells with a tegument-enriched antigenic extract of FhNEJ (FhNEJ-TEG) significantly reduced infection by both vesicular stomatitis virus particles pseudotyped with the SARS-CoV-2 Spike protein (VSV-S2) and live SARS-CoV-2. Pre-treatment of the virus itself with FhNEJ-TEG prior to infection also resulted in reduced infection efficiency similar to that obtained by remdesivir pre-treatment. Remarkably, treatment of Vero cells with FhNEJ-TEG after VSV-S2 entry also resulted in reduced infection efficiency, suggesting that FhNEJ-TEG may also affect post-entry steps of the VSV replication cycle. Altogether, our results could potentially encourage the production of FhNEJ-derived molecules in a safe, synthetic format for their application as therapeutic agents against SARS-CoV-2 and other related respiratory viruses.
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Affiliation(s)
- Judit Serrat
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Clara Francés-Gómez
- Institute for Integrative Systems Biology (I2SysBio), Universidad de Valencia-CSIC, 46980 Valencia, Spain
| | - David Becerro-Recio
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Javier González-Miguel
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Ron Geller
- Institute for Integrative Systems Biology (I2SysBio), Universidad de Valencia-CSIC, 46980 Valencia, Spain
| | - Mar Siles-Lucas
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), C/Cordel de Merinas 40-52, 37008 Salamanca, Spain
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13
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Jacob RA, Zhang A, Ajoge HO, D'Agostino MR, Nirmalarajah K, Shigayeva A, Demian WL, Baker SJC, Derakhshani H, Rossi L, Nasir JA, Panousis EM, Draia AN, Vermeiren C, Gilchrist J, Smieja N, Bulir D, Smieja M, Surette MG, McArthur AG, McGeer AJ, Mubareka S, Banerjee A, Miller MS, Mossman K. Sensitivity to Neutralizing Antibodies and Resistance to Type I Interferons in SARS-CoV-2 R.1 Lineage Variants, Canada. Emerg Infect Dis 2023; 29:1386-1396. [PMID: 37308158 PMCID: PMC10310370 DOI: 10.3201/eid2907.230198] [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: 06/14/2023] Open
Abstract
Isolating and characterizing emerging SARS-CoV-2 variants is key to understanding virus pathogenesis. In this study, we isolated samples of the SARS-CoV-2 R.1 lineage, categorized as a variant under monitoring by the World Health Organization, and evaluated their sensitivity to neutralizing antibodies and type I interferons. We used convalescent serum samples from persons in Canada infected either with ancestral virus (wave 1) or the B.1.1.7 (Alpha) variant of concern (wave 3) for testing neutralization sensitivity. The R.1 isolates were potently neutralized by both the wave 1 and wave 3 convalescent serum samples, unlike the B.1.351 (Beta) variant of concern. Of note, the R.1 variant was significantly more resistant to type I interferons (IFN-α/β) than was the ancestral isolate. Our study demonstrates that the R.1 variant retained sensitivity to neutralizing antibodies but evolved resistance to type I interferons. This critical driving force will influence the trajectory of the pandemic.
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14
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Ma D, Wang X, Li M, Hu C, Tang L. Reconsideration of interferon treatment for viral diseases: Lessons from SARS, MERS, and COVID-19. Int Immunopharmacol 2023; 121:110485. [PMID: 37348227 PMCID: PMC10272952 DOI: 10.1016/j.intimp.2023.110485] [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: 04/04/2023] [Revised: 06/01/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023]
Abstract
Periodic pandemics of coronavirus (CoV)-related pneumonia have been a major challenging issue since the outbreak of severe acute respiratory syndrome (SARS) in 2002 and Middle East respiratory syndrome (MERS) in 2012. The ongoing pandemic of CoV disease (COVID-19) poses a substantial threat to public health. As for the treatment options, only limited antiviral agents have been approved hitherto, and clinicians mainly focus on currently available drugs including the conventional antiviral interferons (IFNs). In clinical practice, IFNs, when used either alone or in combination with ribavirin and/or lopinavir/ritonavir, have shown promising outcomes, to some extent, in SARS-CoV or MERS-CoV treatment. Although the efficacy and safety of IFNs in COVID-19 treatment remain unclear, their possible use merits further evaluation. We present a review that summarizes current evidence of IFN treatment for COVID-19 and elaborates on other challenges in terms of the timing of IFN treatment initiation, treatment duration, and IFN type to be used. The review findings suggested that IFN acts by directly inhibiting viral replication and activating immune cell subsets. However, there is a lack of well-designed and controlled clinical trials providing firm evidence for the efficacy or safety of IFN therapy for CoVs. Additionally, critically ill patients with multiple immunosuppression-associated comorbidities may not benefit from IFN therapy, necessitating screening of those patients who would most benefit from IFN treatment.
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Affiliation(s)
- Dan Ma
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, GuiZhou, China; Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang 550004, GuiZhou, China
| | - Ximin Wang
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Min Li
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Chujiao Hu
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang 550004, GuiZhou, China.
| | - Lei Tang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang 550004, GuiZhou, China.
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15
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Chiok KR, Dhar N, Banerjee A. Mycobacterium tuberculosis and SARS-CoV-2 co-infections: The knowns and unknowns. iScience 2023; 26:106629. [PMID: 37091987 PMCID: PMC10082467 DOI: 10.1016/j.isci.2023.106629] [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] [Indexed: 04/25/2023] Open
Abstract
Health impacts of Mycobacterium tuberculosis (Mtb) and SARS-CoV-2 co-infections are not fully understood. Both pathogens modulate host responses and induce immunopathology with extensive lung damage. With a quarter of the world's population harboring latent TB, exploring the relationship between SARS-CoV-2 infection and its effect on the transition of Mtb from latent to active form is paramount to control this pathogen. The effects of active Mtb infection on establishment and severity of COVID-19 are also unknown, despite the ability of TB to orchestrate profound long-lasting immunopathologies in the lungs. Absence of mechanistic studies and co-infection models hinder the development of effective interventions to reduce the health impacts of SARS-CoV-2 and Mtb co-infection. Here, we highlight dysregulated immune responses induced by SARS-CoV-2 and Mtb, their potential interplay, and implications for co-infection in the lungs. As both pathogens master immunomodulation, we discuss relevant converging and diverging immune-related pathways underlying SARS-CoV-2 and Mtb co-infections.
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Affiliation(s)
- Kim R Chiok
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Neeraj Dhar
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Respiratory Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Respiratory Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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16
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Dual mechanism: Epigenetic inhibitor apabetalone reduces SARS-CoV-2 Delta and Omicron variant spike binding and attenuates SARS-CoV-2 RNA induced inflammation. Int Immunopharmacol 2023; 117:109929. [PMID: 36857935 PMCID: PMC9946890 DOI: 10.1016/j.intimp.2023.109929] [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: 12/14/2022] [Revised: 02/03/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
The SARS-CoV-2 virus initiates infection via interactions between the viral spike protein and the ACE2 receptors on host cells. Variants of concern have mutations in the spike protein that enhance ACE2 binding affinity, leading to increased virulence and transmission. Viral RNAs released after entry into host cells trigger interferon-I (IFN-I) mediated inflammatory responses for viral clearance and resolution of infection. However, overreactive host IFN-I responses and pro-inflammatory signals drive COVID-19 pathophysiology and disease severity during acute infection. These immune abnormalities also lead to the development of post-COVID syndrome if persistent. Novel therapeutics are urgently required to reduce short- and long-term pathologic consequences associated with SARS-CoV-2 infection. Apabetalone, an inhibitor of epigenetic regulators of the BET protein family, is a candidate for COVID-19 treatment via a dual mechanism of action. In vitro, apabetalone downregulates ACE2 gene expression to limit SARS-CoV-2 entry and propagation. In pre-clinical models and patients treated for cardiovascular disease, apabetalone inhibits expression of inflammatory mediators involved in the pathologic cytokine storm (CS) stimulated by various cytokines. Here we show apabetalone treatment of human lung epithelial cells reduces binding of viral spike protein regardless of mutations found in the highly contagious Delta variant and heavily mutated Omicron. Additionally, we demonstrate that apabetalone counters expression of pro-inflammatory factors with roles in CS and IFN-I signaling in lung cells stimulated with SARS-CoV-2 RNA. Our results support clinical evaluation of apabetalone to treat COVID-19 and post-COVID syndrome regardless of the SARS-CoV-2 variant.
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17
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Diallo I, Jacob RA, Vion E, Kozak RA, Mossman K, Provost P. Altered microRNA Transcriptome in Cultured Human Airway Cells upon Infection with SARS-CoV-2. Viruses 2023; 15:v15020496. [PMID: 36851710 PMCID: PMC9962802 DOI: 10.3390/v15020496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Numerous proteomic and transcriptomic studies have been carried out to better understand the current multi-variant SARS-CoV-2 virus mechanisms of action and effects. However, they are mostly centered on mRNAs and proteins. The effect of the virus on human post-transcriptional regulatory agents such as microRNAs (miRNAs), which are involved in the regulation of 60% of human gene activity, remains poorly explored. Similar to research we have previously undertaken with other viruses such as Ebola and HIV, in this study we investigated the miRNA profile of lung epithelial cells following infection with SARS-CoV-2. At the 24 and 72 h post-infection time points, SARS-CoV-2 did not drastically alter the miRNome. About 90% of the miRNAs remained non-differentially expressed. The results revealed that miR-1246, miR-1290 and miR-4728-5p were the most upregulated over time. miR-196b-5p and miR-196a-5p were the most downregulated at 24 h, whereas at 72 h, miR-3924, miR-30e-5p and miR-145-3p showed the highest level of downregulation. In the top significantly enriched KEGG pathways of genes targeted by differentially expressed miRNAs we found, among others, MAPK, RAS, P13K-Akt and renin secretion signaling pathways. Using RT-qPCR, we also showed that SARS-CoV-2 may regulate several predicted host mRNA targets involved in the entry of the virus into host cells (ACE2, TMPRSS2, ADAM17, FURIN), renin-angiotensin system (RAS) (Renin, Angiotensinogen, ACE), innate immune response (IL-6, IFN1β, CXCL10, SOCS4) and fundamental cellular processes (AKT, NOTCH, WNT). Finally, we demonstrated by dual-luciferase assay a direct interaction between miR-1246 and ACE-2 mRNA. This study highlights the modulatory role of miRNAs in the pathogenesis of SARS-CoV-2.
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Affiliation(s)
- Idrissa Diallo
- CHU de Québec Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Rajesh Abraham Jacob
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Elodie Vion
- CHU de Québec Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Robert A. Kozak
- Division of Microbiology, Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Karen Mossman
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Patrick Provost
- CHU de Québec Research Center/CHUL Pavilion, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +1-418-525-4444 (ext. 48842)
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18
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Jagoda E, Marnetto D, Senevirathne G, Gonzalez V, Baid K, Montinaro F, Richard D, Falzarano D, LeBlanc EV, Colpitts CC, Banerjee A, Pagani L, Capellini TD. Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals. eLife 2023; 12:e71235. [PMID: 36763080 PMCID: PMC9917435 DOI: 10.7554/elife.71235] [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: 06/12/2021] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
Individuals infected with the SARS-CoV-2 virus present with a wide variety of symptoms ranging from asymptomatic to severe and even lethal outcomes. Past research has revealed a genetic haplotype on chromosome 3 that entered the human population via introgression from Neanderthals as the strongest genetic risk factor for the severe response to COVID-19. However, the specific variants along this introgressed haplotype that contribute to this risk and the biological mechanisms that are involved remain unclear. Here, we assess the variants present on the risk haplotype for their likelihood of driving the genetic predisposition to severe COVID-19 outcomes. We do this by first exploring their impact on the regulation of genes involved in COVID-19 infection using a variety of population genetics and functional genomics tools. We then perform a locus-specific massively parallel reporter assay to individually assess the regulatory potential of each allele on the haplotype in a multipotent immune-related cell line. We ultimately reduce the set of over 600 linked genetic variants to identify four introgressed alleles that are strong functional candidates for driving the association between this locus and severe COVID-19. Using reporter assays in the presence/absence of SARS-CoV-2, we find evidence that these variants respond to viral infection. These variants likely drive the locus' impact on severity by modulating the regulation of two critical chemokine receptor genes: CCR1 and CCR5. These alleles are ideal targets for future functional investigations into the interaction between host genomics and COVID-19 outcomes.
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Affiliation(s)
- Evelyn Jagoda
- Department of Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Davide Marnetto
- Estonian Biocentre, Institute of Genomics, University of TartuTartuEstonia
| | - Gayani Senevirathne
- Department of Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Victoria Gonzalez
- Department of Veterinary Microbiology, University of SaskatchewanSaskatoonCanada
- Vaccine and Infectious Disease Organization, University of SaskatchewanSaskatoonCanada
| | - Kaushal Baid
- Vaccine and Infectious Disease Organization, University of SaskatchewanSaskatoonCanada
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of TartuTartuEstonia
- Department of Biology, University of BariBariItaly
| | - Daniel Richard
- Department of Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Darryl Falzarano
- Department of Veterinary Microbiology, University of SaskatchewanSaskatoonCanada
- Vaccine and Infectious Disease Organization, University of SaskatchewanSaskatoonCanada
| | - Emmanuelle V LeBlanc
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
| | - Che C Colpitts
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
| | - Arinjay Banerjee
- Department of Veterinary Microbiology, University of SaskatchewanSaskatoonCanada
- Vaccine and Infectious Disease Organization, University of SaskatchewanSaskatoonCanada
- Department of Biology, University of WaterlooWaterlooCanada
- Department of Laboratory Medicine and Pathobiology, University of TorontoTorontoCanada
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of TartuTartuEstonia
- Department of Biology, University of PadovaPadovaItaly
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
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19
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Lacasse É, Gudimard L, Dubuc I, Gravel A, Allaeys I, Boilard É, Flamand L. SARS-CoV-2 Nsp2 Contributes to Inflammation by Activating NF-κB. Viruses 2023; 15:v15020334. [PMID: 36851549 PMCID: PMC9964531 DOI: 10.3390/v15020334] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
COVID-19 is associated with robust inflammation and partially impaired antiviral responses. The modulation of inflammatory gene expression by SARS-CoV-2 is not completely understood. In this study, we characterized the inflammatory and antiviral responses mounted during SARS-CoV-2 infection. K18-hACE2 mice were infected with a Wuhan-like strain of SARS-CoV-2, and the transcriptional and translational expression interferons (IFNs), cytokines, and chemokines were analyzed in mouse lung homogenates. Our results show that the infection of mice with SARS-CoV-2 induces the expression of several pro-inflammatory CC and CXC chemokines activated through NF-κB but weakly IL1β and IL18 whose expression are more characteristic of inflammasome formation. We also observed the downregulation of several inflammasome effectors. The modulation of innate response, following expressions of non-structural protein 2 (Nsp2) and SARS-CoV-2 infection, was assessed by measuring IFNβ expression and NF-κB modulation in human pulmonary cells. A robust activation of the NF-κB p65 subunit was induced following the infection of human cells with the corresponding NF-κB-driven inflammatory signature. We identified that Nsp2 expression induced the activation of the IFNβ promoter through its NF-κB regulatory domain as well as activation of p65 subunit phosphorylation. The present studies suggest that SARS-CoV-2 skews the antiviral response in favor of an NF-κB-driven inflammatory response, a hallmark of acute COVID-19 and for which Nsp2 should be considered an important contributor.
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Affiliation(s)
- Émile Lacasse
- Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC G1V 4G2, Canada
- Département de Microbiologie-Infectiologie et d’Immunologie, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Leslie Gudimard
- Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC G1V 4G2, Canada
| | - Isabelle Dubuc
- Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC G1V 4G2, Canada
| | - Annie Gravel
- Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC G1V 4G2, Canada
| | - Isabelle Allaeys
- Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC G1V 4G2, Canada
| | - Éric Boilard
- Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC G1V 4G2, Canada
- Département de Microbiologie-Infectiologie et d’Immunologie, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Louis Flamand
- Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Québec City, QC G1V 4G2, Canada
- Département de Microbiologie-Infectiologie et d’Immunologie, Université Laval, Québec City, QC G1V 0A6, Canada
- Correspondence:
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20
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Chan K, Farias AG, Lee H, Guvenc F, Mero P, Brown KR, Ward H, Billmann M, Aulakh K, Astori A, Haider S, Marcon E, Braunschweig U, Pu S, Habsid A, Yan Tong AH, Christie-Holmes N, Budylowski P, Ghalami A, Mubareka S, Maguire F, Banerjee A, Mossman KL, Greenblatt J, Gray-Owen SD, Raught B, Blencowe BJ, Taipale M, Myers C, Moffat J. Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors. Heliyon 2023; 9:e12744. [PMID: 36597481 PMCID: PMC9800021 DOI: 10.1016/j.heliyon.2022.e12744] [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: 12/16/2021] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection and replication. If druggable, host factor dependencies may present an attractive strategy for anti-viral therapy. In this study, we performed genome wide CRISPR knockout screens in Vero E6 cells and four human cell lines including Calu-3, UM-UC-4, HEK-293 and HuH-7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while other host genes identified were largely cell line specific, including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, immune-related pathways, and chromatin modification. Notably, the chromatin modifier gene KMT2C in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed.
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Affiliation(s)
- Katherine Chan
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Corresponding author
| | - Adrian Granda Farias
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Hunsang Lee
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Furkan Guvenc
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Patricia Mero
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Kevin R. Brown
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Henry Ward
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Kamaldeep Aulakh
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Audrey Astori
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Shahan Haider
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Edyta Marcon
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Ulrich Braunschweig
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Shuye Pu
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Andrea Habsid
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Amy Hin Yan Tong
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
| | - Natasha Christie-Holmes
- Combined Containment Level 3 Unit, Temerty Faculty of Medicine, University of Toronto Toronto, Ontario, Canada, M5S3E1
| | - Patrick Budylowski
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Ayoob Ghalami
- Office of Environmental Health & Safety, University of Toronto, Toronto, Ontario, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, Ontario, Canada, M5S3E1,Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Finlay Maguire
- Department of Community Health and Epidemiology, Faculty of Medicine Dalhousie University, Halifax, Nova Scotia, Canada,Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Karen L. Mossman
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jack Greenblatt
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Scott D. Gray-Owen
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Brian Raught
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Benjamin J. Blencowe
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Mikko Taipale
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
| | - Chad Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Jason Moffat
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1,Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8,Institute for Biomedical Engineering, Rosebrugh Building, 164 College Street, Room 407, University of Toronto, Toronto, Ontario, Canada, M5S3G9,Corresponding author. Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
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21
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Pinto SM, Subbannayya Y, Kim H, Hagen L, Górna MW, Nieminen AI, Bjørås M, Espevik T, Kainov D, Kandasamy RK. Multi-OMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells. iScience 2022; 26:105895. [PMID: 36590899 PMCID: PMC9794516 DOI: 10.1016/j.isci.2022.105895] [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: 09/09/2022] [Revised: 12/03/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
COVID-19 pandemic continues to remain a global health concern owing to the emergence of newer variants. Several multi-Omics studies have produced extensive evidence on host-pathogen interactions and potential therapeutic targets. Nonetheless, an increased understanding of host signaling networks regulated by post-translational modifications and their ensuing effect on the cellular dynamics is critical to expanding the current knowledge on SARS-CoV-2 infections. Through an unbiased transcriptomics, proteomics, acetylomics, phosphoproteomics, and exometabolome analysis of a lung-derived human cell line, we show that SARS-CoV-2 Norway/Trondheim-S15 strain induces time-dependent alterations in the induction of type I IFN response, activation of DNA damage response, dysregulated Hippo signaling, among others. We identified interplay of phosphorylation and acetylation dynamics on host proteins and its effect on the altered release of metabolites, especially organic acids and ketone bodies. Together, our findings serve as a resource of potential targets that can aid in designing novel host-directed therapeutic strategies.
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Affiliation(s)
- Sneha M. Pinto
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway,Corresponding author
| | - Yashwanth Subbannayya
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hera Kim
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway,Proteomics and Modomics Experimental Core, PROMEC, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Maria W. Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Anni I. Nieminen
- Institute for Molecular Medicine Finland, University of Helsinki, 00014Helsinki, Finland
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Terje Espevik
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway,Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA,Corresponding author
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22
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Archer SL, Dasgupta A, Chen KH, Wu D, Baid K, Mamatis JE, Gonzalez V, Read A, Bentley RET, Martin AY, Mewburn JD, Dunham-Snary KJ, Evans GA, Levy G, Jones O, Al-Qazazi R, Ring B, Alizadeh E, Hindmarch CCT, Rossi J, Lima PDA, Falzarano D, Banerjee A, Colpitts CC. SARS-CoV-2 mitochondriopathy in COVID-19 pneumonia exacerbates hypoxemia. Redox Biol 2022; 58:102508. [PMID: 36334378 PMCID: PMC9558649 DOI: 10.1016/j.redox.2022.102508] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/09/2022] [Indexed: 11/05/2022] Open
Abstract
Rationale Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 pneumonia. We hypothesize that SARS-CoV-2 causes alveolar injury and hypoxemia by damaging mitochondria in airway epithelial cells (AEC) and pulmonary artery smooth muscle cells (PASMC), triggering apoptosis and bioenergetic impairment, and impairing hypoxic pulmonary vasoconstriction (HPV), respectively. Objectives We examined the effects of: A) human betacoronaviruses, SARS-CoV-2 and HCoV-OC43, and individual SARS-CoV-2 proteins on apoptosis, mitochondrial fission, and bioenergetics in AEC; and B) SARS-CoV-2 proteins and mouse hepatitis virus (MHV-1) infection on HPV. Methods We used transcriptomic data to identify temporal changes in mitochondrial-relevant gene ontology (GO) pathways post-SARS-CoV-2 infection. We also transduced AECs with SARS-CoV-2 proteins (M, Nsp7 or Nsp9) and determined effects on mitochondrial permeability transition pore (mPTP) activity, relative membrane potential, apoptosis, mitochondrial fission, and oxygen consumption rates (OCR). In human PASMC, we assessed the effects of SARS-CoV-2 proteins on hypoxic increases in cytosolic calcium, an HPV proxy. In MHV-1 pneumonia, we assessed HPV via cardiac catheterization and apoptosis using the TUNEL assay. Results SARS-CoV-2 regulated mitochondrial apoptosis, mitochondrial membrane permeabilization and electron transport chain (ETC) GO pathways within 2 hours of infection. SARS-CoV-2 downregulated ETC Complex I and ATP synthase genes, and upregulated apoptosis-inducing genes. SARS-CoV-2 and HCoV-OC43 upregulated and activated dynamin-related protein 1 (Drp1) and increased mitochondrial fission. SARS-CoV-2 and transduced SARS-CoV-2 proteins increased apoptosis inducing factor (AIF) expression and activated caspase 7, resulting in apoptosis. Coronaviruses also reduced OCR, decreased ETC Complex I activity and lowered ATP levels in AEC. M protein transduction also increased mPTP opening. In human PASMC, M and Nsp9 proteins inhibited HPV. In MHV-1 pneumonia, infected AEC displayed apoptosis and HPV was suppressed. BAY K8644, a calcium channel agonist, increased HPV and improved SpO2. Conclusions Coronaviruses, including SARS-CoV-2, cause AEC apoptosis, mitochondrial fission, and bioenergetic impairment. SARS-CoV-2 also suppresses HPV by targeting mitochondria. This mitochondriopathy is replicated by transduction with SARS-CoV-2 proteins, indicating a mechanistic role for viral-host mitochondrial protein interactions. Mitochondriopathy is a conserved feature of coronaviral pneumonia that may exacerbate hypoxemia and constitutes a therapeutic target.
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Affiliation(s)
- Stephen L. Archer
- Department of Medicine, Queen’s University, Kingston, ON, Canada,Queen’s Cardiopulmonary Unit (QCPU), Queen’s University, Kingston, ON, Canada,Corresponding author. Head Department of Medicine, Queen's University Etherington Hall, Room 3041 94 Stuart St., Kingston, Ontario, K7L 3N6, Canada
| | - Asish Dasgupta
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Kuang-Hueih Chen
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Danchen Wu
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Kaushal Baid
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - John E. Mamatis
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
| | - Victoria Gonzalez
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan; Saskatoon, SK, Canada
| | - Austin Read
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | | | - Ashley Y. Martin
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | | | - Kimberly J. Dunham-Snary
- Department of Medicine, Queen’s University, Kingston, ON, Canada,Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
| | - Gerald A. Evans
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Gary Levy
- University of Toronto, Toronto, ON, Canada
| | - Oliver Jones
- Queen’s Cardiopulmonary Unit (QCPU), Queen’s University, Kingston, ON, Canada
| | - Ruaa Al-Qazazi
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Brooke Ring
- Queen’s Cardiopulmonary Unit (QCPU), Queen’s University, Kingston, ON, Canada
| | - Elahe Alizadeh
- Queen’s Cardiopulmonary Unit (QCPU), Queen’s University, Kingston, ON, Canada
| | | | - Jenna Rossi
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Patricia DA. Lima
- Queen’s Cardiopulmonary Unit (QCPU), Queen’s University, Kingston, ON, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan; Saskatoon, SK, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan; Saskatoon, SK, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Department of Biology, University of Waterloo; Waterloo, ON, Canada
| | - Che C. Colpitts
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
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23
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Ruiz MJ, Siracusano G, Cottignies-Calamarte A, Tudor D, Real F, Zhu A, Pastori C, Capron C, Rosenberg AR, Temperton N, Cantoni D, Liao H, Ternette N, Moine P, Godement M, Geri G, Chiche JD, Annane D, Cramer Bordé E, Lopalco L, Bomsel M. Persistent but dysfunctional mucosal SARS-CoV-2-specific IgA and low lung IL-1β associate with COVID-19 fatal outcome: A cross-sectional analysis. Front Immunol 2022; 13:842468. [PMID: 36248831 PMCID: PMC9560774 DOI: 10.3389/fimmu.2022.842468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
The role of the mucosal pulmonary antibody response in coronavirus disease 2019 (COVID-19) outcome remains unclear. Here, we found that in bronchoalveolar lavage (BAL) samples from 48 patients with severe COVID-19-infected with the ancestral Wuhan virus, mucosal IgG and IgA specific for S1, receptor-binding domain (RBD), S2, and nucleocapsid protein (NP) emerged in BAL containing viruses early in infection and persist after virus elimination, with more IgA than IgG for all antigens tested. Furthermore, spike-IgA and spike-IgG immune complexes were detected in BAL, especially when the lung virus has been cleared. BAL IgG and IgA recognized the four main RBD variants. BAL neutralizing titers were higher early in COVID-19 when virus replicates in the lung than later in infection after viral clearance. Patients with fatal COVID-19, in contrast to survivors, developed higher levels of mucosal spike-specific IgA than IgG but lost neutralizing activities over time and had reduced IL-1β in the lung. Altogether, mucosal spike and NP-specific IgG and S1-specific IgA persisting after lung severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance and low pulmonary IL-1β correlate with COVID-19 fatal outcome. Thus, mucosal SARS-CoV-2-specific antibodies may have adverse functions in addition to protective neutralization.
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Affiliation(s)
- Maria Julia Ruiz
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Gabriel Siracusano
- Immunobiology of HIV Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Andréa Cottignies-Calamarte
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Daniela Tudor
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Fernando Real
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Aiwei Zhu
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
| | - Claudia Pastori
- Immunobiology of HIV Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Claude Capron
- AP-HP, Hôpital Ambroise Paré, Service d'Hématologie, Boulogne-Billancourt, France
| | - Arielle R. Rosenberg
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
- AP-HP, Hôpital Cochin, Service de Virologie, Paris, France
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, United Kingdom
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, United Kingdom
| | - Hanqing Liao
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Pierre Moine
- FHU SEPSIS (Saclay and Paris Seine Nord Endeavour to PerSonalize Interventions for Sepsis), RHU RECORDS (Rapid rEcognition of CORticosteroiD resistant or sensitive Sepsis), Department of Intensive Care, Hôpital Raymond Poincaré (APHP), Laboratory of Infection and Inflammation – U1173, School of Medicine Simone Veil, University Versailles Saint Quentin – University Paris Saclay, INSERM, Garches, France
| | - Mathieu Godement
- FHU SEPSIS (Saclay and Paris Seine Nord Endeavour to PerSonalize Interventions for Sepsis), RHU RECORDS (Rapid rEcognition of CORticosteroiD resistant or sensitive Sepsis), Department of Intensive Care, Hôpital Raymond Poincaré (APHP), Laboratory of Infection and Inflammation – U1173, School of Medicine Simone Veil, University Versailles Saint Quentin – University Paris Saclay, INSERM, Garches, France
| | - Guillaume Geri
- AP-HP, Hôpital Ambroise Paré, Service de Réanimation, Boulogne-Billancourt, France
- Université de Versailles-St Quentin en Yvelines, Versailles, France
| | | | - Djillali Annane
- FHU SEPSIS (Saclay and Paris Seine Nord Endeavour to PerSonalize Interventions for Sepsis), RHU RECORDS (Rapid rEcognition of CORticosteroiD resistant or sensitive Sepsis), Department of Intensive Care, Hôpital Raymond Poincaré (APHP), Laboratory of Infection and Inflammation – U1173, School of Medicine Simone Veil, University Versailles Saint Quentin – University Paris Saclay, INSERM, Garches, France
| | | | - Lucia Lopalco
- Immunobiology of HIV Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Morgane Bomsel
- Mucosal Entry of HIV and Mucosal Immunity, Institut Cochin, Paris-Descartes University, Paris, France
- INSERM U1016, Paris, France
- CNRS UMR8104, Paris, France
- *Correspondence: Morgane Bomsel,
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24
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Kleer M, Mulloy RP, Robinson CA, Evseev D, Bui-Marinos MP, Castle EL, Banerjee A, Mubareka S, Mossman K, Corcoran JA. Human coronaviruses disassemble processing bodies. PLoS Pathog 2022; 18:e1010724. [PMID: 35998203 PMCID: PMC9439236 DOI: 10.1371/journal.ppat.1010724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 09/02/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022] Open
Abstract
A dysregulated proinflammatory cytokine response is characteristic of severe coronavirus infections caused by SARS-CoV-2, yet our understanding of the underlying mechanism responsible for this imbalanced immune response remains incomplete. Processing bodies (PBs) are cytoplasmic membraneless ribonucleoprotein granules that control innate immune responses by mediating the constitutive decay or suppression of mRNA transcripts, including many that encode proinflammatory cytokines. PB formation promotes turnover or suppression of cytokine RNAs, whereas PB disassembly corresponds with the increased stability and/or translation of these cytokine RNAs. Many viruses cause PB disassembly, an event that can be viewed as a switch that rapidly relieves cytokine RNA repression and permits the infected cell to respond to viral infection. Prior to this submission, no information was known about how human coronaviruses (CoVs) impacted PBs. Here, we show SARS-CoV-2 and the common cold CoVs, OC43 and 229E, induced PB loss. We screened a SARS-CoV-2 gene library and identified that expression of the viral nucleocapsid (N) protein from SARS-CoV-2 was sufficient to mediate PB disassembly. RNA fluorescent in situ hybridization revealed that transcripts encoding TNF and IL-6 localized to PBs in control cells. PB loss correlated with the increased cytoplasmic localization of these transcripts in SARS-CoV-2 N protein-expressing cells. Ectopic expression of the N proteins from five other human coronaviruses (OC43, MERS, 229E, NL63 and SARS-CoV) did not cause significant PB disassembly, suggesting that this feature is unique to SARS-CoV-2 N protein. These data suggest that SARS-CoV-2-mediated PB disassembly contributes to the dysregulation of proinflammatory cytokine production observed during severe SARS-CoV-2 infection.
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Affiliation(s)
- Mariel Kleer
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Rory P. Mulloy
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Carolyn-Ann Robinson
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Danyel Evseev
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Maxwell P. Bui-Marinos
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Elizabeth L. Castle
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan; Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan; Saskatoon, Saskatchewan, Canada
- Department of Biology, University of Waterloo; Waterloo, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Karen Mossman
- Department of Medicine, Master University, Hamilton, Ontario, Canada
- Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer A. Corcoran
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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25
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Bronchial epithelia from adults and children: SARS-CoV-2 spread via syncytia formation and type III interferon infectivity restriction. Proc Natl Acad Sci U S A 2022; 119:e2202370119. [PMID: 35749382 DOI: 10.1073/pnas.2202370119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections initiate in the bronchi of the upper respiratory tract and are able to disseminate to the lower respiratory tract, where infections can cause an acute respiratory distress syndrome with a high degree of mortality in elderly patients. We used reconstituted primary bronchial epithelia from adult and child donors to follow the SARS-CoV-2 infection dynamics. We show that, in epithelia from adult donors, infections initiate in multiciliated cells and spread within 24 to 48 h throughout the whole epithelia. Syncytia formed of ciliated and basal cells appeared at the apical side of the epithelia within 3 to 4 d and were released into the apical lumen, where they contributed to the transmittable virus dose. A small number of reconstituted epithelia were intrinsically more resistant to virus infection, limiting virus spread to different degrees. This phenotype was more frequent in epithelia derived from children versus adults and correlated with an accelerated release of type III interferon. Treatment of permissive adult epithelia with exogenous type III interferon restricted infection, while type III interferon gene knockout promoted infection. Furthermore, a transcript analysis revealed that the inflammatory response was specifically attenuated in children. Taken together, our findings suggest that apical syncytia formation is an underappreciated source of virus propagation for tissue or environmental dissemination, whereas a robust type III interferon response such as commonly seen in young donors restricted SARS-CoV-2 infection. Thus, the combination of interferon restriction and attenuated inflammatory response in children might explain the epidemiological observation of age-related susceptibility to COVID-19.
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26
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Richard D, Muthuirulan P, Aguiar J, Doxey AC, Banerjee A, Mossman K, Hirota J, Capellini TD. Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways. iScience 2022; 25:104614. [PMID: 35756893 PMCID: PMC9213013 DOI: 10.1016/j.isci.2022.104614] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 03/19/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022] Open
Abstract
The angiotensin-converting enzyme 2 (ACE2) protein is a key catalytic regulator of the renin-angiotensin system (RAS), involved in fluid homeostasis and blood pressure modulation. ACE2 also serves as a cell-surface receptor for some coronaviruses such as SARS-CoV and SARS-CoV-2. Improved characterization of ACE2 regulation may help us understand the effects of pre-existing conditions on COVID-19 incidence, as well as pathogenic dysregulation following viral infection. Here, we perform bioinformatic analyses to hypothesize on ACE2 gene regulation in two different physiological contexts, identifying putative regulatory elements of ACE2 expression. We perform functional validation of our computational predictions via targeted CRISPR-Cas9 deletions of these elements in vitro, finding them responsive to immune signaling and oxidative-stress pathways. This contributes to our understanding of ACE2 gene regulation at baseline and immune challenge. Our work supports pursuit of these putative mechanisms in our understanding of infection/disease caused by current, and future, SARS-related viruses such as SARS-CoV-2. Lung expression patterns suggest ACE2 regulation by immune and oxidative signaling CRISPR deletion of intronic regulatory elements (REs) alters ACE2 expression Effects of RE deletion are modified by immune stimulation and oxidative stress Propose two mechanisms for regulating ACE2 at baseline and after immune challenge
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Affiliation(s)
- Daniel Richard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138 USA
| | | | - Jennifer Aguiar
- Department of Biology, University of Waterloo, Waterloo, ON, N2L3G1 Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, N2L3G1 Canada
| | - Arinjay Banerjee
- Department of Biology, University of Waterloo, Waterloo, ON, N2L3G1 Canada.,Vaccine and Infectious Disease Organization, University of Saskatchewan; Saskatoon, SK, S7N 5E3 Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan; Saskatoon, SK, S7N5B4 Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, ON, L8N 3Z5 Canada
| | - Jeremy Hirota
- Department of Biology, University of Waterloo, Waterloo, ON, N2L3G1 Canada.,Department of Medicine, McMaster University, Hamilton, ON, L8N 3Z5 Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, V5Z 1M9 Canada
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138 USA.,Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA
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27
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Shalamova L, Felgenhauer U, Wilhelm J, Schaubmar AR, Büttner K, Schoen A, Widera M, Ciesek S, Weber F. Omicron variant of SARS-CoV-2 exhibits an increased resilience to the antiviral type I interferon response. PNAS NEXUS 2022; 1:pgac067. [PMID: 36713328 PMCID: PMC9802332 DOI: 10.1093/pnasnexus/pgac067] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023]
Abstract
The new variant of concern (VOC) of SARS-CoV-2, Omicron (B.1.1.529), is genetically very different from other VOCs. We compared Omicron with the preceding VOC Delta (B.1.617.2) and the wildtype (wt) strain (B.1) with respect to their interactions with the antiviral interferon (IFN-alpha/beta) response in infected cells. Our data indicate that IFN induction by Omicron is low and comparable to the wt, whereas Delta showed an increased IFN induction. However, Omicron exceeded both the wt and the Delta strain with respect to the ability to withstand the antiviral state imposed by IFN-alpha.
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Affiliation(s)
- Lyudmila Shalamova
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, D-35392 Giessen, Germany
| | - Ulrike Felgenhauer
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, D-35392 Giessen, Germany
| | - Jochen Wilhelm
- Institute for Lung Health (ILH), Justus-Liebig-University Giessen
, D-35392 Giessen, Germany
| | - Andreas R Schaubmar
- Unit for Biomathematics and Data processing, FB10-Veterinary Medicine, Justus-Liebig University, D-35392 Giessen, Germany
| | - Kathrin Büttner
- Unit for Biomathematics and Data processing, FB10-Veterinary Medicine, Justus-Liebig University, D-35392 Giessen, Germany
| | - Andreas Schoen
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, D-35392 Giessen, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital, Goethe University, D-60596 Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University, D-60596 Frankfurt am Main, Germany,German Centre for Infection Research (DZIF), D-35392 Giessen and D-60596 Frankfurt, Germany,Branch Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 60596 Frankfurt am Main, Germany
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28
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Nelson RW, Geha RS, McDonald DR. Inborn Errors of the Immune System Associated With Atopy. Front Immunol 2022; 13:860821. [PMID: 35572516 PMCID: PMC9094424 DOI: 10.3389/fimmu.2022.860821] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Atopic disorders, including atopic dermatitis, food and environmental allergies, and asthma, are increasingly prevalent diseases. Atopic disorders are often associated with eosinophilia, driven by T helper type 2 (Th2) immune responses, and triggered by disrupted barrier function leading to abnormal immune priming in a susceptible host. Immune deficiencies, in contrast, occur with a significantly lower incidence, but are associated with greater morbidity and mortality. A subset of atopic disorders with eosinophilia and elevated IgE are associated with monogenic inborn errors of immunity (IEI). In this review, we discuss current knowledge of IEI that are associated with atopy and the lessons these immunologic disorders provide regarding the fundamental mechanisms that regulate type 2 immunity in humans. We also discuss further mechanistic insights provided by animal models.
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Affiliation(s)
- Ryan W Nelson
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Douglas R McDonald
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
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29
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Wang Q, Wu X, Mao Q, Gao F, Liu M, Song Z, Bian L, Liang Z. How SARS-CoV-2 dodges immune surveillance and facilitates infection: an analytical review. Expert Rev Anti Infect Ther 2022; 20:1119-1127. [PMID: 35574688 DOI: 10.1080/14787210.2022.2078307] [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: 11/04/2022]
Abstract
INTRODUCTION Effective treatments for the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic are limited. The virus has evolved strategies to evade the immune system or hijack immune responses to facilitate infection and escape immune surveillance. Mechanistically, SARS-CoV-2 takes advantage of TLR4 and cytokine-induced integrins to promote its entrance into the cell. Furthermore, the activation of pattern recognition receptors (PRR)-mediated signaling pathways is compromised by SARS-CoV-2 non-structural proteins (NSPs), accessory protein open reading frames (ORFs), and structural proteins upon infection, contributing to viral infection and replication. Host factors necessary for cellular protein synthesis, metabolism, and viral replication can also be inhibited by the SARS-CoV-2 proteins. Exploring specific mechanisms would optimize the therapy methods and benefit drug research and development. AREAS COVERED : We describe pathways and mechanisms by which SARS-CoV-2 evades immune system; these include the mechanisms that operate during virus entry, signaling pathways involved, and processes at RNA and protein levels. EXPERT OPINION : Increased understanding of how viruses interfere with immune responses would provide more evidence for drug development. Drugs targeting conserved viral proteins to inhibit their replication or host factors to enhance immune responses would minimize the impact of virus mutations and prepare for future coronavirus outbreaks.
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Affiliation(s)
- Qian Wang
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Xing Wu
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Qunying Mao
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Fan Gao
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Mingchen Liu
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Ziyang Song
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Lianlian Bian
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Zhenglun Liang
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
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30
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Jiménez D, Torres Arias M. Immunouniverse of SARS-CoV-2. Immunol Med 2022; 45:186-224. [PMID: 35502127 DOI: 10.1080/25785826.2022.2066251] [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: 10/18/2022] Open
Abstract
SARS-CoV-2 virus has become a global health problem that has caused millions of deaths worldwide. The infection can present with multiple clinical features ranging from asymptomatic or mildly symptomatic patients to patients with severe or critical illness that can even lead to death. Although the immune system plays an important role in pathogen control, SARS-CoV-2 can drive dysregulation of this response and trigger severe immunopathology. Exploring the mechanisms of the immune response involved in host defense against SARS-CoV-2 allows us to understand its immunopathogenesis and possibly detect features that can be used as potential therapies to eliminate the virus. The main objective of this review on SARS-CoV-2 is to highlight the interaction between the virus and the immune response. We explore the function and action of the immune system, the expression of molecules at the site of infection that cause hyperinflammation and hypercoagulation disorders, the factors leading to the development of pneumonia and subsequent severe acute respiratory distress syndrome which is the leading cause of death in patients with COVID-19.
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Affiliation(s)
- Dennis Jiménez
- Departamento de Ciencias de la Vida y Agricultura, Carrera de Ingeniería en Biotecnología, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Pichincha, Ecuador
| | - Marbel Torres Arias
- Departamento de Ciencias de la Vida y Agricultura, Carrera de Ingeniería en Biotecnología, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Pichincha, Ecuador.,Laboratorio de Inmunología y Virología, CENCINAT, GISAH, Universidad de las Fuerzas Armadas, Sangolquí, Pichincha, Ecuador
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31
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Peng Y, Wang ZN, Chen SY, Xu AR, Fang ZF, Sun J, Zhou ZQ, Hou XT, Cen LJ, Ma JJ, Zhao JC, Guan WJ, Wang DY, Zhong NS. Angiotensin-converting enzyme 2 in peripheral lung club cells modulates the susceptibility to SARS-CoV-2 in chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2022; 322:L712-L721. [PMID: 35318858 PMCID: PMC9054324 DOI: 10.1152/ajplung.00305.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Accumulating evidence has confirmed that chronic obstructive pulmonary disease (COPD) is a risk factor for development of severe pathological changes in the peripheral lungs of patients with COVID-19. However, the underlying molecular mechanisms remain unclear. Because bronchiolar club cells are crucial for maintaining small airway homeostasis, we sought to explore whether the altered susceptibility to SARS-CoV-2 infection of the club cells might have contributed to the severe COVID-19 pneumonia in COPD patients. Our investigation on the quantity and distribution patterns of angiotensin-converting enzyme 2 (ACE2) in airway epithelium via immunofluorescence staining revealed that the mean fluorescence intensity of the ACE2-positive epithelial cells was significantly higher in club cells than those in other epithelial cells (including ciliated cells, basal cells, goblet cells, neuroendocrine cells, and alveolar type 2 cells). Compared with nonsmokers, the median percentage of club cells in bronchiolar epithelium and ACE2-positive club cells was significantly higher in COPD patients. In vitro, SARS-CoV-2 infection (at a multiplicity of infection of 1.0) of primary small airway epithelial cells, cultured on air-liquid interface, confirmed a higher percentage of infected ACE2-positive club cells in COPD patients than in nonsmokers. Our findings have indicated the role of club cells in modulating the pathogenesis of SARS-CoV-2-related severe pneumonia and the poor clinical outcomes, which may help physicians to formulate a novel therapeutic strategy for COVID-19 patients with coexisting COPD.
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Affiliation(s)
- Yang Peng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China.,Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zhao-Ni Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shi-Ying Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ai-Ru Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhang-Fu Fang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zi-Qing Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao-Tao Hou
- Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, China
| | - Lai-Jian Cen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jian-Juan Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jin-Cun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China.,Department of Thoracic Surgery, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China.,Department of Respiratory and Critical Care Medicine, Foshan Second People's Hospital, Affiliated Foshan Hospital of Southern Medical University, Foshan, Guangdong, China
| | - De Yun Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Nan-Shan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
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Pasquero S, Gugliesi F, Griffante G, Dell’Oste V, Biolatti M, Albano C, Bajetto G, Delbue S, Signorini L, Dolci M, Landolfo S, De Andrea M. Novel antiviral activity of PAD inhibitors against human beta-coronaviruses HCoV-OC43 and SARS-CoV-2. Antiviral Res 2022; 200:105278. [PMID: 35288208 PMCID: PMC8915624 DOI: 10.1016/j.antiviral.2022.105278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 11/25/2022]
Abstract
The current SARS-CoV-2 pandemic, along with the likelihood that new coronavirus strains will appear in the nearby future, highlights the urgent need to develop new effective antiviral agents. In this scenario, emerging host-targeting antivirals (HTAs), which act on host-cell factors essential for viral replication, are a promising class of antiviral compounds. Here we show that a new class of HTAs targeting peptidylarginine deiminases (PADs), a family of calcium-dependent enzymes catalyzing protein citrullination, is endowed with a potent inhibitory activity against human beta-coronaviruses (HCoVs). Specifically, we show that infection of human fetal lung fibroblasts with HCoV-OC43 leads to enhanced protein citrullination through transcriptional activation of PAD4, and that inhibition of PAD4-mediated citrullination with either of the two pan-PAD inhibitors Cl-A and BB-Cl or the PAD4-specific inhibitor GSK199 curbs HCoV-OC43 replication. Furthermore, we show that either Cl-A or BB-Cl treatment of African green monkey kidney Vero-E6 cells, a widely used cell system to study beta-CoV replication, potently suppresses HCoV-OC43 and SARS-CoV-2 replication. Overall, our results demonstrate the potential efficacy of PAD inhibitors, in suppressing HCoV infection, which may provide the rationale for the repurposing of this class of inhibitors for the treatment of COVID-19 patients.
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BCG vaccination provides protection against IAV but not SARS-CoV-2. Cell Rep 2022; 38:110502. [PMID: 35235831 PMCID: PMC8858710 DOI: 10.1016/j.celrep.2022.110502] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/30/2021] [Accepted: 02/15/2022] [Indexed: 11/25/2022] Open
Abstract
Since the vast majority of species solely rely on innate immunity for host defense, it stands to reason that a critical evolutionary trait like immunological memory evolved in this primitive branch of our immune system. There is ample evidence that vaccines such as bacillus Calmette-Guérin (BCG) induce protective innate immune memory responses (trained immunity) against heterologous pathogens. Here we show that while BCG vaccination significantly reduces morbidity and mortality against influenza A virus (IAV), it fails to provide protection against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In contrast to IAV, SARS-CoV-2 infection leads to unique pulmonary vasculature damage facilitating viral dissemination to other organs, including the bone marrow (BM), a central site for BCG-mediated trained immunity. Finally, monocytes from BCG-vaccinated individuals mount an efficient cytokine response to IAV infection, while this response is minimal following SARS-CoV-2. Collectively, our data suggest that the protective capacity of BCG vaccination is contingent on viral pathogenesis and tissue tropism.
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Ferraccioli G, Gremese E, Goletti D, Petrone L, Cantini F, Ugel S, Canè S, Bronte V. Immune-guided therapy of COVID-19. Cancer Immunol Res 2022; 10:384-402. [DOI: 10.1158/2326-6066.cir-21-0675] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/04/2021] [Accepted: 01/20/2022] [Indexed: 01/08/2023]
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35
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Jouvenet N, Goujon C, Banerjee A. Clash of the titans: interferons and SARS-CoV-2. Trends Immunol 2021; 42:1069-1072. [PMID: 34742657 PMCID: PMC8519778 DOI: 10.1016/j.it.2021.10.009] [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] [Received: 08/07/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 12/02/2022]
Abstract
Interferons are our first line of defense against invading viruses. However, viruses encode effector proteins that can modulate human interferon responses. In this forum article, we highlight important discoveries and discuss outstanding questions that will enable us to better understand the nuances of this evolutionary battle between interferons and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR3569, Virus Sensing and Signaling Unit, Paris, France.
| | - Caroline Goujon
- IRIM, CNRS, Montpellier University, Montpellier 34090, France.
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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36
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Interfering with SARS-CoV-2: are interferons friends or foes in COVID-19? Curr Opin Virol 2021; 50:119-127. [PMID: 34454352 PMCID: PMC8367741 DOI: 10.1016/j.coviro.2021.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 01/06/2023]
Abstract
Type I and type III interferons are among the most potent anti-viral cytokines produced by the immune system. The recent outbreak of SARS-CoV-2, which causes COVID-19, underscores the vital role of these cytokines in controlling the virus and dictating disease severity. Here we delineate the pathways that lead to interferon production in response to SARS-CoV-2 encounter, and elucidate how this virus hinders the production and action of these cytokines; we also highlight that these interferon families serve protective as well as detrimental roles in patients with COVID-19, and conclude that a better understanding of the time, dose, localization, and activity of specific members of the interferon families is imperative for designing more efficient therapeutic interventions against this disease.
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37
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Galani IE, Andreakos E. Impaired innate antiviral defenses in COVID-19: Causes, consequences and therapeutic opportunities. Semin Immunol 2021; 55:101522. [PMID: 34815163 PMCID: PMC8576141 DOI: 10.1016/j.smim.2021.101522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged pathogen that has caused coronavirus disease 2019 (COVID-19), the worst pandemic of our times leading to tremendous loss of human life and unprecedented measures of social distancing. COVID-19 symptom manifestations range from asymptomatic disease to severe and lethal outcomes. Lack of previous exposure and immunity to SARS-CoV-2, and high infectivity of the virus have contributed to its broad spread across the globe. In the absence of specific adaptive immunity, innate immune mechanisms are crucial for efficient antiviral defenses and control of the infection. Accumulating evidence now suggests that the remarkable heterogeneity in COVID-19 disease manifestations is due to variable degrees of impairment of innate immune mechanisms. In this review, we summarize recent findings describing both viral and host intrinsic factors that have been linked to defective innate immune responses and account for severe COVID-19. We also discuss emerging therapeutic opportunities for targeting innate immunity for the treatment of COVID-19.
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Affiliation(s)
- Ioanna-Evdokia Galani
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece
| | - Evangelos Andreakos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece.
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38
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Nemudryi A, Nemudraia A, Wiegand T, Nichols J, Snyder DT, Hedges JF, Cicha C, Lee H, Vanderwood KK, Bimczok D, Jutila MA, Wiedenheft B. SARS-CoV-2 genomic surveillance identifies naturally occurring truncation of ORF7a that limits immune suppression. Cell Rep 2021; 35:109197. [PMID: 34043946 PMCID: PMC8118641 DOI: 10.1016/j.celrep.2021.109197] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/04/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
Over 950,000 whole-genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been determined for viruses isolated from around the world. These sequences are critical for understanding the spread and evolution of SARS-CoV-2. Using global phylogenomics, we show that mutations frequently occur in the C-terminal end of ORF7a. We isolate one of these mutant viruses from a patient sample and use viral challenge experiments to link this isolate (ORF7aΔ115) to a growth defect. ORF7a is implicated in immune modulation, and we show that the C-terminal truncation negates anti-immune activities of the protein, which results in elevated type I interferon response to the viral infection. Collectively, this work indicates that ORF7a mutations occur frequently, and that these changes affect viral mechanisms responsible for suppressing the immune response.
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Affiliation(s)
- Artem Nemudryi
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Anna Nemudraia
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Joseph Nichols
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Deann T Snyder
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Jodi F Hedges
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Calvin Cicha
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Helen Lee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | | | - Diane Bimczok
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Mark A Jutila
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
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