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Joharinia N, Bonneil É, Grandvaux N, Thibault P, Lippé R. Comprehensive proteomic analysis of HCoV-OC43 virions and virus-modulated extracellular vesicles. J Virol 2024; 98:e0085024. [PMID: 38953378 PMCID: PMC11265355 DOI: 10.1128/jvi.00850-24] [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: 05/15/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024] Open
Abstract
Viruses are obligate parasites that depend on the cellular machinery for their propagation. Several viruses also incorporate cellular proteins that facilitate viral spread. Defining these cellular proteins is critical to decipher viral life cycles and delineate novel therapeutic strategies. While numerous studies have explored the importance of host proteins in coronavirus spread, information about their presence in mature virions is limited. In this study, we developed a protocol to highly enrich mature HCoV-OC43 virions and characterize them by proteomics. Recognizing that cells release extracellular vesicles whose content is modulated by viruses, and given our ability to separate virions from these vesicles, we also analyzed their protein content in both uninfected and infected cells. We uncovered 69 unique cellular proteins associated with virions including 31 high-confidence hits. These proteins primarily regulate RNA metabolism, enzymatic activities, vesicular transport, cell adhesion, metabolite interconversion, and translation. We further discovered that the virus had a profound impact on exosome composition, incorporating 47 novel cellular proteins (11 high confidence) and excluding 92 others (61 high confidence) in virus-associated extracellular vesicles compared to uninfected cells. Moreover, a dsiRNA screen revealed that 11 of 18 select targets significantly impacted viral yields, including proteins found in virions or extracellular vesicles. Overall, this study provides new and important insights into the incorporation of numerous host proteins into HCoV-OC43 virions, their biological significance, and the ability of the virus to modulate extracellular vesicles. IMPORTANCE In recent years, coronaviruses have dominated global attention, making it crucial to develop methods to control them and prevent future pandemics. Besides viral proteins, host proteins play a significant role in viral propagation and offer potential therapeutic targets. Targeting host proteins is advantageous because they are less likely to mutate and develop resistance compared to viral proteins, a common issue with many antiviral treatments. In this study, we examined the protein content of the less virulent biosafety level 2 HCoV-OC43 virus as a stand-in for the more virulent SARS-CoV-2. Our findings reveal that several cellular proteins incorporated into the virion regulate viral spread. In addition, we report that the virus extensively modulates the content of extracellular vesicles, enhancing viral dissemination. This underscores the critical interplay between the virus, host proteins, and extracellular vesicles.
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Affiliation(s)
- Negar Joharinia
- Azrieli Research center of the CHU Sainte-Justine, Montreal, Quebec, Canada
- Department of Microbiology, Infectiology and Immunology, University of Montreal, Montreal, Quebec, Canada
| | - Éric Bonneil
- IRIC, University of Montreal, Montreal, Quebec, Canada
| | - Nathalie Grandvaux
- Research center of the CHUM (CRCHUM), Montreal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Pierre Thibault
- IRIC, University of Montreal, Montreal, Quebec, Canada
- Department of Chemistry, University of Montreal, Montreal, Quebec, Canada
| | - Roger Lippé
- Azrieli Research center of the CHU Sainte-Justine, Montreal, Quebec, Canada
- Department of Pathology and Cell biology, University of Montreal, Montreal, Quebec, Canada
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2
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McGirr T, Onar O, Jafarnejad SM. Dysregulated ribosome quality control in human diseases. FEBS J 2024. [PMID: 38949989 DOI: 10.1111/febs.17217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/31/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Precise regulation of mRNA translation is of fundamental importance for maintaining homeostasis. Conversely, dysregulated general or transcript-specific translation, as well as abnormal translation events, have been linked to a multitude of diseases. However, driven by the misconception that the transient nature of mRNAs renders their abnormalities inconsequential, the importance of mechanisms that monitor the quality and fidelity of the translation process has been largely overlooked. In recent years, there has been a dramatic shift in this paradigm, evidenced by several seminal discoveries on the role of a key mechanism in monitoring the quality of mRNA translation - namely, Ribosome Quality Control (RQC) - in the maintenance of homeostasis and the prevention of diseases. Here, we will review recent advances in the field and emphasize the biological significance of the RQC mechanism, particularly its implications in human diseases.
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Affiliation(s)
- Tom McGirr
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Okan Onar
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
- Department of Biology, Faculty of Science, Ankara University, Turkey
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3
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Kober DL, Caballero Van Dyke MC, Eitson JL, Boys IN, McDougal MB, Rosenbaum DM, Schoggins JW. Development of a mutant aerosolized ACE2 that neutralizes SARS-CoV-2 in vivo. mBio 2024; 15:e0076824. [PMID: 38771062 PMCID: PMC11237572 DOI: 10.1128/mbio.00768-24] [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: 03/14/2024] [Accepted: 04/17/2024] [Indexed: 05/22/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 variants highlights the need for new therapies to prevent disease spread. SARS-CoV-2, like SARS-CoV-1, uses the human cell surface protein angiotensin-converting enzyme 2 (ACE2) as its native receptor. Here, we design and characterize a mutant ACE2 that enables rapid affinity purification of a dimeric protein by altering the active site to prevent autoproteolytic digestion of a C-terminal His10 epitope tag. In cultured cells, mutant ACE2 competitively inhibits lentiviral vectors pseudotyped with spikes from multiple SARS-CoV-2 variants and infectious SARS-CoV-2. Moreover, the protein can be nebulized and retains virus-binding properties. We developed a system for the delivery of aerosolized ACE2 to K18-hACE2 mice and demonstrated protection by our modified ACE2 when delivered as a prophylactic agent. These results show proof-of-concept for an aerosolized delivery method to evaluate anti-SARS-CoV-2 agents in vivo and suggest a new tool in the ongoing fight against SARS-CoV-2 and other ACE2-dependent viruses. IMPORTANCE The rapid evolution of SARS-CoV-2 variants poses a challenge for immune recognition and antibody therapies. However, the virus is constrained by the requirement that it recognizes a human host receptor protein. A recombinant ACE2 could protect against SARS-CoV-2 infection by functioning as a soluble decoy receptor. We designed a mutant version of ACE2 with impaired catalytic activity to enable the purification of the protein using a single affinity purification step. This protein can be nebulized and retains the ability to bind the relevant domains from SARS-CoV-1 and SARS-CoV-2. Moreover, this protein inhibits viral infection against a panel of coronaviruses in cells. Finally, we developed an aerosolized delivery system for animal studies and show the modified ACE2 offers protection in an animal model of COVID-19. These results show proof-of-concept for an aerosolized delivery method to evaluate anti-SARS-CoV-2 agents in vivo and suggest a new tool in the ongoing fight against SARS-CoV-2.
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Affiliation(s)
- Daniel L Kober
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Jennifer L Eitson
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ian N Boys
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Matthew B McDougal
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John W Schoggins
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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4
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Wang X, Chen Y, Qi C, Li F, Zhang Y, Zhou J, Wu H, Zhang T, Qi A, Ouyang H, Xie Z, Pang D. Mechanism, structural and functional insights into nidovirus-induced double-membrane vesicles. Front Immunol 2024; 15:1340332. [PMID: 38919631 PMCID: PMC11196420 DOI: 10.3389/fimmu.2024.1340332] [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: 11/17/2023] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
During infection, positive-stranded RNA causes a rearrangement of the host cell membrane, resulting in specialized membrane structure formation aiding viral genome replication. Double-membrane vesicles (DMVs), typical structures produced by virus-induced membrane rearrangements, are platforms for viral replication. Nidoviruses, one of the most complex positive-strand RNA viruses, have the ability to infect not only mammals and a few birds but also invertebrates. Nidoviruses possess a distinctive replication mechanism, wherein their nonstructural proteins (nsps) play a crucial role in DMV biogenesis. With the participation of host factors related to autophagy and lipid synthesis pathways, several viral nsps hijack the membrane rearrangement process of host endoplasmic reticulum (ER), Golgi apparatus, and other organelles to induce DMV formation. An understanding of the mechanisms of DMV formation and its structure and function in the infectious cycle of nidovirus may be essential for the development of new and effective antiviral strategies in the future.
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Affiliation(s)
- Xi Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Yiwu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Chunyun Qi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Feng Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Yuanzhu Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Jian Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Heyong Wu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Tianyi Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Aosi Qi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Hongsheng Ouyang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
- Chongqing Research Institute, Jilin University, Chongqing, China
- Center for Animal Science and Technology Research, Chongqing Jitang Biotechnology Research Institute Co., Ltd, Chongqing, China
| | - Zicong Xie
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
- Chongqing Research Institute, Jilin University, Chongqing, China
| | - Daxin Pang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
- Chongqing Research Institute, Jilin University, Chongqing, China
- Center for Animal Science and Technology Research, Chongqing Jitang Biotechnology Research Institute Co., Ltd, Chongqing, China
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5
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Schäfer A, Gralinski LE, Leist SR, Hampton BK, Mooney MA, Jensen KL, Graham RL, Agnihothram S, Jeng S, Chamberlin S, Bell TA, Scobey DT, Linnertz CL, VanBlargan LA, Thackray LB, Hock P, Miller DR, Shaw GD, Diamond MS, de Villena FPM, McWeeney SK, Heise MT, Menachery VD, Ferris MT, Baric RS. Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans. Virus Res 2024; 344:199357. [PMID: 38508400 PMCID: PMC10981091 DOI: 10.1016/j.virusres.2024.199357] [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: 09/28/2023] [Revised: 02/15/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Coronavirus (CoV) cause considerable morbidity and mortality in humans and other mammals, as evidenced by the emergence of Severe Acute Respiratory CoV (SARS-CoV) in 2003, Middle East Respiratory CoV (MERS-CoV) in 2012, and SARS-CoV-2 in 2019. Although poorly characterized, natural genetic variation in human and other mammals modulate virus pathogenesis, as reflected by the spectrum of clinical outcomes ranging from asymptomatic infections to lethal disease. Using multiple human epidemic and zoonotic Sarbecoviruses, coupled with murine Collaborative Cross genetic reference populations, we identify several dozen quantitative trait loci that regulate SARS-like group-2B CoV pathogenesis and replication. Under a Chr4 QTL, we deleted a candidate interferon stimulated gene, Trim14 which resulted in enhanced SARS-CoV titers and clinical disease, suggesting an antiviral role during infection. Importantly, about 60 % of the murine QTL encode susceptibility genes identified as priority candidates from human genome-wide association studies (GWAS) studies after SARS-CoV-2 infection, suggesting that similar selective forces have targeted analogous genes and pathways to regulate Sarbecovirus disease across diverse mammalian hosts. These studies provide an experimental platform in rodents to investigate the molecular-genetic mechanisms by which potential cross mammalian susceptibility loci and genes regulate type-specific and cross-SARS-like group 2B CoV replication, immunity, and pathogenesis in rodent models. Our study also provides a paradigm for identifying susceptibility loci for other highly heterogeneous and virulent viruses that sporadically emerge from zoonotic reservoirs to plague human and animal populations.
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Affiliation(s)
- Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael A Mooney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Kara L Jensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Steven Chamberlin
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology2, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology3, Washington University School of Medicine, St. Louis, MO, USA
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA; Department of Pathology and Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA.
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6
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Zhang Y, Chen S, Tian Y, Fu X. Host factors of SARS-CoV-2 in infection, pathogenesis, and long-term effects. Front Cell Infect Microbiol 2024; 14:1407261. [PMID: 38846354 PMCID: PMC11155306 DOI: 10.3389/fcimb.2024.1407261] [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: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
SARS-CoV-2 is the causative virus of the devastating COVID-19 pandemic that results in an unparalleled global health and economic crisis. Despite unprecedented scientific efforts and therapeutic interventions, the fight against COVID-19 continues as the rapid emergence of different SARS-CoV-2 variants of concern and the increasing challenge of long COVID-19, raising a vast demand to understand the pathomechanisms of COVID-19 and its long-term sequelae and develop therapeutic strategies beyond the virus per se. Notably, in addition to the virus itself, the replication cycle of SARS-CoV-2 and clinical severity of COVID-19 is also governed by host factors. In this review, we therefore comprehensively overview the replication cycle and pathogenesis of SARS-CoV-2 from the perspective of host factors and host-virus interactions. We sequentially outline the pathological implications of molecular interactions between host factors and SARS-CoV-2 in multi-organ and multi-system long COVID-19, and summarize current therapeutic strategies and agents targeting host factors for treating these diseases. This knowledge would be key for the identification of new pathophysiological aspects and mechanisms, and the development of actionable therapeutic targets and strategies for tackling COVID-19 and its sequelae.
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Affiliation(s)
| | | | - Yan Tian
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
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7
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Viox EG, Bosinger SE, Douek DC, Schreiber G, Paiardini M. Harnessing the power of IFN for therapeutic approaches to COVID-19. J Virol 2024; 98:e0120423. [PMID: 38651899 PMCID: PMC11092331 DOI: 10.1128/jvi.01204-23] [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] [Indexed: 04/25/2024] Open
Abstract
Interferons (IFNs) are essential for defense against viral infections but also drive recruitment of inflammatory cells to sites of infection, a key feature of severe COVID-19. Here, we explore the complexity of the IFN response in COVID-19, examine the effects of manipulating IFN on SARS-CoV-2 viral replication and pathogenesis, and highlight pre-clinical and clinical studies evaluating the therapeutic efficacy of IFN in limiting COVID-19 severity.
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Affiliation(s)
- Elise G. Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
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Shivaprasad S, Qiao W, Weng KF, Umashankar P, Carette JE, Sarnow P. CRISPR Screen Reveals PACT as a Pro-Viral Factor for Dengue Viral Replication. Viruses 2024; 16:725. [PMID: 38793607 PMCID: PMC11125577 DOI: 10.3390/v16050725] [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: 03/13/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
The dengue virus is a single-stranded, positive-sense RNA virus that infects ~400 million people worldwide. Currently, there are no approved antivirals available. CRISPR-based screening methods have greatly accelerated the discovery of host factors that are essential for DENV infection and that can be targeted in host-directed antiviral interventions. In the present study, we performed a focused CRISPR (Clustered Regularly Interspaced Palindromic Repeats) library screen to discover the key host factors that are essential for DENV infection in human Huh7 cells and identified the Protein Activator of Interferon-Induced Protein Kinase (PACT) as a novel pro-viral factor for DENV. PACT is a double-stranded RNA-binding protein generally known to activate antiviral responses in virus-infected cells and block viral replication. However, in our studies, we observed that PACT plays a pro-viral role in DENV infection and specifically promotes viral RNA replication. Knockout of PACT resulted in a significant decrease in DENV RNA and protein abundances in infected cells, which was rescued upon ectopic expression of full-length PACT. An analysis of global gene expression changes indicated that several ER-associated pro-viral genes such as ERN1, DDIT3, HERPUD1, and EIF2AK3 are not upregulated in DENV-infected PACT knockout cells as compared to infected wildtype cells. Thus, our study demonstrates a novel role for PACT in promoting DENV replication, possibly through modulating the expression of ER-associated pro-viral genes.
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Affiliation(s)
- Shwetha Shivaprasad
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, CA 94305, USA; (W.Q.); (J.E.C.); (P.S.)
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, Karnataka, India;
| | - Wenjie Qiao
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, CA 94305, USA; (W.Q.); (J.E.C.); (P.S.)
| | - Kuo-Feng Weng
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, CA 94305, USA; (W.Q.); (J.E.C.); (P.S.)
| | - Pavithra Umashankar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, Karnataka, India;
| | - Jan E. Carette
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, CA 94305, USA; (W.Q.); (J.E.C.); (P.S.)
| | - Peter Sarnow
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, CA 94305, USA; (W.Q.); (J.E.C.); (P.S.)
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9
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Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf JP, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar WL, Maecker HT, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Sekaly RP, Ehrlich LI, Fourati S, Peters B, Kleinstein SH, Guan L. Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. J Clin Invest 2024; 134:e176640. [PMID: 38690733 PMCID: PMC11060740 DOI: 10.1172/jci176640] [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: 10/26/2023] [Accepted: 03/12/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUNDPatients hospitalized for COVID-19 exhibit diverse clinical outcomes, with outcomes for some individuals diverging over time even though their initial disease severity appears similar to that of other patients. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity.METHODSWe performed deep immunophenotyping and conducted longitudinal multiomics modeling, integrating 10 assays for 1,152 Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study participants and identifying several immune cascades that were significant drivers of differential clinical outcomes.RESULTSIncreasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, formation of neutrophil extracellular traps, and T cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma Igs and B cells and dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to failure of viral clearance in patients with fatal illness.CONCLUSIONOur longitudinal multiomics profiling study revealed temporal coordination across diverse omics that potentially explain the disease progression, providing insights that can inform the targeted development of therapies for patients hospitalized with COVID-19, especially those who are critically ill.TRIAL REGISTRATIONClinicalTrials.gov NCT04378777.FUNDINGNIH (5R01AI135803-03, 5U19AI118608-04, 5U19AI128910-04, 4U19AI090023-11, 4U19AI118610-06, R01AI145835-01A1S1, 5U19AI062629-17, 5U19AI057229-17, 5U19AI125357-05, 5U19AI128913-03, 3U19AI077439-13, 5U54AI142766-03, 5R01AI104870-07, 3U19AI089992-09, 3U19AI128913-03, and 5T32DA018926-18); NIAID, NIH (3U19AI1289130, U19AI128913-04S1, and R01AI122220); and National Science Foundation (DMS2310836).
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Affiliation(s)
| | - Cole Maguire
- The University of Texas at Austin, Austin, Texas, USA
| | | | - Pramod Shinde
- La Jolla Institute for Immunology, La Jolla, California, USA
| | | | - Casey P. Shannon
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Providence Research, Vancouver, British Columbia, Canada
| | - Leqi Xu
- Yale School of Public Health, New Haven, Connecticut, USA
| | - Annmarie Hoch
- Clinical and Data Coordinating Center (CDCC) and
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Elias K. Haddad
- Drexel University, Tower Health Hospital, Philadelphia, Pennsylvania, USA
| | - IMPACC Network
- The Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) Network is detailed in Supplemental Acknowledgments
| | - Elaine F. Reed
- David Geffen School of Medicine at the UCLA, Los Angeles, California, USA
| | - Monica Kraft
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Grace A. McComsey
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Jordan P. Metcalf
- Oklahoma University Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Al Ozonoff
- Clinical and Data Coordinating Center (CDCC) and
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Charles B. Cairns
- Drexel University, Tower Health Hospital, Philadelphia, Pennsylvania, USA
| | | | | | | | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Lindsey B. Rosen
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | | | - Hanno Steen
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Ofer Levy
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Bali Pulendran
- Stanford University School of Medicine, Palo Alto, California, USA
| | - Joann Diray-Arce
- Clinical and Data Coordinating Center (CDCC) and
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kinga K. Smolen
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Rafick P. Sekaly
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | | | - Slim Fourati
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, UCSD, La Jolla, California, USA
| | | | - Leying Guan
- Yale School of Public Health, New Haven, Connecticut, USA
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10
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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11
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Sergio MC, Ricciardi S, Guarino AM, Giaquinto L, De Matteis MA. Membrane remodeling and trafficking piloted by SARS-CoV-2. Trends Cell Biol 2024:S0962-8924(23)00256-8. [PMID: 38262893 DOI: 10.1016/j.tcb.2023.12.006] [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: 10/20/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024]
Abstract
The molecular mechanisms underlying SARS-CoV-2 host cell invasion and life cycle have been studied extensively in recent years, with a primary focus on viral entry and internalization with the aim of identifying antiviral therapies. By contrast, our understanding of the molecular mechanisms involved in the later steps of the coronavirus life cycle is relatively limited. In this review, we describe what is known about the host factors and viral proteins involved in the replication, assembly, and egress phases of SARS-CoV-2, which induce significant host membrane rearrangements. We also discuss the limits of the current approaches and the knowledge gaps still to be addressed.
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Affiliation(s)
- Maria Concetta Sergio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | | | - Andrea M Guarino
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | - Laura Giaquinto
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy.
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12
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Bragazzi Cunha J, Leix K, Sherman EJ, Mirabelli C, Frum T, Zhang CJ, Kennedy AA, Lauring AS, Tai AW, Sexton JZ, Spence JR, Wobus CE, Emmer BT. Type I interferon signaling induces a delayed antiproliferative response in respiratory epithelial cells during SARS-CoV-2 infection. J Virol 2023; 97:e0127623. [PMID: 37975674 PMCID: PMC10734423 DOI: 10.1128/jvi.01276-23] [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: 08/29/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023] Open
Abstract
ABSTRACT Disease progression during SARS-CoV-2 infection is tightly linked to the fate of lung epithelial cells, with severe cases of COVID-19 characterized by direct injury of the alveolar epithelium and an impairment in its regeneration from progenitor cells. The molecular pathways that govern respiratory epithelial cell death and proliferation during SARS-CoV-2 infection, however, remain unclear. We now report a high-throughput CRISPR screen for host genetic modifiers of the survival and proliferation of SARS-CoV-2-infected Calu-3 respiratory epithelial cells. The top four genes identified in our screen encode components of the same type I interferon (IFN-I) signaling complex—IFNAR1, IFNAR2, JAK1, and TYK2. The fifth gene, ACE2, was an expected control encoding the SARS-CoV-2 viral receptor. Surprisingly, despite the antiviral properties of IFN-I signaling, its disruption in our screen was associated with an increase in Calu-3 cell fitness. We validated this effect and found that IFN-I signaling did not sensitize SARS-CoV-2-infected cultures to cell death but rather inhibited the proliferation of surviving cells after the early peak of viral replication and cytopathic effect. We also found that IFN-I signaling alone, in the absence of viral infection, was sufficient to induce this delayed antiproliferative response in both Calu-3 cells and iPSC-derived type 2 alveolar epithelial cells. Together, these findings highlight a cell autonomous antiproliferative response by respiratory epithelial cells to persistent IFN-I signaling during SARS-CoV-2 infection. This response may contribute to the deficient alveolar regeneration that has been associated with COVID-19 lung injury and represents a promising area for host-targeted therapeutic development.
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Affiliation(s)
- Juliana Bragazzi Cunha
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kyle Leix
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Emily J. Sherman
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tristan Frum
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Charles J. Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew A. Kennedy
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Adam S. Lauring
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Andrew W. Tai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- VA Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Jonathan Z. Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R. Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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13
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Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Network I, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf J, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Augustine AD, Sekaly RP, Ehrlich LIR, Fourati S, Peters B, Kleinstein SH, Guan L. Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565292. [PMID: 37986828 PMCID: PMC10659275 DOI: 10.1101/2023.11.03.565292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Hospitalized COVID-19 patients exhibit diverse clinical outcomes, with some individuals diverging over time even though their initial disease severity appears similar. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity. In this study, we carried out deep immunophenotyping and conducted longitudinal multi-omics modeling integrating ten distinct assays on a total of 1,152 IMPACC participants and identified several immune cascades that were significant drivers of differential clinical outcomes. Increasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, NETosis, and T-cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma immunoglobulins and B cells, as well as dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to the failure of viral clearance in patients with fatal illness. Our longitudinal multi-omics profiling study revealed novel temporal coordination across diverse omics that potentially explain disease progression, providing insights that inform the targeted development of therapies for hospitalized COVID-19 patients, especially those critically ill.
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14
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Shi W, Chen M, Pan T, Chen M, Cheng Y, Hao Y, Chen S, Tang Y. Integration of risk variants from GWAS with SARS-CoV-2 RNA interactome prioritizes FUBP1 and RAB2A as risk genes for COVID-19. Sci Rep 2023; 13:19194. [PMID: 37932299 PMCID: PMC10628159 DOI: 10.1038/s41598-023-44705-3] [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: 08/21/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
The role of host genetic factors in COVID-19 outcomes remains unclear despite various genome-wide association studies (GWAS). We annotate all significant variants and those variants in high LD (R2 > 0.8) from the COVID-19 host genetics initiative (HGI) and identify risk genes by recognizing genes intolerant nonsynonymous mutations in coding regions and genes associated with cis-expression quantitative trait loci (cis-eQTL) in non-coding regions. These genes are enriched in the immune response pathway and viral life cycle. It has been found that host RNA binding proteins (RBPs) participate in different phases of the SARS-CoV-2 life cycle. We collect 503 RBPs that interact with SARS-CoV-2 RNA concluded from in vitro studies. Combining risk genes from the HGI with RBPs, we identify two COVID-19 risk loci that regulate the expression levels of FUBP1 and RAB2A in the lung. Due to the risk allele, COVID-19 patients show downregulation of FUBP1 and upregulation of RAB2A. Using single-cell RNA sequencing data, we show that FUBP1 and RAB2A are expressed in SARS-CoV-2-infected upper respiratory tract epithelial cells. We further identify NC_000001.11:g.77984833C>A and NC_000008.11:g.60559280T>C as functional variants by surveying allele-specific transcription factor sites and cis-regulatory elements and performing motif analysis. To sum up, our research, which associates human genetics with expression levels of RBPs, identifies FUBP1 and RAB2A as two risk genes for COVID-19 and reveals the anti-viral role of FUBP1 and the pro-viral role of RAB2A in the infection of SARS-CoV-2.
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Affiliation(s)
- Weiwen Shi
- Shanghai Institute of Rheumatology/Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengke Chen
- Shanghai Institute of Rheumatology/Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingting Pan
- Shanghai Institute of Rheumatology/Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengjie Chen
- Department of Rheumatology, the First People's Hospital of Wenling, Taizhou, China
| | - Yongjun Cheng
- Department of Rheumatology, the First People's Hospital of Wenling, Taizhou, China
| | - Yimei Hao
- Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Sheng Chen
- Shanghai Institute of Rheumatology/Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology/Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai, China.
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15
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Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nat Commun 2023; 14:6245. [PMID: 37803001 PMCID: PMC10558542 DOI: 10.1038/s41467-023-41788-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023] Open
Abstract
Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.
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Affiliation(s)
- Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California, Berkeley-UCSF Joint Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oren S Rosenberg
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| | - Marco Y Hein
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Center for Medical Biochemistry, Vienna, Austria.
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16
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Kober DL, Caballero Van Dyke MC, Eitson JL, Boys IN, McDougal MB, Rosenbaum DM, Schoggins JW. Development of a mutant aerosolized ACE2 that neutralizes SARS-CoV-2 in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559550. [PMID: 37808801 PMCID: PMC10557691 DOI: 10.1101/2023.09.26.559550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The rapid evolution of SARS-CoV-2 variants highlights the need for new therapies to prevent disease spread. SARS-CoV-2, like SARS-CoV-1, uses the human cell surface protein angiotensin-converting enzyme 2 (ACE2) as its native receptor. Here, we design and characterize a mutant ACE2 that enables rapid affinity purification of a dimeric protein by altering the active site to prevent autoproteolytic digestion of a C-terminal His10 epitope tag. In cultured cells, mutant ACE2 competitively inhibits lentiviral vectors pseudotyped with spike from multiple SARS-CoV-2 variants, and infectious SARS-CoV-2. Moreover, the protein can be nebulized and retains virus-binding properties. We developed a system for delivery of aerosolized ACE2 to K18-hACE2 mice and demonstrate protection by our modified ACE2 when delivered as a prophylactic agent. These results show proof-of-concept for an aerosolized delivery method to evaluate anti-SARS-CoV-2 agents in vivo and suggest a new tool in the ongoing fight against SARS-CoV-2 and other ACE2-dependent viruses.
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Affiliation(s)
- Daniel L. Kober
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Jennifer L. Eitson
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ian N. Boys
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Matthew B. McDougal
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel M. Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John W. Schoggins
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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17
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Tayal S, Bhatnagar S. Role of molecular mimicry in the SARS-CoV-2-human interactome for pathogenesis of cardiovascular diseases: An update to ImitateDB. Comput Biol Chem 2023; 106:107919. [PMID: 37463554 DOI: 10.1016/j.compbiolchem.2023.107919] [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: 01/15/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Mimicry of host proteins is a strategy employed by pathogens to hijack host functions. Domain and motif mimicry was explored in the experimental and predicted SARS-CoV-2-human interactome. The host first interactor proteins were also added to capture the continuum of the interactions. The domains and motifs of the proteins were annotated using NCBI CD Search and ScanProsite, respectively. Host and pathogen proteins with a common host interactor and similar domain/motif constitute a mimicry pair indicating global structural similarity (domain mimicry pair; DMP) or local sequence similarity (motif mimicry pair; MMP). 593 DMPs and 7,02,472 MMPs were determined. AAA, DEXDc and Macro domains were frequent among DMPs whereas glycosylation, myristoylation and RGD motifs were abundant among MMP. The proteins involved in mimicry were visualised as a SARS-CoV-2 mimicry interaction network. The host proteins were enriched in multiple CVD pathways indicating the role of mimicry in COVID-19 associated CVDs. Bridging nodes were identified as potential drug targets. Approved antihypertensive and anti-inflammatory drugs are proposed for repurposing against COVID-19 associated CVDs. The SARS-CoV-2 mimicry data has been updated in ImitateDB (http://imitatedb.sblab-nsit.net/SARSCoV2Mimicry). Determination of key mechanisms, proteins, pathways, drug targets and repurposing candidates is critical for developing therapeutics for SARS CoV-2 associated CVDs.
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Affiliation(s)
- Sonali Tayal
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India.
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18
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Yi J, Zhang M, Zhu L, Xu C, Li B, Wu P, Wu H, Zhang B. High-efficiency genetic engineering toolkit for virus based on lambda red-mediated recombination. Biotechnol Lett 2023; 45:1327-1337. [PMID: 37526868 DOI: 10.1007/s10529-023-03412-9] [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: 02/21/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
PURPOSE Viruses, such as Ebola virus (EBOV), evolve rapidly and threaten the human health. There is a great demand to exploit efficient gene-editing techniques for the identification of virus to probe virulence mechanism for drug development. METHODS Based on lambda Red recombination in Escherichia coli (E. coli), counter-selection, and in vitro annealing, a high-efficiency genetic method was utilized here for precisely engineering viruses. EBOV trVLPs assay and dual luciferase reporter assay were used to further test the effect of mutations on virus replication. RESULTS Considering the significance of matrix protein VP24 in EBOV replication, the types of mutations within vp24, including several single-base substitutions, one double-base substitution, two seamless deletions, and one targeted insertion, were generated on the multi-copy plasmid of E. coli. Further, the length of the homology arms for recombination and in vitro annealing, and the amount of DNA cassettes and linear plasmids were optimized to create a more elaborate and cost-efficient protocol than original approach. The effects of VP24 mutations on the expression of a reporter gene (luciferase) from the EBOV minigenome were determined, and results indicated that mutations of key sites within VP24 have significant impacts on EBOV replication. CONCLUSION This precise mutagenesis method will facilitate effective and simple editing of viral genes in E. coli.
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Affiliation(s)
- Jing Yi
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Maifei Zhang
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Lin Zhu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Changzhi Xu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Binglin Li
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Panpan Wu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Hang Wu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China.
| | - Buchang Zhang
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
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19
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Savan R, Gale M. Innate immunity and interferon in SARS-CoV-2 infection outcome. Immunity 2023; 56:1443-1450. [PMID: 37437537 PMCID: PMC10361255 DOI: 10.1016/j.immuni.2023.06.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/14/2023]
Abstract
Innate immunity and the actions of type I and III interferons (IFNs) are essential for protection from SARS-CoV-2 and COVID-19. Each is induced in response to infection and serves to restrict viral replication and spread while directing the polarization and modulation of the adaptive immune response. Owing to the distribution of their specific receptors, type I and III IFNs, respectively, impart systemic and local actions. Therapeutic IFN has been administered to combat COVID-19 but with differential outcomes when given early or late in infection. In this perspective, we sort out the role of innate immunity and complex actions of IFNs in the context of SARS-CoV-2 infection and COVID-19. We conclude that IFNs are a beneficial component of innate immunity that has mediated natural clearance of infection in over 700 million people. Therapeutic induction of innate immunity and use of IFN should be featured in strategies to treat acute SARS-CoV-2 infection in people at risk for severe COVID-19.
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Affiliation(s)
- Ram Savan
- Department of Immunology and Center for Innate Immunity and Immune Disease, University of Washington, 750 Republican St., Seattle, WA 98109, USA
| | - Michael Gale
- Department of Immunology and Center for Innate Immunity and Immune Disease, University of Washington, 750 Republican St., Seattle, WA 98109, USA.
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20
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Wing PAC, Schmidt NM, Peters R, Erdmann M, Brown R, Wang H, Swadling L, Newman J, Thakur N, Shionoya K, Morgan SB, Hinks TSC, Watashi K, Bailey D, Hansen SB, Davidson AD, Maini MK, McKeating JA. An ACAT inhibitor suppresses SARS-CoV-2 replication and boosts antiviral T cell activity. PLoS Pathog 2023; 19:e1011323. [PMID: 37134108 PMCID: PMC10202285 DOI: 10.1371/journal.ppat.1011323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 05/22/2023] [Accepted: 03/27/2023] [Indexed: 05/04/2023] Open
Abstract
The severity of disease following infection with SARS-CoV-2 is determined by viral replication kinetics and host immunity, with early T cell responses and/or suppression of viraemia driving a favourable outcome. Recent studies uncovered a role for cholesterol metabolism in the SARS-CoV-2 life cycle and in T cell function. Here we show that blockade of the enzyme Acyl-CoA:cholesterol acyltransferase (ACAT) with Avasimibe inhibits SARS-CoV-2 pseudoparticle infection and disrupts the association of ACE2 and GM1 lipid rafts on the cell membrane, perturbing viral attachment. Imaging SARS-CoV-2 RNAs at the single cell level using a viral replicon model identifies the capacity of Avasimibe to limit the establishment of replication complexes required for RNA replication. Genetic studies to transiently silence or overexpress ACAT isoforms confirmed a role for ACAT in SARS-CoV-2 infection. Furthermore, Avasimibe boosts the expansion of functional SARS-CoV-2-specific T cells from the blood of patients sampled during the acute phase of infection. Thus, re-purposing of ACAT inhibitors provides a compelling therapeutic strategy for the treatment of COVID-19 to achieve both antiviral and immunomodulatory effects. Trial registration: NCT04318314.
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Affiliation(s)
- Peter A. C. Wing
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nathalie M. Schmidt
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, United Kingdom
| | - Rory Peters
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Maximilian Erdmann
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Rachel Brown
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, United Kingdom
- UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Hao Wang
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, San Diego, California, United States of America
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, San Diego, California, United States of America
| | - Leo Swadling
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, United Kingdom
| | | | | | | | - Kaho Shionoya
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Research Centre for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sophie B. Morgan
- Respiratory Medicine Unit and National Institute for Health Research Oxford Biomedical Research Centre, Nuffield Department of Medicine, Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Timothy SC Hinks
- Respiratory Medicine Unit and National Institute for Health Research Oxford Biomedical Research Centre, Nuffield Department of Medicine, Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Research Centre for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Scott B. Hansen
- UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Mala K. Maini
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, United Kingdom
| | - Jane A. McKeating
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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21
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Fang L, Yang L, Han M, Xu H, Ding W, Dong X. CRISPR-cas technology: A key approach for SARS-CoV-2 detection. Front Bioeng Biotechnol 2023; 11:1158672. [PMID: 37214290 PMCID: PMC10198440 DOI: 10.3389/fbioe.2023.1158672] [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: 02/09/2023] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
The CRISPR (Clustered Regularly Spaced Short Palindromic Repeats) system was first discovered in prokaryotes as a unique immune mechanism to clear foreign nucleic acids. It has been rapidly and extensively used in basic and applied research owing to its strong ability of gene editing, regulation and detection in eukaryotes. Hererin in this article, we reviewed the biology, mechanisms and relevance of CRISPR-Cas technology and its applications in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. CRISPR-Cas nucleic acid detection tools include CRISPR-Cas9, CRISPR-Cas12, CRISPR-Cas13, CRISPR-Cas14, CRISPR nucleic acid amplification detection technology, and CRISPR colorimetric readout detection system. The above CRISPR technologies have been applied to the nucleic acid detection, including SARS-CoV-2 detection. Common nucleic acid detection based on CRISPR derivation technology include SHERLOCK, DETECTR, and STOPCovid. CRISPR-Cas biosensing technology has been widely applied to point-of-care testing (POCT) by targeting recognition of both DNA molecules and RNA Molecules.
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Affiliation(s)
- Lijuan Fang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Lusen Yang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Mingyue Han
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Huimei Xu
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Wenshuai Ding
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Xuejun Dong
- Medical Laboratory, Zhejiang University Shaoxing Hospital, Shaoxing, China
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22
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Rosado-Olivieri EA, Razooky B, Le Pen J, De Santis R, Barrows D, Sabry Z, Hoffmann HH, Park J, Carroll TS, Poirier JT, Rice CM, Brivanlou AH. Organotypic human lung bud microarrays identify BMP-dependent SARS-CoV-2 infection in lung cells. Stem Cell Reports 2023; 18:1107-1122. [PMID: 37084725 PMCID: PMC10116630 DOI: 10.1016/j.stemcr.2023.03.015] [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: 08/24/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/23/2023] Open
Abstract
Although lung disease is the primary clinical outcome in COVID-19 patients, how SARS-CoV-2 induces lung pathology remains elusive. Here we describe a high-throughput platform to generate self-organizing and commensurate human lung buds derived from hESCs cultured on micropatterned substrates. Lung buds resemble human fetal lungs and display proximodistal patterning of alveolar and airway tissue directed by KGF. These lung buds are susceptible to infection by SARS-CoV-2 and endemic coronaviruses and can be used to track cell type-specific cytopathic effects in hundreds of lung buds in parallel. Transcriptomic comparisons of infected lung buds and postmortem tissue of COVID-19 patients identified an induction of BMP signaling pathway. BMP activity renders lung cells more susceptible to SARS-CoV-2 infection and its pharmacological inhibition impairs infection by this virus. These data highlight the rapid and scalable access to disease-relevant tissue using lung buds that recapitulate key features of human lung morphogenesis and viral infection biology.
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Affiliation(s)
- E A Rosado-Olivieri
- Laboratory of Synthetic Embryology, the Rockefeller University, New York, NY, USA
| | - B Razooky
- Laboratory of Virology and Infectious Diseases, the Rockefeller University, New York, NY, USA
| | - J Le Pen
- Laboratory of Virology and Infectious Diseases, the Rockefeller University, New York, NY, USA
| | - R De Santis
- Laboratory of Synthetic Embryology, the Rockefeller University, New York, NY, USA
| | - D Barrows
- Bioinformatics Resource Center, the Rockefeller University, New York, NY, USA
| | - Z Sabry
- Laboratory of Synthetic Embryology, the Rockefeller University, New York, NY, USA
| | - H-H Hoffmann
- Laboratory of Virology and Infectious Diseases, the Rockefeller University, New York, NY, USA
| | - J Park
- Laboratory of Virology and Infectious Diseases, the Rockefeller University, New York, NY, USA
| | - T S Carroll
- Bioinformatics Resource Center, the Rockefeller University, New York, NY, USA
| | - J T Poirier
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - C M Rice
- Laboratory of Virology and Infectious Diseases, the Rockefeller University, New York, NY, USA.
| | - A H Brivanlou
- Laboratory of Synthetic Embryology, the Rockefeller University, New York, NY, USA.
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23
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Klestova Z. Possible spread of SARS-CoV-2 in domestic and wild animals and body temperature role. Virus Res 2023; 327:199066. [PMID: 36754290 PMCID: PMC9911306 DOI: 10.1016/j.virusres.2023.199066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
The COVID-19 pandemic was officially announced in March 2020 and is still moving around the world. Virus strains, their pathogenicity and infectivity are changing, but the ability is fast to spread and harm people's health remained, despite the seasonality seasons and other circumstances. Most likely, humanity is doomed for a long time to coexistence with this emergent pathogen, since it is already circulating not only among the human population, but and among fauna, especially among wild animals in different regions of the planet. Thus, the range the virus has expanded, the material and conditions for its evolution are more than enough. The detection of SARS-CoV-2 in known infected fauna species is analyzed and possible spread and ongoing circulation of the virus in domestic and wild animals are discussed. One of the main focus of the article is the role of animal body temperature, its fluctuations and the presence of entry receptors in the susceptibility of different animal species to SARS-CoV-2 infection and virus spreading in possible new ecological niches. The possibility of long-term circulation of the pathogen among susceptible organisms is discussed.
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Affiliation(s)
- Zinaida Klestova
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Elfriede-Aulhorn-Straße 6, Tübingen 72076, Germany.
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24
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Autophagy in Inflammatory Response against SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24054928. [PMID: 36902354 PMCID: PMC10002778 DOI: 10.3390/ijms24054928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
The coronavirus disease pandemic, which profoundly reshaped the world in 2019 (COVID-19), and is currently ongoing, has affected over 200 countries, caused over 500 million cumulative cases, and claimed the lives of over 6.4 million people worldwide as of August 2022. The causative agent is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Depicting this virus' life cycle and pathogenic mechanisms, as well as the cellular host factors and pathways involved during infection, has great relevance for the development of therapeutic strategies. Autophagy is a catabolic process that sequesters damaged cell organelles, proteins, and external invading microbes, and delivers them to the lysosomes for degradation. Autophagy would be involved in the entry, endo, and release, as well as the transcription and translation, of the viral particles in the host cell. Secretory autophagy would also be involved in developing the thrombotic immune-inflammatory syndrome seen in a significant number of COVID-19 patients that can lead to severe illness and even death. This review aims to review the main aspects that characterize the complex and not yet fully elucidated relationship between SARS-CoV-2 infection and autophagy. It briefly describes the key concepts regarding autophagy and mentions its pro- and antiviral roles, while also noting the reciprocal effect of viral infection in autophagic pathways and their clinical aspects.
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25
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Cunha JB, Leix K, Sherman EJ, Mirabelli C, Kennedy AA, Lauring AS, Tai AW, Wobus CE, Emmer BT. Type I interferon signaling induces a delayed antiproliferative response in Calu-3 cells during SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530557. [PMID: 36909579 PMCID: PMC10002732 DOI: 10.1101/2023.02.28.530557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Disease progression during SARS-CoV-2 infection is tightly linked to the fate of lung epithelial cells, with severe cases of COVID-19 characterized by direct injury of the alveolar epithelium and an impairment in its regeneration from progenitor cells. The molecular pathways that govern respiratory epithelial cell death and proliferation during SARS-CoV-2 infection, however, remain poorly understood. We now report a high-throughput CRISPR screen for host genetic modifiers of the survival and proliferation of SARS-CoV-2-infected Calu-3 respiratory epithelial cells. The top 4 genes identified in our screen encode components of the same type I interferon signaling complex - IFNAR1, IFNAR2, JAK1, and TYK2. The 5th gene, ACE2, was an expected control encoding the SARS-CoV-2 viral receptor. Surprisingly, despite the antiviral properties of IFN-I signaling, its disruption in our screen was associated with an increase in Calu-3 cell fitness. We validated this effect and found that IFN-I signaling did not sensitize SARS-CoV-2-infected cultures to cell death but rather inhibited the proliferation of surviving cells after the early peak of viral replication and cytopathic effect. We also found that IFN-I signaling alone, in the absence of viral infection, was sufficient to induce this delayed antiproliferative response. Together, these findings highlight a cell autonomous antiproliferative response by respiratory epithelial cells to persistent IFN-I signaling during SARS-CoV-2 infection. This response may contribute to the deficient alveolar regeneration that has been associated with COVID-19 lung injury and represents a promising area for host-targeted therapeutic development.
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Affiliation(s)
| | - Kyle Leix
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
| | - Emily J. Sherman
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor MI
| | - Andrew A. Kennedy
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
| | - Adam S. Lauring
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor MI
| | - Andrew W. Tai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor MI
- VA Ann Arbor Healthcare System, Ann Arbor MI
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor MI
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
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26
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Kim MI, Lee C. Human Coronavirus OC43 as a Low-Risk Model to Study COVID-19. Viruses 2023; 15:v15020578. [PMID: 36851792 PMCID: PMC9965565 DOI: 10.3390/v15020578] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had irreversible and devastating impacts on every aspect of human life. To better prepare for the next similar pandemic, a clear understanding of coronavirus biology is a prerequisite. Nevertheless, the high-risk nature of the causative agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), requires the use of a cumbersome biosafety level-3 (BSL-3) confinement facility. To facilitate the development of preventive and therapeutic measures against SARS-CoV-2, one of the endemic strains of low-risk coronaviruses has gained attention as a useful research alternative: human coronavirus OC43 (HCoV-OC43). In this review, its history, classification, and clinical manifestations are first summarized. The characteristics of its viral genomes, genes, and evolution process are then further explained. In addition, the host factors necessary to support the life cycle of HCoV-OC43 and the innate, as well as adaptive, immunological responses to HCoV-OC43 infection are discussed. Finally, the development of in vitro and in vivo systems to study HCoV-OC43 and its application to the discovery of potential antivirals for COVID-19 by using HCoV-OC43 models are also presented. This review should serve as a concise guide for those who wish to use HCoV-OC43 to study coronaviruses in a low-risk research setting.
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27
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Horlacher M, Oleshko S, Hu Y, Ghanbari M, Cantini G, Schinke P, Vergara EE, Bittner F, Mueller NS, Ohler U, Moyon L, Marsico A. A computational map of the human-SARS-CoV-2 protein-RNA interactome predicted at single-nucleotide resolution. NAR Genom Bioinform 2023; 5:lqad010. [PMID: 36814457 PMCID: PMC9940458 DOI: 10.1093/nargab/lqad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/10/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
RNA-binding proteins (RBPs) are critical host factors for viral infection, however, large scale experimental investigation of the binding landscape of human RBPs to viral RNAs is costly and further complicated due to sequence variation between viral strains. To fill this gap, we investigated the role of RBPs in the context of SARS-CoV-2 by constructing the first in silico map of human RBP-viral RNA interactions at nucleotide-resolution using two deep learning methods (pysster and DeepRiPe) trained on data from CLIP-seq experiments on more than 100 human RBPs. We evaluated conservation of RBP binding between six other human pathogenic coronaviruses and identified sites of conserved and differential binding in the UTRs of SARS-CoV-1, SARS-CoV-2 and MERS. We scored the impact of mutations from 11 variants of concern on protein-RNA interaction, identifying a set of gain- and loss-of-binding events, as well as predicted the regulatory impact of putative future mutations. Lastly, we linked RBPs to functional, OMICs and COVID-19 patient data from other studies, and identified MBNL1, FTO and FXR2 RBPs as potential clinical biomarkers. Our results contribute towards a deeper understanding of how viruses hijack host cellular pathways and open new avenues for therapeutic intervention.
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Affiliation(s)
- Marc Horlacher
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Svitlana Oleshko
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Yue Hu
- Computational Health Center, Helmholtz Center Munich, Munich, Germany,Informatics 12 Chair of Bioinformatics, Technical University Munich, Garching, Germany
| | - Mahsa Ghanbari
- Institutes of Biology and Computer Science, Humboldt University, Berlin, Germany,Max Delbruck Center, Computational Regulatory Genomics, Berlin, Germany
| | - Giulia Cantini
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Patrick Schinke
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | | | | | | | - Uwe Ohler
- Institutes of Biology and Computer Science, Humboldt University, Berlin, Germany,Max Delbruck Center, Computational Regulatory Genomics, Berlin, Germany
| | - Lambert Moyon
- To whom correspondence should be addressed. Tel: +49 89318749193;
| | - Annalisa Marsico
- Correspondence may also be addressed to Annalisa Marsico. Tel: +49 89318743073;
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28
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Innate Immunity in Cardiovascular Diseases-Identification of Novel Molecular Players and Targets. J Clin Med 2023; 12:jcm12010335. [PMID: 36615135 PMCID: PMC9821340 DOI: 10.3390/jcm12010335] [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: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
During the past few years, unexpected developments have driven studies in the field of clinical immunology. One driver of immense impact was the outbreak of a pandemic caused by the novel virus SARS-CoV-2. Excellent recent reviews address diverse aspects of immunological re-search into cardiovascular diseases. Here, we specifically focus on selected studies taking advantage of advanced state-of-the-art molecular genetic methods ranging from genome-wide epi/transcriptome mapping and variant scanning to optogenetics and chemogenetics. First, we discuss the emerging clinical relevance of advanced diagnostics for cardiovascular diseases, including those associated with COVID-19-with a focus on the role of inflammation in cardiomyopathies and arrhythmias. Second, we consider newly identified immunological interactions at organ and system levels which affect cardiovascular pathogenesis. Thus, studies into immune influences arising from the intestinal system are moving towards therapeutic exploitation. Further, powerful new research tools have enabled novel insight into brain-immune system interactions at unprecedented resolution. This latter line of investigation emphasizes the strength of influence of emotional stress-acting through defined brain regions-upon viral and cardiovascular disorders. Several challenges need to be overcome before the full impact of these far-reaching new findings will hit the clinical arena.
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29
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Najafabadi ZY, Fanuel S, Falak R, Kaboli S, Kardar GA. The Trend of CRISPR-Based Technologies in COVID-19 Disease: Beyond Genome Editing. Mol Biotechnol 2023; 65:146-161. [PMID: 35091986 PMCID: PMC8799426 DOI: 10.1007/s12033-021-00431-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023]
Abstract
Biotechnological approaches have always sought to utilize novel and efficient methods in the prevention, diagnosis, and treatment of diseases. This science has consistently tried to revolutionize medical science by employing state-of-the-art technologies in genomic and proteomic engineering. CRISPR-Cas system is one of the emerging techniques in the field of biotechnology. To date, the CRISPR-Cas system has been extensively applied in gene editing, targeting genomic sequences for diagnosis, treatment of diseases through genomic manipulation, and in creating animal models for preclinical researches. With the emergence of the COVID-19 pandemic in 2019, there is need for the development and modification of novel tools such as the CRISPR-Cas system for use in diagnostic emergencies. This system can compete with other existing biotechnological methods in accuracy, precision, and wide performance that could guarantee its future in these conditions. In this article, we review the various platforms of the CRISPR-Cas system meant for SARS-CoV-2 diagnosis, anti-viral therapeutic procedures, producing animal models for preclinical studies, and genome-wide screening studies toward drug and vaccine development.
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Affiliation(s)
- Zeinab Yousefi Najafabadi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Immunology, Asthma Allergy Research Institute (IAARI), Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Songwe Fanuel
- Department of Applied Biosciences and Biotechnology, Faculty of Science and Technology, Midlands State University (MSU), Gweru, Zimbabwe
| | - Reza Falak
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Kaboli
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Gholam Ali Kardar
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Immunology, Asthma Allergy Research Institute (IAARI), Tehran University of Medical Sciences, Tehran, Iran
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30
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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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31
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Christie M, Igreja C. eIF4E-homologous protein (4EHP): a multifarious cap-binding protein. FEBS J 2023; 290:266-285. [PMID: 34758096 DOI: 10.1111/febs.16275] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 02/05/2023]
Abstract
The cap-binding protein 4EHP/eIF4E2 has been a recent object of interest in the field of post-transcriptional gene regulation and translational control. From ribosome-associated quality control, to RNA decay and microRNA-mediated gene silencing, this member of the eIF4E protein family regulates gene expression through numerous pathways. Low in abundance but ubiquitously expressed, 4EHP interacts with different binding partners to form multiple protein complexes that regulate translation in a variety of biological contexts. Documented functions of 4EHP primarily relate to its role as a translational repressor, but recent findings indicate that it might also participate in the activation of translation in specific settings. In this review, we discuss the known functions, properties and mechanisms that involve 4EHP in the control of gene expression. We also discuss our current understanding of how 4EHP processes are regulated in eukaryotic cells, and the diseases implicated with dysregulation of 4EHP-mediated translational control.
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Affiliation(s)
- Mary Christie
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
| | - Cátia Igreja
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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32
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Significance of Catecholamine Biosynthetic/Metabolic Pathway in SARS-CoV-2 Infection and COVID-19 Severity. Cells 2022; 12:cells12010012. [PMID: 36611805 PMCID: PMC9818320 DOI: 10.3390/cells12010012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The SARS-CoV-2 infection was previously associated with the expression of the dopamine biosynthetic enzyme L-Dopa decarboxylase (DDC). Specifically, a negative correlation was detected between DDC mRNA and SARS-CoV-2 RNA levels in in vitro infected epithelial cells and the nasopharyngeal tissue of COVID-19 patients with mild/no symptoms. However, DDC, among other genes related to both DDC expression and SARS-CoV-2-infection (ACE2, dACE2, EPO), was upregulated in these patients, possibly attributed to an orchestrated host antiviral response. Herein, by comparing DDC expression in the nasopharyngeal swab samples of severe/critical to mild COVID-19 cases, we showed a 20 mean-fold reduction, highlighting the importance of the expression of this gene as a potential marker of COVID-19 severity. Moreover, we identified an association of SARS-CoV-2 infection with the expression of key catecholamine biosynthesis/metabolism-related genes, in whole blood samples from hospitalized patients and in cultured cells. Specifically, viral infection downregulated the biosynthetic part of the dopamine pathway (reduction in DDC expression up to 7.5 mean-fold), while enhanced the catabolizing part (increase in monoamine oxidases A and B expression up to 15 and 10 mean-fold, respectively) in vivo, irrespectively of the presence of comorbidities. In accordance, dopamine levels in the sera of severe cases were reduced (up to 3.8 mean-fold). Additionally, a moderate positive correlation between DDC and MAOA mRNA levels (r = 0.527, p < 00001) in the blood was identified upon SARS-CoV-2-infection. These observations were consistent to the gene expression data from SARS-CoV-2-infected Vero E6 and A549 epithelial cells. Furthermore, L-Dopa or dopamine treatment of infected cells attenuated the virus-derived cytopathic effect by 55% and 59%, respectively. The SARS-CoV-2 mediated suppression of dopamine biosynthesis in cell culture was, at least in part, attributed to hypoxia-like conditions triggered by viral infection. These findings suggest that L-Dopa/dopamine intake may have a preventive or therapeutic value for COVID-19 patients.
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33
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Rabaan AA, Mutair AA, Aljeldah M, Shammari BRA, Sulaiman T, Alshukairi AN, Alfaresi M, Al-Jishi JM, Al Bati NA, Al-Mozaini MA, Bshabshe AA, Almatouq JA, Abuzaid AA, Alfaraj AH, Al-Adsani W, Alabdullah M, Alwarthan S, Alsalman F, Alwashmi ASS, Alhumaid S. Genetic Variants and Protective Immunity against SARS-CoV-2. Genes (Basel) 2022; 13:genes13122355. [PMID: 36553622 PMCID: PMC9778397 DOI: 10.3390/genes13122355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/16/2022] Open
Abstract
The novel coronavirus-19 (SARS-CoV-2), has infected numerous individuals worldwide, resulting in millions of fatalities. The pandemic spread with high mortality rates in multiple waves, leaving others with moderate to severe symptoms. Co-morbidity variables, including hypertension, diabetes, and immunosuppression, have exacerbated the severity of COVID-19. In addition, numerous efforts have been made to comprehend the pathogenic and host variables that contribute to COVID-19 susceptibility and pathogenesis. One of these endeavours is understanding the host genetic factors predisposing an individual to COVID-19. Genome-Wide Association Studies (GWAS) have demonstrated the host predisposition factors in different populations. These factors are involved in the appropriate immune response, their imbalance influences susceptibility or resistance to viral infection. This review investigated the host genetic components implicated at the various stages of viral pathogenesis, including viral entry, pathophysiological alterations, and immunological responses. In addition, the recent and most updated genetic variations associated with multiple host factors affecting COVID-19 pathogenesis are described in the study.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
- Correspondence:
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia
- College of Nursing, Princess Norah Bint Abdulrahman University, Riyadh 11564, Saudi Arabia
- School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia
- Nursing Department, Prince Sultan Military College of Health Sciences, Dhahran 33048, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Tarek Sulaiman
- Infectious Diseases Section, Medical Specialties Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Abeer N. Alshukairi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah 21499, Saudi Arabia
| | - Mubarak Alfaresi
- Department of Pathology and Laboratory Medicine, Sheikh Khalifa General Hospital, Umm Al Quwain 499, United Arab Emirates
- Department of Pathology, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
| | - Jumana M. Al-Jishi
- Internal Medicine Department, Qatif Central Hospital, Qatif 35342, Saudi Arabia
| | - Neda A. Al Bati
- Medical and Clinical Affairs, Rural Health Network, Eastern Health Cluster, Dammam 31444, Saudi Arabia
| | - Maha A. Al-Mozaini
- Immunocompromised Host Research Section, Department of Infection and Immunity, King Faisal, Specialist Hospital and Research Centre, Riyadh 11564, Saudi Arabia
| | - Ali Al Bshabshe
- Adult Critical Care Department of Medicine, Division of Adult Critical Care, College of Medicine, King Khalid University, Abha 62561, Saudi Arabia
| | - Jenan A. Almatouq
- Department of Clinical Laboratory Sciences, Mohammed Al-Mana College of Health Sciences, Dammam 34222, Saudi Arabia
| | - Abdulmonem A. Abuzaid
- Medical Microbiology Department, Security Forces Hospital Programme, Dammam 32314, Saudi Arabia
| | - Amal H. Alfaraj
- Pediatric Department, Abqaiq General Hospital, First Eastern Health Cluster, Abqaiq 33261, Saudi Arabia
| | - Wasl Al-Adsani
- Department of Medicine, Infectious Diseases Hospital, Kuwait City 63537, Kuwait
- Department of Infectious Diseases, Hampton Veterans Administration Medical Center, Hampton, VA 23667, USA
| | - Mohammed Alabdullah
- Department of Infectious Diseases, Almoosa Specialist Hospital, Al Mubarraz 36342, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Fatimah Alsalman
- Department of Emergency Medicine, Oyun City Hospital, Al-Ahsa 36312, Saudi Arabia
| | - Ameen S. S. Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia
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34
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Ostendorf BN, Patel MA, Bilanovic J, Hoffmann HH, Carrasco SE, Rice CM, Tavazoie SF. Common human genetic variants of APOE impact murine COVID-19 mortality. Nature 2022; 611:346-351. [PMID: 36130725 PMCID: PMC10957240 DOI: 10.1038/s41586-022-05344-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 09/13/2022] [Indexed: 11/08/2022]
Abstract
Clinical outcomes of severe acute respiratory syndrome 2 (SARS-CoV-2) infection are highly heterogeneous, ranging from asymptomatic infection to lethal coronavirus disease 2019 (COVID-19). The factors underlying this heterogeneity remain insufficiently understood. Genetic association studies have suggested that genetic variants contribute to the heterogeneity of COVID-19 outcomes, but the underlying potential causal mechanisms are insufficiently understood. Here we show that common variants of the apolipoprotein E (APOE) gene, homozygous in approximately 3% of the world's population1 and associated with Alzheimer's disease, atherosclerosis and anti-tumour immunity2-5, affect COVID-19 outcome in a mouse model that recapitulates increased susceptibility conferred by male sex and advanced age. Mice bearing the APOE2 or APOE4 variant exhibited rapid disease progression and poor survival outcomes relative to mice bearing the most prevalent APOE3 allele. APOE2 and APOE4 mice exhibited increased viral loads as well as suppressed adaptive immune responses early after infection. In vitro assays demonstrated increased infection in the presence of APOE2 and APOE4 relative to APOE3, indicating that differential outcomes are mediated by differential effects of APOE variants on both viral infection and antiviral immunity. Consistent with these in vivo findings in mice, our results also show that APOE genotype is associated with survival in patients infected with SARS-CoV-2 in the UK Biobank (candidate variant analysis, P = 2.6 × 10-7). Our findings suggest APOE genotype to partially explain the heterogeneity of COVID-19 outcomes and warrant prospective studies to assess APOE genotyping as a means of identifying patients at high risk for adverse outcomes.
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Affiliation(s)
- Benjamin N Ostendorf
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
- Department of Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin, Germany.
| | - Mira A Patel
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Jana Bilanovic
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - H-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Sebastian E Carrasco
- Laboratory of Comparative Pathology, Weill Cornell Medicine, Memorial Sloan Kettering Cancer Center, and Rockefeller University, New York, NY, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
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Atlas of interactions between SARS-CoV-2 macromolecules and host proteins. CELL INSIGHT 2022; 2:100068. [PMID: 37192911 PMCID: PMC9670597 DOI: 10.1016/j.cellin.2022.100068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]
Abstract
The proteins and RNAs of viruses extensively interact with host proteins after infection. We collected and reanalyzed all available datasets of protein-protein and RNA-protein interactions related to SARS-CoV-2. We investigated the reproducibility of those interactions and made strict filters to identify highly confident interactions. We systematically analyzed the interaction network and identified preferred subcellular localizations of viral proteins, some of which such as ORF8 in ER and ORF7A/B in ER membrane were validated using dual fluorescence imaging. Moreover, we showed that viral proteins frequently interact with host machinery related to protein processing in ER and vesicle-associated processes. Integrating the protein- and RNA-interactomes, we found that SARS-CoV-2 RNA and its N protein closely interacted with stress granules including 40 core factors, of which we specifically validated G3BP1, IGF2BP1, and MOV10 using RIP and Co-IP assays. Combining CRISPR screening results, we further identified 86 antiviral and 62 proviral factors and associated drugs. Using network diffusion, we found additional 44 interacting proteins including two proviral factors previously validated. Furthermore, we showed that this atlas could be applied to identify the complications associated with COVID-19. All data are available in the AIMaP database (https://mvip.whu.edu.cn/aimap/) for users to easily explore the interaction map.
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36
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Zhu X, Trimarco JD, Williams CA, Barrera A, Reddy TE, Heaton NS. ZBTB7A promotes virus-host homeostasis during human coronavirus 229E infection. Cell Rep 2022; 41:111540. [PMID: 36243002 PMCID: PMC9533670 DOI: 10.1016/j.celrep.2022.111540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/24/2022] [Accepted: 09/29/2022] [Indexed: 11/22/2022] Open
Abstract
The cellular fate after infection with human coronaviruses (HCoVs) is typically death. Previous data suggest, however, that the transcriptional state of an individual cell may sometimes allow additional outcomes of infection. Here, to probe the range of interactions a permissive cell type can have with a HCoV, we perform a CRISPR activation screen with HCoV-229E. The screen identified the transcription factor ZBTB7A, which strongly promotes cell survival after infection. Rather than suppressing viral infection, ZBTB7A upregulation allows the virus to induce a persistent infection and homeostatic state with the cell. We also find that control of oxidative stress is a primary driver of cellular survival during HCoV-229E infection. These data illustrate that, in addition to the nature of the infecting virus and the type of cell that it encounters, the cellular gene expression profile prior to infection can affect the eventual fate.
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Affiliation(s)
- Xinyu Zhu
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Joseph D. Trimarco
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Courtney A. Williams
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA,Center for Genomic and Computational Biology, Duke University, Durham, NC, USA,Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Alejandro Barrera
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA,Center for Genomic and Computational Biology, Duke University, Durham, NC, USA,Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Timothy E. Reddy
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA,Center for Genomic and Computational Biology, Duke University, Durham, NC, USA,Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA,Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA,Corresponding author
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37
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Amahong K, Zhang W, Zhou Y, Zhang S, Yin J, Li F, Xu H, Yan T, Yue Z, Liu Y, Hou T, Qiu Y, Tao L, Han L, Zhu F. CovInter: interaction data between coronavirus RNAs and host proteins. Nucleic Acids Res 2022; 51:D546-D556. [PMID: 36200814 PMCID: PMC9825556 DOI: 10.1093/nar/gkac834] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/07/2022] [Accepted: 09/16/2022] [Indexed: 01/29/2023] Open
Abstract
Coronavirus has brought about three massive outbreaks in the past two decades. Each step of its life cycle invariably depends on the interactions among virus and host molecules. The interaction between virus RNA and host protein (IVRHP) is unique compared to other virus-host molecular interactions and represents not only an attempt by viruses to promote their translation/replication, but also the host's endeavor to combat viral pathogenicity. In other words, there is an urgent need to develop a database for providing such IVRHP data. In this study, a new database was therefore constructed to describe the interactions between coronavirus RNAs and host proteins (CovInter). This database is unique in (a) unambiguously characterizing the interactions between virus RNA and host protein, (b) comprehensively providing experimentally validated biological function for hundreds of host proteins key in viral infection and (c) systematically quantifying the differential expression patterns (before and after infection) of these key proteins. Given the devastating and persistent threat of coronaviruses, CovInter is highly expected to fill the gap in the whole process of the 'molecular arms race' between viruses and their hosts, which will then aid in the discovery of new antiviral therapies. It's now free and publicly accessible at: https://idrblab.org/covinter/.
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Affiliation(s)
| | | | | | - Song Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Hongquan Xu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Tianci Yan
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Zixuan Yue
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuhong Liu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Lin Tao
- Correspondence may also be addressed to Lin Tao.
| | - Lianyi Han
- Correspondence may also be addressed to Lianyi Han.
| | - Feng Zhu
- To whom correspondence should be addressed. Tel: +86 189 8946 6518; Fax: +86 571 8820 8444;
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38
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Duan X, Lacko LA, Chen S. Druggable targets and therapeutic development for COVID-19. Front Chem 2022; 10:963701. [PMID: 36277347 PMCID: PMC9581228 DOI: 10.3389/fchem.2022.963701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/11/2022] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease (COVID-19), which is caused by SARS-CoV-2, is the biggest challenge to the global public health and economy in recent years. Until now, only limited therapeutic regimens have been available for COVID-19 patients, sparking unprecedented efforts to study coronavirus biology. The genome of SARS-CoV-2 encodes 16 non-structural, four structural, and nine accessory proteins, which mediate the viral life cycle, including viral entry, RNA replication and transcription, virion assembly and release. These processes depend on the interactions between viral polypeptides and host proteins, both of which could be potential therapeutic targets for COVID-19. Here, we will discuss the potential medicinal value of essential proteins of SARS-CoV-2 and key host factors. We summarize the most updated therapeutic interventions for COVID-19 patients, including those approved clinically or in clinical trials.
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Song J, Chow RD, Peña-Hernández MA, Zhang L, Loeb SA, So EY, Liang OD, Ren P, Chen S, Wilen CB, Lee S. LRRC15 inhibits SARS-CoV-2 cellular entry in trans. PLoS Biol 2022; 20:e3001805. [PMID: 36228039 PMCID: PMC9595563 DOI: 10.1371/journal.pbio.3001805] [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: 11/25/2021] [Revised: 10/25/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is mediated by the entry receptor angiotensin-converting enzyme 2 (ACE2). Although attachment factors and coreceptors facilitating entry are extensively studied, cellular entry factors inhibiting viral entry are largely unknown. Using a surfaceome CRISPR activation screen, we identified human LRRC15 as an inhibitory attachment factor for SARS-CoV-2 entry. LRRC15 directly binds to the receptor-binding domain (RBD) of spike protein with a moderate affinity and inhibits spike-mediated entry. Analysis of human lung single-cell RNA sequencing dataset reveals that expression of LRRC15 is primarily detected in fibroblasts and particularly enriched in pathological fibroblasts in COVID-19 patients. ACE2 and LRRC15 are not coexpressed in the same cell types in the lung. Strikingly, expression of LRRC15 in ACE2-negative cells blocks spike-mediated viral entry in ACE2+ cell in trans, suggesting a protective role of LRRC15 in a physiological context. Therefore, LRRC15 represents an inhibitory attachment factor for SARS-CoV-2 that regulates viral entry in trans.
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Affiliation(s)
- Jaewon Song
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, Rhode Island, United States of America
| | - Ryan D. Chow
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Mario A. Peña-Hernández
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Li Zhang
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, Rhode Island, United States of America
| | - Skylar A. Loeb
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, Rhode Island, United States of America
| | - Eui-Young So
- Division of Hematology/Oncology, Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, United States of America
| | - Olin D. Liang
- Division of Hematology/Oncology, Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, United States of America
| | - Ping Ren
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Sidi Chen
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Sanghyun Lee
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, Brown University, Providence, Rhode Island, United States of America
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Zhou H, Møhlenberg M, Thakor JC, Tuli HS, Wang P, Assaraf YG, Dhama K, Jiang S. Sensitivity to Vaccines, Therapeutic Antibodies, and Viral Entry Inhibitors and Advances To Counter the SARS-CoV-2 Omicron Variant. Clin Microbiol Rev 2022; 35:e0001422. [PMID: 35862736 PMCID: PMC9491202 DOI: 10.1128/cmr.00014-22] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) keeps evolving and mutating into newer variants over time, which gain higher transmissibility, disease severity, and spread in communities at a faster rate, resulting in multiple waves of surge in Coronavirus Disease 2019 (COVID-19) cases. A highly mutated and transmissible SARS-CoV-2 Omicron variant has recently emerged, driving the extremely high peak of infections in almost all continents at an unprecedented speed and scale. The Omicron variant evades the protection rendered by vaccine-induced antibodies and natural infection, as well as overpowers the antibody-based immunotherapies, raising the concerns of current effectiveness of available vaccines and monoclonal antibody-based therapies. This review outlines the most recent advancements in studying the virology and biology of the Omicron variant, highlighting its increased resistance to current antibody-based therapeutics and its immune escape against vaccines. However, the Omicron variant is highly sensitive to viral fusion inhibitors targeting the HR1 motif in the spike protein, enzyme inhibitors, involving the endosomal fusion pathway, and ACE2-based entry inhibitors. Omicron variant-associated infectivity and entry mechanisms of Omicron variant are essentially distinct from previous characterized variants. Innate sensing and immune evasion of SARS-CoV-2 and T cell immunity to the virus provide new perspectives of vaccine and drug development. These findings are important for understanding SARS-CoV-2 viral biology and advances in developing vaccines, antibody-based therapies, and more effective strategies to mitigate the transmission of the Omicron variant or the next SARS-CoV-2 variant of concern.
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Affiliation(s)
- Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Michelle Møhlenberg
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Cancer Biology, Department of Oncology, VIB-KU Leuven, Leuven, Belgium
| | - Jigarji C. Thakor
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed University), Mullana, Ambala, Haryana, India
| | - Pengfei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, China
| | - Yehuda G. Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Faculty of Biology, Technion Israel Institute of Technology, Haifa, Israel
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
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Serum microRNAs targeting ACE2 and RAB14 genes distinguish asymptomatic from critical COVID-19 patients. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:76-87. [PMID: 35721225 PMCID: PMC9188110 DOI: 10.1016/j.omtn.2022.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/05/2022] [Indexed: 01/08/2023]
Abstract
Despite the extraordinary advances achieved to beat COVID-19 disease, many questions remain unsolved, including the mechanisms of action of SARS-CoV-2 and which factors determine why individuals respond so differently to the viral infection. Herein, we performed an in silico analysis to identify host microRNA targeting ACE2, TMPRSS2, and/or RAB14, all genes known to participate in viral entry and replication. Next, the levels of six microRNA candidates previously linked to viral and respiratory-related pathologies were measured in the serum of COVID-19-negative controls (n = 16), IgG-positive COVID-19 asymptomatic individuals (n = 16), and critical COVID-19 patients (n = 17). Four of the peripheral microRNAs analyzed (hsa-miR-32-5p, hsa-miR-98-3p, hsa-miR-423-3p, and hsa-miR-1246) were upregulated in COVID-19 critical patients compared with COVID-19-negative controls. Moreover, hsa-miR-32-5p and hsa-miR-1246 levels were also altered in critical versus asymptomatic individuals. Furthermore, these microRNA target genes were related to viral infection, inflammatory response, and coagulation-related processes. In conclusion, SARS-CoV-2 promotes the alteration of microRNAs targeting the expression of key proteins for viral entry and replication, and these changes are associated with disease severity. The microRNAs identified could be taken as potential biomarkers of COVID-19 progression as well as candidates for future therapeutic approaches against this disease.
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Roingeard P, Eymieux S, Burlaud-Gaillard J, Hourioux C, Patient R, Blanchard E. The double-membrane vesicle (DMV): a virus-induced organelle dedicated to the replication of SARS-CoV-2 and other positive-sense single-stranded RNA viruses. Cell Mol Life Sci 2022; 79:425. [PMID: 35841484 PMCID: PMC9287701 DOI: 10.1007/s00018-022-04469-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/16/2022] [Accepted: 06/30/2022] [Indexed: 12/18/2022]
Abstract
Positive single-strand RNA (+ RNA) viruses can remodel host cell membranes to induce a replication organelle (RO) isolating the replication of their genome from innate immunity mechanisms. Some of these viruses, including severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), induce double-membrane vesicles (DMVs) for this purpose. Viral non-structural proteins are essential for DMV biogenesis, but they cannot form without an original membrane from a host cell organelle and a significant supply of lipids. The endoplasmic reticulum (ER) and the initial mechanisms of autophagic processes have been shown to be essential for the biogenesis of SARS-CoV-2 DMVs. However, by analogy with other DMV-inducing viruses, it seems likely that the Golgi apparatus, mitochondria and lipid droplets are also involved. As for hepatitis C virus (HCV), pores crossing both membranes of SARS-CoV-2-induced DMVs have been identified. These pores presumably allow the supply of metabolites essential for viral replication within the DMV, together with the export of the newly synthesized viral RNA to form the genome of future virions. It remains unknown whether, as for HCV, DMVs with open pores can coexist with the fully sealed DMVs required for the storage of large amounts of viral RNA. Interestingly, recent studies have revealed many similarities in the mechanisms of DMV biogenesis and morphology between these two phylogenetically distant viruses. An understanding of the mechanisms of DMV formation and their role in the infectious cycle of SARS-CoV-2 may be essential for the development of new antiviral approaches against this pathogen or other coronaviruses that may emerge in the future.
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Affiliation(s)
- Philippe Roingeard
- INSERM U1259, Faculté de Médecine, Université François Rabelais de Tours and CHRU de Tours, 10 boulevard Tonnellé, 37032, Tours Cedex, France. .,Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France.
| | - Sébastien Eymieux
- INSERM U1259, Faculté de Médecine, Université François Rabelais de Tours and CHRU de Tours, 10 boulevard Tonnellé, 37032, Tours Cedex, France.,Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Julien Burlaud-Gaillard
- INSERM U1259, Faculté de Médecine, Université François Rabelais de Tours and CHRU de Tours, 10 boulevard Tonnellé, 37032, Tours Cedex, France.,Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Christophe Hourioux
- INSERM U1259, Faculté de Médecine, Université François Rabelais de Tours and CHRU de Tours, 10 boulevard Tonnellé, 37032, Tours Cedex, France.,Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Romuald Patient
- INSERM U1259, Faculté de Médecine, Université François Rabelais de Tours and CHRU de Tours, 10 boulevard Tonnellé, 37032, Tours Cedex, France.,Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Emmanuelle Blanchard
- INSERM U1259, Faculté de Médecine, Université François Rabelais de Tours and CHRU de Tours, 10 boulevard Tonnellé, 37032, Tours Cedex, France.,Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
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Eskandarzade N, Ghorbani A, Samarfard S, Diaz J, Guzzi PH, Fariborzi N, Tahmasebi A, Izadpanah K. Network for network concept offers new insights into host- SARS-CoV-2 protein interactions and potential novel targets for developing antiviral drugs. Comput Biol Med 2022; 146:105575. [PMID: 35533462 PMCID: PMC9055686 DOI: 10.1016/j.compbiomed.2022.105575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2, the causal agent of COVID-19, is primarily a pulmonary virus that can directly or indirectly infect several organs. Despite many studies carried out during the current COVID-19 pandemic, some pathological features of SARS-CoV-2 have remained unclear. It has been recently attempted to address the current knowledge gaps on the viral pathogenicity and pathological mechanisms via cellular-level tropism of SARS-CoV-2 using human proteomics, visualization of virus-host protein-protein interactions (PPIs), and enrichment analysis of experimental results. The synergistic use of models and methods that rely on graph theory has enabled the visualization and analysis of the molecular context of virus/host PPIs. We review current knowledge on the SARS-COV-2/host interactome cascade involved in the viral pathogenicity through the graph theory concept and highlight the hub proteins in the intra-viral network that create a subnet with a small number of host central proteins, leading to cell disintegration and infectivity. Then we discuss the putative principle of the "gene-for-gene and "network for network" concepts as platforms for future directions toward designing efficient anti-viral therapies.
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Affiliation(s)
- Neda Eskandarzade
- Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran,Corresponding author
| | - Samira Samarfard
- Berrimah Veterinary Laboratory, Department of Primary Industry and Resources, Berrimah, NT, 0828, Australia
| | - Jose Diaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Pietro H. Guzzi
- Department of Medical and Surgical Sciences, Laboratory of Bioinformatics Unit, Italy
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Tahmasebi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
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Production of a functionally active recombinant SARS-CoV-2 (COVID-19) 3C-Like protease and a soluble inactive 3C-like protease-RBD chimeric in a prokaryotic expression system. Epidemiol Infect 2022; 150:e128. [PMID: 35723031 PMCID: PMC9300977 DOI: 10.1017/s0950268822001078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) intracellular life-cycle, two large polyproteins, pp1a and pp1ab, are produced. Processing of these by viral cysteine proteases, the papain-like protease (PLpro) and the chymotrypsin-like 3C-like protease (3CL-pro) release non-structural proteins necessary for the establishment of the viral replication and transcription complex (RTC), crucial for viral replication. Hence, these proteases are considered prime targets against which anti-coronavirus disease 2019 (COVID-19) drugs could be developed. Here, we describe the expression of a highly soluble and functionally active recombinant 3CL-pro using Escherichia coli BL21 cells. We show that the enzyme functions in a dimeric form and exhibits an unexpected inhibitory profile because its activity is potently blocked by serine rather than cysteine protease inhibitors. In addition, we assessed the ability of our 3CL-pro to function as a carrier for the receptor binding domain (RBD) of the Spike protein. The co-expressed chimeric protein, 3CLpro-RBD, did not exhibit 3CL-pro activity, but its enhanced solubility made purification easier and improved RBD antigenicity when tested against serum from vaccinated individuals in ELISAs. Chimeric proteins containing the 3CL-pro could represent an innovative approach to developing new COVID-19 vaccines.
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45
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Zou L, Moch C, Graille M, Chapat C. The SARS-CoV-2 protein NSP2 impairs the silencing capacity of the human 4EHP-GIGYF2 complex. iScience 2022; 25:104646. [PMID: 35756894 PMCID: PMC9213009 DOI: 10.1016/j.isci.2022.104646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/12/2022] [Accepted: 06/15/2022] [Indexed: 01/20/2023] Open
Abstract
There is an urgent need for a molecular understanding of how SARS-CoV-2 influences the machineries of the host cell. Herein, we focused our attention on the capacity of the SARS-CoV-2 protein NSP2 to bind the human 4EHP-GIGYF2 complex, a key factor involved in microRNA-mediated silencing of gene expression. Using in vitro interaction assays, our data demonstrate that NSP2 physically associates with both 4EHP and a central segment in GIGYF2 in the cytoplasm. We also provide functional evidence showing that NSP2 impairs the function of GIGYF2 in mediating translation repression using reporter-based assays. Collectively, these data reveal the potential impact of NSP2 on the post-transcriptional silencing of gene expression in human cells, pointing out 4EHP-GIGYF2 targeting as a possible strategy of SARS-CoV-2 to take over the silencing machinery and to suppress host defenses.
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Affiliation(s)
- Limei Zou
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| | - Clara Moch
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| | - Clément Chapat
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
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46
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Los B, Preußner M, Eschke K, Vidal RM, Abdelgawad A, Olofsson D, Keiper S, Paulo-Pedro M, Grindel A, Meinke S, Trimpert J, Heyd F. Body temperature variation controls pre-mRNA processing and transcription of antiviral genes and SARS-CoV-2 replication. Nucleic Acids Res 2022; 50:6769-6785. [PMID: 35713540 PMCID: PMC9262603 DOI: 10.1093/nar/gkac513] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/07/2022] [Accepted: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
Antiviral innate immunity represents the first defense against invading viruses and is key to control viral infections, including SARS-CoV-2. Body temperature is an omnipresent variable but was neglected when addressing host defense mechanisms and susceptibility to SARS-CoV-2 infection. Here, we show that increasing temperature in a 1.5°C window, between 36.5 and 38°C, strongly increases the expression of genes in two branches of antiviral immunity, nitric oxide production and type I interferon response. We show that alternative splicing coupled to nonsense-mediated decay decreases STAT2 expression in colder conditions and suggest that increased STAT2 expression at elevated temperature induces the expression of diverse antiviral genes and SARS-CoV-2 restriction factors. This cascade is activated in a remarkably narrow temperature range below febrile temperature, which reflects individual, circadian and age-dependent variation. We suggest that decreased body temperature with aging contributes to reduced expression of antiviral genes in older individuals. Using cell culture and in vivo models, we show that higher body temperature correlates with reduced SARS-CoV-2 replication, which may affect the different vulnerability of children versus seniors toward severe SARS-CoV-2 infection. Altogether, our data connect body temperature and pre-mRNA processing to provide new mechanistic insight into the regulation of antiviral innate immunity.
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Affiliation(s)
- Bruna Los
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Marco Preußner
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Kathrin Eschke
- Omiqa Bioinformatics, Altensteinstraße 40, 14195 Berlin, Germany
| | | | - Azza Abdelgawad
- Omiqa Bioinformatics, Altensteinstraße 40, 14195 Berlin, Germany
| | - Didrik Olofsson
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163 Berlin, Germany
| | - Sandra Keiper
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Margarida Paulo-Pedro
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Alica Grindel
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Stefan Meinke
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Jakob Trimpert
- Omiqa Bioinformatics, Altensteinstraße 40, 14195 Berlin, Germany
| | - Florian Heyd
- To whom correspondence should be addressed. Tel: +49 30 83862938; Fax: +49 30 838 4 62938;
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Shah T, Shah Z, Yasmeen N, Baloch Z, Xia X. Pathogenesis of SARS-CoV-2 and Mycobacterium tuberculosis Coinfection. Front Immunol 2022; 13:909011. [PMID: 35784278 PMCID: PMC9246416 DOI: 10.3389/fimmu.2022.909011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/23/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease-2019 (COVID-19), caused by SARS-CoV-2, is an infectious disease that poses severe threats to global public health and significant economic losses. The COVID-19 global burden is rapidly increasing, with over 246.53 million COVID-19 cases and 49.97 million deaths reported in the WHO 2021 report. People with compromised immunity, such as tuberculosis (TB) patients, are highly exposed to severe COVID-19. Both COVID-19 and TB diseases spread primarily through respiratory droplets from an infected person to a healthy person, which may cause pneumonia and cytokine storms, leading to severe respiratory disorders. The COVID-19-TB coinfection could be fatal, exacerbating the current COVID-19 pandemic apart from cellular immune deficiency, coagulation activation, myocardial infarction, and other organ dysfunction. This study aimed to assess the pathogenesis of SARS-CoV-2-Mycobacterium tuberculosis coinfections. We provide a brief overview of COVID19-TB coinfection and discuss SARS-CoV-2 host cellular receptors and pathogenesis. In addition, we discuss M. tuberculosis host cellular receptors and pathogenesis. Moreover, we highlight the impact of SARS-CoV-2 on TB patients and the pathological pathways that connect SARS-CoV-2 and M. tuberculosis infection. Further, we discuss the impact of BCG vaccination on SARS-CoV-2 cases coinfected with M. tuberculosis, as well as the diagnostic challenges associated with the coinfection.
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Affiliation(s)
- Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Zahir Shah
- College of Veterinary Sciences, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Nafeesa Yasmeen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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48
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Kung YA, Lee KM, Chiang HJ, Huang SY, Wu CJ, Shih SR. Molecular Virology of SARS-CoV-2 and Related Coronaviruses. Microbiol Mol Biol Rev 2022; 86:e0002621. [PMID: 35343760 PMCID: PMC9199417 DOI: 10.1128/mmbr.00026-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global COVID-19 pandemic continues to threaten the lives of hundreds of millions of people, with a severe negative impact on the global economy. Although several COVID-19 vaccines are currently being administered, none of them is 100% effective. Moreover, SARS-CoV-2 variants remain an important worldwide public health issue. Hence, the accelerated development of efficacious antiviral agents is urgently needed. Coronavirus depends on various host cell factors for replication. An ongoing research objective is the identification of host factors that could be exploited as targets for drugs and compounds effective against SARS-CoV-2. In the present review, we discuss the molecular mechanisms of SARS-CoV-2 and related coronaviruses, focusing on the host factors or pathways involved in SARS-CoV-2 replication that have been identified by genome-wide CRISPR screening.
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Affiliation(s)
- Yu-An Kung
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Huan-Jung Chiang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sheng-Yu Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Jung Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
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Režen T, Martins A, Mraz M, Zimic N, Rozman D, Moškon M. Integration of omics data to generate and analyse COVID-19 specific genome-scale metabolic models. Comput Biol Med 2022; 145:105428. [PMID: 35339845 PMCID: PMC8940269 DOI: 10.1016/j.compbiomed.2022.105428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 12/16/2022]
Abstract
COVID-19 presents a complex disease that needs to be addressed using systems medicine approaches that include genome-scale metabolic models (GEMs). Previous studies have used a single model extraction method (MEM) and/or a single transcriptomic dataset to reconstruct context-specific models, which proved to be insufficient for the broader biological contexts. We have applied four MEMs in combination with five COVID-19 datasets. Models produced by GIMME were separated by infection, while tINIT preserved the biological variability in the data and enabled the best prediction of the enrichment of metabolic subsystems. Vitamin D3 metabolism was predicted to be down-regulated in one dataset by GIMME, and in all by tINIT. Models generated by tINIT and GIMME predicted downregulation of retinol metabolism in different datasets, while downregulated cholesterol metabolism was predicted only by tINIT-generated models. Predictions are in line with the observations in COVID-19 patients. Our data indicated that GIMME and tINIT models provided the most biologically relevant results and should have a larger emphasis in further analyses. Particularly tINIT models identified the metabolic pathways that are a part of the host response and are potential antiviral targets. The code and the results of the analyses are available to download from https://github.com/CompBioLj/COVID_GEMs_and_MEMs.
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Affiliation(s)
- Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Miha Mraz
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Nikolaj Zimic
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Moškon
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
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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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