151
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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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152
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Banerjee S, Baidya SK, Adhikari N, Ghosh B, Jha T. Glycyrrhizin as a promising kryptonite against SARS-CoV-2: Clinical, experimental, and theoretical evidences. J Mol Struct 2022; 1275:134642. [DOI: 10.1016/j.molstruc.2022.134642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/24/2022] [Accepted: 11/24/2022] [Indexed: 11/27/2022]
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153
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Yazdani M, Zamani J, Fatemi SSA. Identification of a potent dual-function inhibitor for hIMPDH isoforms by computer-aided drug discovery approaches. Front Pharmacol 2022; 13:977568. [PMID: 36386211 PMCID: PMC9643795 DOI: 10.3389/fphar.2022.977568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2023] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is a key enzyme in de novo biosynthesis of purine nucleotides. Due to this important role, it is a great target to drug discovery for a wide range of activities, especially immunosuppressant in heart and kidney transplantation. Both human IMPDH isoforms are expressed in stimulated lymphocytes. In addition to the side effects of existing drugs, previous studies have mainly focused on the type II isoform. In this study, virtual screening and computer-aided approaches were employed to identify potential drugs with simultaneous inhibitory effects on both human IMPDH isoforms. After Re-docking, Double-step docking, and identification of virtual hits based on the PLANTS scoring function, drug-likeness and ADME-Tox assessments of the topmost ligands were performed. Following further evaluation, the best ligand was selected and, in complex with both isoforms, simulated in monomeric and tetrameric forms using molecular dynamics to evaluate its stability and binding pattern. The results showed a potential drug candidate [(S)-N-(3-hydroxy-1-(4-hydroxyphenyl) propyl)-2-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl) acetamide] with a high inhibitory effect on the two human IMPDH isoforms. This drug-like inhibitor could potentially serve as an immunosuppressant to prevent transplant rejection response by inhibiting B- and T-lymphocyte proliferation. In addition, its effect can be evaluated in various therapeutic targets in which IMPDH is known as a therapeutic target, especially in Covid-19 patients.
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Affiliation(s)
- Meysam Yazdani
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Javad Zamani
- Department of Plant Molecular Biotechnology, Institute of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Seyed Safa-Ali Fatemi
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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154
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A Review of Potential Therapeutic Strategies for COVID-19. Viruses 2022; 14:v14112346. [PMID: 36366444 PMCID: PMC9696587 DOI: 10.3390/v14112346] [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: 09/18/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 02/01/2023] Open
Abstract
Coronavirus disease 2019 is a rather heterogeneous disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The ongoing pandemic is a global threat with increasing death tolls worldwide. SARS-CoV-2 belongs to lineage B β-CoV, a subgroup of Sarbecovirus. These enveloped, large, positive-sense single-stranded RNA viruses are easily spread among individuals, mainly via the respiratory system and droplets. Although the disease has been gradually controlled in many countries, once social restrictions are relaxed the virus may rebound, leading to a more severe and uncontrollable situation again, as occurred in Shanghai, China, in 2022. The current global health threat calls for the urgent development of effective therapeutic options for the treatment and prevention of SARS-CoV-2 infection. This systematic overview of possible SARS-CoV-2 therapeutic strategies from 2019 to 2022 indicates three potential targets: virus entry, virus replication, and the immune system. The information provided in this review will aid the development of more potent and specific antiviral compounds.
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155
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Pires De Souza GA, Le Bideau M, Boschi C, Wurtz N, Colson P, Aherfi S, Devaux C, La Scola B. Choosing a cellular model to study SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:1003608. [PMID: 36339347 PMCID: PMC9634005 DOI: 10.3389/fcimb.2022.1003608] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/03/2022] [Indexed: 08/04/2023] Open
Abstract
As new pathogens emerge, new challenges must be faced. This is no different in infectious disease research, where identifying the best tools available in laboratories to conduct an investigation can, at least initially, be particularly complicated. However, in the context of an emerging virus, such as SARS-CoV-2, which was recently detected in China and has become a global threat to healthcare systems, developing models of infection and pathogenesis is urgently required. Cell-based approaches are crucial to understanding coronavirus infection biology, growth kinetics, and tropism. Usually, laboratory cell lines are the first line in experimental models to study viral pathogenicity and perform assays aimed at screening antiviral compounds which are efficient at blocking the replication of emerging viruses, saving time and resources, reducing the use of experimental animals. However, determining the ideal cell type can be challenging, especially when several researchers have to adapt their studies to specific requirements. This review strives to guide scientists who are venturing into studying SARS-CoV-2 and help them choose the right cellular models. It revisits basic concepts of virology and presents the currently available in vitro models, their advantages and disadvantages, and the known consequences of each choice.
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Affiliation(s)
- Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Marion Le Bideau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Céline Boschi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Christian Devaux
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Department of Biological Sciences (INSB), Centre National de la Recherche Scientifique, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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156
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Xing J, Shankar R, Ko M, Zhang K, Zhang S, Drelich A, Paithankar S, Chekalin E, Chua MS, Rajasekaran S, Kent Tseng CT, Zheng M, Kim S, Chen B. Deciphering COVID-19 host transcriptomic complexity and variations for therapeutic discovery against new variants. iScience 2022; 25:105068. [PMID: 36093376 PMCID: PMC9439871 DOI: 10.1016/j.isci.2022.105068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/11/2022] [Accepted: 08/30/2022] [Indexed: 12/04/2022] Open
Abstract
The molecular manifestations of host cells responding to SARS-CoV-2 and its evolving variants of infection are vastly different across the studied models and conditions, imposing challenges for host-based antiviral drug discovery. Based on the postulation that antiviral drugs tend to reverse the global host gene expression induced by viral infection, we retrospectively evaluated hundreds of signatures derived from 1,700 published host transcriptomic profiles of SARS/MERS/SARS-CoV-2 infection using an iterative data-driven approach. A few of these signatures could be reversed by known anti-SARS-CoV-2 inhibitors, suggesting the potential of extrapolating the biology for new variant research. We discovered IMD-0354 as a promising candidate to reverse the signatures globally with nanomolar IC50 against SARS-CoV-2 and its five variants. IMD-0354 stimulated type I interferon antiviral response, inhibited viral entry, and down-regulated hijacked proteins. This study demonstrates that the conserved coronavirus signatures and the transcriptomic reversal approach that leverages polypharmacological effects could guide new variant therapeutic discovery.
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Affiliation(s)
- Jing Xing
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Rama Shankar
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Meehyun Ko
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, 13488, Korea
| | - Keke Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Aleksandra Drelich
- Departments of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shreya Paithankar
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Eugene Chekalin
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Mei-Sze Chua
- Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
- Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
| | - Chien-Te Kent Tseng
- Departments of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Center of Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, 13488, Korea
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
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157
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Wang X, Rimal S, Tantray I, Geng J, Bhurtel S, Khaket TP, Li W, Han Z, Lu B. Prevention of ribosome collision-induced neuromuscular degeneration by SARS CoV-2-encoded Nsp1. Proc Natl Acad Sci U S A 2022; 119:e2202322119. [PMID: 36170200 PMCID: PMC9586304 DOI: 10.1073/pnas.2202322119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022] Open
Abstract
An overarching goal of aging and age-related neurodegenerative disease research is to discover effective therapeutic strategies applicable to a broad spectrum of neurodegenerative diseases. Little is known about the extent to which targetable pathogenic mechanisms are shared among these seemingly diverse diseases. Translational control is critical for maintaining proteostasis during aging. Gaining control of the translation machinery is also crucial in the battle between viruses and their hosts. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing COVID-19 pandemic. Here, we show that overexpression of SARS-CoV-2-encoded nonstructural protein 1 (Nsp1) robustly rescued neuromuscular degeneration and behavioral phenotypes in Drosophila models of Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. These diseases share a common mechanism: the accumulation of aberrant protein species due to the stalling and collision of translating ribosomes, leading to proteostasis failure. Our genetic and biochemical analyses revealed that Nsp1 acted in a multipronged manner to resolve collided ribosomes, abort stalled translation, and remove faulty translation products causative of disease in these models, at least in part through the ribosome recycling factor ABCE1, ribosome-associated quality-control factors, autophagy, and AKT signaling. Nsp1 exhibited exquisite specificity in its action, as it did not modify other neurodegenerative conditions not known to be associated with ribosome stalling. These findings uncover a previously unrecognized mechanism of Nsp1 in manipulating host translation, which can be leveraged for combating age-related neurodegenerative diseases that are affecting millions of people worldwide and currently without effective treatment.
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Affiliation(s)
- Xingjun Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94350
| | - Suman Rimal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94350
| | - Ishaq Tantray
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94350
| | - Ji Geng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94350
| | - Sunil Bhurtel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94350
| | - Tejinder Pal Khaket
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94350
| | - Wen Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94350
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Bingwei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94350
- Programs of Neuroscience and Cancer Biology, Stanford University School of Medicine, Stanford, CA 94350
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158
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Wang J, Liu J, Luo M, Cui H, Zhang W, Zhao K, Dai H, Song F, Chen K, Yu Y, Zhou D, Li MJ, Yang H. Rational drug repositioning for coronavirus-associated diseases using directional mapping and side-effect inference. iScience 2022; 25:105348. [PMID: 36267550 PMCID: PMC9556799 DOI: 10.1016/j.isci.2022.105348] [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: 06/03/2022] [Revised: 09/02/2022] [Accepted: 10/11/2022] [Indexed: 02/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen of coronavirus disease 2019 (COVID-19), has infected hundreds of millions of people and caused millions of deaths. Looking for valid druggable targets with minimal side effects for the treatment of COVID-19 remains critical. After discovering host genes from multiscale omics data, we developed an end-to-end network method to investigate drug-host gene(s)-coronavirus (CoV) paths and the mechanism of action between the drug and the host factor in a directional network. We also inspected the potential side effect of the candidate drug on several common comorbidities. We established a catalog of host genes associated with three CoVs. Rule-based prioritization yielded 29 Food and Drug Administration (FDA)-approved drugs via accounting for the effects of drugs on CoVs, comorbidities, and drug-target confidence information. Seven drugs are currently undergoing clinical trials as COVID-19 treatment. This catalog of druggable host genes associated with CoVs and the prioritized repurposed drugs will provide a new sight in therapeutics discovery for severe COVID-19 patients.
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Affiliation(s)
- Jianhua Wang
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China,Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiaojiao Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Menghan Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hui Cui
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wenwen Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ke Zhao
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hongji Dai
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Fangfang Song
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ying Yu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dongming Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Corresponding author
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China,Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Corresponding author
| | - Hongxi Yang
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China,Corresponding author
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159
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Rashid MU, Glover KKM, Lao Y, Spicer V, Coombs KM. Temporal proteomic analyses of human lung cells distinguish high pathogenicity influenza viruses and coronaviruses from low pathogenicity viruses. Front Microbiol 2022; 13:994512. [PMID: 36299731 PMCID: PMC9589293 DOI: 10.3389/fmicb.2022.994512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022] Open
Abstract
Newly re-emerging viruses are of significant global concern. In late 2019, a new coronavirus, SARS-CoV-2, emerged in China and soon spread worldwide, causing the COVID-19 pandemic, which to date has caused >6 M deaths. There has been a wealth of studies on this new virus since its emergence. The coronaviruses consist of many animal and human pathogens, with some of the human coronavirus, such as strain OC43, normally causing only mild cold-like symptoms. Viruses usurp host cellular processes to successfully replicate. We used tandem mass tag mass spectrometry-based proteomic analyses of human lung MRC-5 cells infected with OC43 for various periods of time to delineate virus-induced host cell alterations. Numerous proteins involved in lipid metabolism, molecular transport, small molecule biochemistry, cell death and survival, humoral immune response, and inflammatory response were dysregulated. Comparison of our findings to previous studies that examined a range of differentially pathogenic influenza A viruses (IAV), and to SARS-CoV-2 data, revealed that proteins involved in the cell cycle, cytokine signaling, DNA replication, and anti-inflammatory responses were generally similarly affected by virtually all tested IAV and CoV. However, proteins involved in necrosis, protein metabolism, ECM regulation, and signal transduction were generally different. In addition, the more pathogenic CoV and IAV activated Rb-dependent repression of E2F-mediated transcription, whereas less pathogenic influenza and coronaviruses either inhibited or had no effect on this pathway.
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Affiliation(s)
- Mahamud-ur Rashid
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Kathleen K. M. Glover
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Ying Lao
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Victor Spicer
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Center for Proteomics and Systems Biology, Winnipeg, MB, Canada
- Children’s Hospital Research Institute of Manitoba, John Buhler Research Center, Winnipeg, MB, Canada
- *Correspondence: Kevin M. Coombs,
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160
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Wang H, Shi D, Jiang P, Yu Z, Han Y, Zhang Z, Wang P, Huang H, Yao H, Qian P. SARS-CoV-2 N protein potentiates host NPM1-snoRNA translation machinery to enhance viral replication. Signal Transduct Target Ther 2022; 7:356. [PMID: 36209261 PMCID: PMC9547094 DOI: 10.1038/s41392-022-01210-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/13/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Hui Wang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Danrong Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Penglei Jiang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Zebin Yu
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Yingli Han
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhaoru Zhang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Peihui Wang
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - He Huang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, China. .,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China. .,School of Medicine, Zhejiang University, Hangzhou, China.
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Yin Y, Liu XZ, Tian Q, Fan YX, Ye Z, Meng TQ, Wei GH, Xiong CL, Li HG, He X, Zhou LQ. Transcriptome and DNA methylome analysis of peripheral blood samples reveals incomplete restoration and transposable element activation after 3-months recovery of COVID-19. Front Cell Dev Biol 2022; 10:1001558. [PMID: 36263014 PMCID: PMC9574079 DOI: 10.3389/fcell.2022.1001558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/15/2022] [Indexed: 01/08/2023] Open
Abstract
Comprehensive analyses showed that SARS-CoV-2 infection caused COVID-19 and induced strong immune responses and sometimes severe illnesses. However, cellular features of recovered patients and long-term health consequences remain largely unexplored. In this study, we collected peripheral blood samples from nine recovered COVID-19 patients (median age of 36 years old) from Hubei province, China, 3 months after discharge as well as 5 age- and gender-matched healthy controls; and carried out RNA-seq and whole-genome bisulfite sequencing to identify hallmarks of recovered COVID-19 patients. Our analyses showed significant changes both in transcript abundance and DNA methylation of genes and transposable elements (TEs) in recovered COVID-19 patients. We identified 425 upregulated genes, 214 downregulated genes, and 18,516 differentially methylated regions (DMRs) in total. Aberrantly expressed genes and DMRs were found to be associated with immune responses and other related biological processes, implicating prolonged overreaction of the immune system in response to SARS-CoV-2 infection. Notably, a significant amount of TEs was aberrantly activated and their activation was positively correlated with COVID-19 severity. Moreover, differentially methylated TEs may regulate adjacent gene expression as regulatory elements. Those identified transcriptomic and epigenomic signatures define and drive the features of recovered COVID-19 patients, helping determine the risks of long COVID-19, and guiding clinical intervention.
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Affiliation(s)
- Ying Yin
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-zhao Liu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Tian
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi-xian Fan
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
| | - Zhen Ye
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tian-qing Meng
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Gong-hong Wei
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
| | - Cheng-liang Xiong
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hong-gang Li
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- *Correspondence: Hong-gang Li, ; Ximiao He, ; Li-quan Zhou,
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Hong-gang Li, ; Ximiao He, ; Li-quan Zhou,
| | - Li-quan Zhou
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- *Correspondence: Hong-gang Li, ; Ximiao He, ; Li-quan Zhou,
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162
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Kee J, Thudium S, Renner DM, Glastad K, Palozola K, Zhang Z, Li Y, Lan Y, Cesare J, Poleshko A, Kiseleva AA, Truitt R, Cardenas-Diaz FL, Zhang X, Xie X, Kotton DN, Alysandratos KD, Epstein JA, Shi PY, Yang W, Morrisey E, Garcia BA, Berger SL, Weiss SR, Korb E. SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry. Nature 2022; 610:381-388. [PMID: 36198800 PMCID: PMC9533993 DOI: 10.1038/s41586-022-05282-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 08/26/2022] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and caused the devastating global pandemic of coronavirus disease 2019 (COVID-19), in part because of its ability to effectively suppress host cell responses1-3. In rare cases, viral proteins dampen antiviral responses by mimicking critical regions of human histone proteins4-8, particularly those containing post-translational modifications required for transcriptional regulation9-11. Recent work has demonstrated that SARS-CoV-2 markedly disrupts host cell epigenetic regulation12-14. However, how SARS-CoV-2 controls the host cell epigenome and whether it uses histone mimicry to do so remain unclear. Here we show that the SARS-CoV-2 protein encoded by ORF8 (ORF8) functions as a histone mimic of the ARKS motifs in histone H3 to disrupt host cell epigenetic regulation. ORF8 is associated with chromatin, disrupts regulation of critical histone post-translational modifications and promotes chromatin compaction. Deletion of either the ORF8 gene or the histone mimic site attenuates the ability of SARS-CoV-2 to disrupt host cell chromatin, affects the transcriptional response to infection and attenuates viral genome copy number. These findings demonstrate a new function of ORF8 and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Further, this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19.
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Affiliation(s)
- John Kee
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel Thudium
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - David M Renner
- Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Karl Glastad
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine Palozola
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Zhen Zhang
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Yize Li
- Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Cesare
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Anna A Kiseleva
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel Truitt
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Fabian L Cardenas-Diaz
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Wenli Yang
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Edward Morrisey
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Susan R Weiss
- Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Erica Korb
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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163
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Zheng W, Zeng Z, Lin S, Hou P. Revisiting potential value of antitumor drugs in the treatment of COVID-19. Cell Biosci 2022; 12:165. [PMID: 36182930 PMCID: PMC9526459 DOI: 10.1186/s13578-022-00899-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 09/12/2022] [Indexed: 01/08/2023] Open
Abstract
Since an outbreak started in China in 2019, coronavirus disease 2019 (COVID-19) has rapidly become a worldwide epidemic with high contagiousness and caused mass mortalities of infected cases around the world. Currently, available treatments for COVID-19, including supportive care, respiratory support and antiviral therapy, have shown limited efficacy. Thus, more effective therapeutic modalities are highly warranted. Drug repurposing, as an efficient strategy to explore a potential broader scope of the application of approved drugs beyond their original indications, accelerates the process of discovering safe and effective agents for a given disease. Since the outbreak of COVID-19 pandemic, drug repurposing strategy has been widely used to discover potential antiviral agents, and some of these drugs have advanced into clinical trials. Antitumor drugs compromise a vast variety of compounds and exhibit extensive mechanism of action, showing promising properties in drug repurposing. In this review, we revisit the potential value of antitumor drugs in the treatment of COVID-19 and systematically discuss their possible underlying mechanisms of the antiviral actions.
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Affiliation(s)
- Wenfang Zheng
- grid.452438.c0000 0004 1760 8119Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 People’s Republic of China
| | - Zekun Zeng
- grid.452438.c0000 0004 1760 8119Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 People’s Republic of China
| | - Shumei Lin
- grid.452438.c0000 0004 1760 8119Department of Infectious Diseases, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 People’s Republic of China
| | - Peng Hou
- grid.452438.c0000 0004 1760 8119Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 People’s Republic of China ,grid.452438.c0000 0004 1760 8119Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 People’s Republic of China
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164
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Zhu JY, Wang G, Huang X, Lee H, Lee JG, Yang P, van de Leemput J, Huang W, Kane MA, Yang P, Han Z. SARS-CoV-2 Nsp6 damages Drosophila heart and mouse cardiomyocytes through MGA/MAX complex-mediated increased glycolysis. Commun Biol 2022; 5:1039. [PMID: 36180527 PMCID: PMC9523645 DOI: 10.1038/s42003-022-03986-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/13/2022] [Indexed: 12/01/2022] Open
Abstract
SARS-CoV-2 infection causes COVID-19, a severe acute respiratory disease associated with cardiovascular complications including long-term outcomes. The presence of virus in cardiac tissue of patients with COVID-19 suggests this is a direct, rather than secondary, effect of infection. Here, by expressing individual SARS-CoV-2 proteins in the Drosophila heart, we demonstrate interaction of virus Nsp6 with host proteins of the MGA/MAX complex (MGA, PCGF6 and TFDP1). Complementing transcriptomic data from the fly heart reveal that this interaction blocks the antagonistic MGA/MAX complex, which shifts the balance towards MYC/MAX and activates glycolysis-with similar findings in mouse cardiomyocytes. Further, the Nsp6-induced glycolysis disrupts cardiac mitochondrial function, known to increase reactive oxygen species (ROS) in heart failure; this could explain COVID-19-associated cardiac pathology. Inhibiting the glycolysis pathway by 2-deoxy-D-glucose (2DG) treatment attenuates the Nsp6-induced cardiac phenotype in flies and mice. These findings point to glycolysis as a potential pharmacological target for treating COVID-19-associated heart failure.
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Affiliation(s)
- Jun-Yi Zhu
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Guanglei Wang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Xiaohu Huang
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Hangnoh Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Jin-Gu Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Penghua Yang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
- University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Peixin Yang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
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165
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Sattar S, Kabat J, Jerome K, Feldmann F, Bailey K, Mehedi M. Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509633. [PMID: 36203551 PMCID: PMC9536038 DOI: 10.1101/2022.09.27.509633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe pathophysiology in vulnerable older populations and appears to be highly pathogenic and more transmissible than SARS-CoV or MERS-CoV [1, 2]. The spike (S) protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal (NLS) "PRRARSV", which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. To our surprise, S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA. While nuclear translocation of nucleoprotein (N) has been shown in many coronaviruses, the nuclear translocation of both S mRNA and S protein reveals a novel pathogenic feature of SARS-CoV-2. Author summary One of the novel sequence insertions resides at the S1/S2 boundary of Spike (S) protein and constitutes a functional nuclear localization signal (NLS) motif "PRRARSV", which may supersede the importance of previously proposed polybasic furin cleavage site "RRAR". Indeed, S protein's NLS-driven nuclear translocation and its possible role in S mRNA's nuclear translocation reveal a novel pathogenic feature of SARS-CoV-2.
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Affiliation(s)
- Sarah Sattar
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, USA
| | - Juraj Kabat
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kailey Jerome
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, USA
| | - Friederike Feldmann
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kristina Bailey
- Department of Internal Medicine, Pulmonary, Critical Care, and Sleep and Allergy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Masfique Mehedi
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, USA
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166
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Identification of the effects of COVID-19 on patients with pulmonary fibrosis and lung cancer: a bioinformatics analysis and literature review. Sci Rep 2022; 12:16040. [PMID: 36163484 PMCID: PMC9512912 DOI: 10.1038/s41598-022-20040-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/07/2022] [Indexed: 11/19/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) poses a serious threat to human health and life. The effective prevention and treatment of COVID-19 complications have become crucial to saving patients’ lives. During the phase of mass spread of the epidemic, a large number of patients with pulmonary fibrosis and lung cancers were inevitably infected with the SARS-CoV-2 virus. Lung cancers have the highest tumor morbidity and mortality rates worldwide, and pulmonary fibrosis itself is one of the complications of COVID-19. Idiopathic lung fibrosis (IPF) and various lung cancers (primary and metastatic) become risk factors for complications of COVID-19 and significantly increase mortality in patients. Therefore, we applied bioinformatics and systems biology approaches to identify molecular biomarkers and common pathways in COVID-19, IPF, colorectal cancer (CRC) lung metastasis, SCLC and NSCLC. We identified 79 DEGs between COVID-19, IPF, CRC lung metastasis, SCLC and NSCLC. Meanwhile, based on the transcriptome features of DSigDB and common DEGs, we identified 10 drug candidates. In this study, 79 DEGs are the common core genes of the 5 diseases. The 10 drugs were found to have positive effects in treating COVID-19 and lung cancer, potentially reducing the risk of pulmonary fibrosis.
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167
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Iacobucci I, Monaco V, Canè L, Bibbò F, Cioffi V, Cozzolino F, Guarino A, Zollo M, Monti M. Spike S1 domain interactome in non-pulmonary systems: A role beyond the receptor recognition. Front Mol Biosci 2022; 9:975570. [PMID: 36225252 PMCID: PMC9550266 DOI: 10.3389/fmolb.2022.975570] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/29/2022] [Indexed: 12/05/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which, since 2019 in China, has rapidly become a worldwide pandemic. The aggressiveness and global spread were enhanced by the many SARS-CoV-2 variants that have been isolated up to now. These mutations affect mostly the viral glycoprotein Spike (S), the capsid protein mainly involved in the early stages of viral entry processes, through the recognition of specific receptors on the host cell surface. In particular, the subunit S1 of the Spike glycoprotein contains the Receptor Binding Domain (RBD) and it is responsible for the interaction with the angiotensin-converting enzyme 2 (ACE2). Although ACE2 is the primary Spike host receptor currently studied, it has been demonstrated that SARS-CoV-2 is also able to infect cells expressing low levels of ACE2, indicating that the virus may have alternative receptors on the host cells. The identification of the alternative receptors can better elucidate the pathogenicity and the tropism of SARS-CoV-2. Therefore, we investigated the Spike S1 interactomes, starting from host membrane proteins of non-pulmonary cell lines, such as human kidney (HK-2), normal colon (NCM460D), and colorectal adenocarcinoma (Caco-2). We employed an affinity purification-mass spectrometry (AP-MS) to pull down, from the membrane protein extracts of all cell lines, the protein partners of the recombinant form of the Spike S1 domain. The purified interactors were identified by a shotgun proteomics approach. The lists of S1 potential interacting proteins were then clusterized according to cellular localization, biological processes, and pathways, highlighting new possible S1 intracellular functions, crucial not only for the entrance mechanisms but also for viral replication and propagation processes.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Vittoria Monaco
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Luisa Canè
- CEINGE Advanced Biotechnologies, Naples, Italy
- Department of Translational Medical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Francesca Bibbò
- CEINGE Advanced Biotechnologies, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies (DMMBM), University of Naples “Federico II”, Naples, Italy
| | - Valentina Cioffi
- Department of Translational Medical Science, Section of Pediatrics, University of Naples “Federico II”, Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Alfredo Guarino
- Department of Translational Medical Science, Section of Pediatrics, University of Naples “Federico II”, Naples, Italy
| | - Massimo Zollo
- CEINGE Advanced Biotechnologies, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies (DMMBM), University of Naples “Federico II”, Naples, Italy
| | - Maria Monti
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
- *Correspondence: Maria Monti,
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168
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Zhong L, Zhao Z, Peng X, Zou J, Yang S. Recent advances in small-molecular therapeutics for COVID-19. PRECISION CLINICAL MEDICINE 2022; 5:pbac024. [PMID: 36268466 PMCID: PMC9579963 DOI: 10.1093/pcmedi/pbac024] [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: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic poses a fundamental challenge to global health. Since the outbreak of SARS-CoV-2, great efforts have been made to identify antiviral strategies and develop therapeutic drugs to combat the disease. There are different strategies for developing small molecular anti-SARS-CoV-2 drugs, including targeting coronavirus structural proteins (e.g. spike protein), non-structural proteins (nsp) (e.g. RdRp, Mpro, PLpro, helicase, nsp14, and nsp16), host proteases (e.g. TMPRSS2, cathepsin, and furin) and the pivotal proteins mediating endocytosis (e.g. PIKfyve), as well as developing endosome acidification agents and immune response modulators. Favipiravir and chloroquine are the anti-SARS-CoV-2 agents that were identified earlier in this epidemic and repurposed for COVID-19 clinical therapy based on these strategies. However, their efficacies are controversial. Currently, three small molecular anti-SARS-CoV-2 agents, remdesivir, molnupiravir, and Paxlovid (PF-07321332 plus ritonavir), have been granted emergency use authorization or approved for COVID-19 therapy in many countries due to their significant curative effects in phase III trials. Meanwhile, a large number of promising anti-SARS-CoV-2 drug candidates have entered clinical evaluation. The development of these drugs brings hope for us to finally conquer COVID-19. In this account, we conducted a comprehensive review of the recent advances in small molecule anti-SARS-CoV-2 agents according to the target classification. Here we present all the approved drugs and most of the important drug candidates for each target, and discuss the challenges and perspectives for the future research and development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
| | | | - Xuerun Peng
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | | | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
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169
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Spectroscopic methods for COVID-19 detection and early diagnosis. Virol J 2022; 19:152. [PMID: 36138463 PMCID: PMC9502632 DOI: 10.1186/s12985-022-01867-2] [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: 04/16/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
The coronavirus pandemic is a worldwide hazard that poses a threat to millions of individuals throughout the world. This pandemic is caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which was initially identified in Wuhan, China's Hubei provincial capital, and has since spread throughout the world. According to the World Health Organization's Weekly Epidemiological Update, there were more than 250 million documented cases of coronavirus infections globally, with five million fatalities. Early detection of coronavirus does not only reduce the spread of the virus, but it also increases the chance of curing the infection. Spectroscopic techniques have been widely used in the early detection and diagnosis of COVID-19 using Raman, Infrared, mass spectrometry and fluorescence spectroscopy. In this review, the reported spectroscopic methods for COVID-19 detection were discussed with emphasis on the practical aspects, limitations and applications.
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170
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Chen M, Yan C, Qin F, Zhang XE. Near-Infrared Luciferase Complementation Assay with Enhanced Bioluminescence for Studying Protein-Protein Interactions and Drug Evaluation Under Physiological Conditions. Anal Chem 2022; 94:13700-13709. [PMID: 36135776 DOI: 10.1021/acs.analchem.2c01238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of protein-protein interactions (PPIs) that occur in various cellular processes helps to reveal their potential molecular mechanisms, and there is still an urgent need to develop the assays to explore PPIs in living subjects. Here, we reported a near-infrared split luciferase complementation assay (SLCA) with enhanced bioluminescence produced by cleaving a luciferase, Akaluc, for exploring and visualizing PPIs in living cells and live mice. Compared with the previously developed and widely used red SLCA based on split firefly luciferase (Fluc-SLCA), the signal intensities for PPI recognition in living cells and live mice of the Akaluc-SLCA increased by ∼3.79-fold and ∼18.06-fold in the measured condition, respectively. Additionally, the interactions between the nucleocapsid protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and cellular RNA processing proteins were identified, and the drug evaluation assays were also performed in living cells using Akaluc-SLCA. This study provides a new tool in the near-infrared region for the identification of PPIs in living cells and in vivo and new information for the understanding and treatment of SARS-CoV-2.
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Affiliation(s)
- Minghai Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chuang Yan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fujun Qin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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171
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Kotani N, Nakano T, Kuwahara R. Host cell membrane proteins located near SARS-CoV-2 spike protein attachment sites are identified using proximity labeling and proteomic analysis. J Biol Chem 2022; 298:102500. [PMID: 36152751 PMCID: PMC9492400 DOI: 10.1016/j.jbc.2022.102500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 11/19/2022] Open
Abstract
Coronavirus disease represents a real threat to the global population, and understanding the biological features of the causative virus, that is, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is imperative for mitigating this threat. Analyses of proteins such as primary receptors and coreceptors (cofactors), which are involved in the entry of SARS-CoV-2 into host cells, will provide important clues to help control the virus. Here, we identified host cell membrane protein candidates present in proximity to the attachment sites of SARS-CoV-2 spike proteins, using proximity labeling and proteomic analysis. The identified proteins represent key candidate factors that may be required for viral entry. We found SARS-CoV-2 host protein DPP4, cell adhesion protein Cadherin 17, and glycoprotein CD133 colocalized with cell membrane–bound SARS-CoV-2 spike proteins in Caco-2 cells and thus showed potential as candidate factors. Additionally, our analysis of the experimental infection of HEK293T cells with a SARS-CoV-2 pseudovirus indicated a 2-fold enhanced infectivity in the CD133-ACE2-coexpressing HEK293T cells compared to that in HEK293T cells expressing ACE-2 alone. The information and resources regarding these coreceptor labeling and analysis techniques could be utilized for the development of antiviral agents against SARS-CoV-2 and other emerging viruses.
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Affiliation(s)
- Norihiro Kotani
- Medical Research Center, Saitama Medical University, Moroyama-machi, Saitama, Japan; Department of Biochemistry, Saitama Medical University, Moroyama-machi, Saitama, Japan.
| | - Takanari Nakano
- Department of Biochemistry, Saitama Medical University, Moroyama-machi, Saitama, Japan
| | - Ryusuke Kuwahara
- Quantum Wave Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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172
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Transcriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection. Int J Mol Sci 2022; 23:ijms231911058. [PMID: 36232363 PMCID: PMC9570475 DOI: 10.3390/ijms231911058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is a coronavirus family member that appeared in China in December 2019 and caused the disease called COVID-19, which was declared a pandemic in 2020 by the World Health Organization. In recent months, great efforts have been made in the field of basic and clinical research to understand the biology and infection processes of SARS-CoV-2. In particular, transcriptome analysis has contributed to generating new knowledge of the viral sequences and intracellular signaling pathways that regulate the infection and pathogenesis of SARS-CoV-2, generating new information about its biology. Furthermore, transcriptomics approaches including spatial transcriptomics, single-cell transcriptomics and direct RNA sequencing have been used for clinical applications in monitoring, detection, diagnosis, and treatment to generate new clinical predictive models for SARS-CoV-2. Consequently, RNA-based therapeutics and their relationship with SARS-CoV-2 have emerged as promising strategies to battle the SARS-CoV-2 pandemic with the assistance of novel approaches such as CRISPR-CAS, ASOs, and siRNA systems. Lastly, we discuss the importance of precision public health in the management of patients infected with SARS-CoV-2 and establish that the fusion of transcriptomics, RNA-based therapeutics, and precision public health will allow a linkage for developing health systems that facilitate the acquisition of relevant clinical strategies for rapid decision making to assist in the management and treatment of the SARS-CoV-2-infected population to combat this global public health problem.
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173
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Yu S, Li X, Xin Z, Sun L, Shi J. Proteomic insights into SARS-CoV-2 infection mechanisms, diagnosis, therapies and prognostic monitoring methods. Front Immunol 2022; 13:923387. [PMID: 36203586 PMCID: PMC9530739 DOI: 10.3389/fimmu.2022.923387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/05/2022] [Indexed: 01/08/2023] Open
Abstract
At the end of 2019, the COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection, seriously damaged world public health security. Several protein markers associated with virus infection have been extensively explored to combat the ever-increasing challenge posed by SARS-CoV-2. The proteomics of COVID-19 deepened our understanding of viral particles and their mechanisms of host invasion, providing us with information on protein changes in host tissues, cells and body fluids following infection in COVID-19 patients. In this review, we summarize the proteomic studies of SARS-CoV-2 infection and review the current understanding of COVID-19 in terms of the quantitative and qualitative proteomics of viral particles and host entry factors from the perspective of protein pathological changes in the organism following host infection.
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Affiliation(s)
- Shengman Yu
- Department of Laboratory Medicine Center, China-Japan Union Hospital, Jilin University, Changchun, China
- School of Laboratory Medicine, Beihua University, Jilin, China
| | - Xiaoyan Li
- Department of Infection Control Department, Hospital of Stomatology, Jilin University, Changchun, China
| | - Zhuoyuan Xin
- The Key Laboratory of Zoonosis Research, Chinese Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Liyuan Sun
- School of Laboratory Medicine, Beihua University, Jilin, China
| | - Jingwei Shi
- Department of Laboratory Medicine Center, China-Japan Union Hospital, Jilin University, Changchun, China
- *Correspondence: Jingwei Shi,
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174
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Stokes W, Berenger BM, Venner AA, Deslandes V, Shaw JLV. Point of care molecular and antigen detection tests for COVID-19: current status and future prospects. Expert Rev Mol Diagn 2022; 22:797-809. [PMID: 36093682 DOI: 10.1080/14737159.2022.2122712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Detection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has been critical to support and management of the COVID-19 pandemic. Point of care testing (POCT) for SARS-CoV-2 has been a widely used tool for detection of SARS-CoV-2. AREAS COVERED POCT nucleic acid amplification tests (NAATs) and rapid antigen tests (RATs) have been the most readily used POCT for SARS-CoV-2. Here, current knowledge on the utility of POCT NAATs and RATs for SARS-CoV-2 are reviewed and discussed alongside aspects of quality assurance factors that must be considered for successful and safe implementation of POCT. EXPERT OPINION Use cases for implementation of POCT must be evidence based, regardless of the test used. A quality assurance framework must be in place to ensure accuracy and safety of POCT.
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Affiliation(s)
- William Stokes
- Alberta Precision Laboratories, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Byron M Berenger
- Alberta Precision Laboratories, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Allison A Venner
- Alberta Precision Laboratories, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Vincent Deslandes
- Eastern Ontario Regional Laboratories Association, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, The University of Ottawa, Ottawa, Ontario, Canada
| | - Julie L V Shaw
- Eastern Ontario Regional Laboratories Association, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, The University of Ottawa, Ottawa, Ontario, Canada
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175
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Fu Z, Rais Y, Dara D, Jackson D, Drabovich AP. Rational Design and Development of SARS-CoV-2 Serological Diagnostics by Immunoprecipitation-Targeted Proteomics. Anal Chem 2022; 94:12990-12999. [PMID: 36095284 PMCID: PMC9523617 DOI: 10.1021/acs.analchem.2c01325] [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] [Indexed: 12/27/2022]
Abstract
![]()
Current design of serological tests utilizes conservative
immunoassay
approaches and is focused on fast and convenient assay development,
throughput, straightforward measurements, and affordability. Limitations
of common serological assays include semiquantitative measurements,
cross-reactivity, lack of reference standards, and no differentiation
between human immunoglobulin subclasses. In this study, we suggested
that a combination of immunoaffinity enrichments with targeted proteomics
would enable rational design and development of serological assays
of infectious diseases, such as COVID-19. Immunoprecipitation-targeted
proteomic assays allowed for sensitive and specific measurements of
NCAP_SARS2 protein with a limit of detection of 313 pg/mL in serum
and enabled differential quantification of anti-SARS-CoV-2 antibody
isotypes (IgG, IgA, IgM, IgD, and IgE) and individual subclasses (IgG1-4
and IgA1-2) in plasma and saliva. Simultaneous evaluation of the numerous
antigen–antibody subclass combinations revealed a receptor-binding
domain (RBD)-IgG1 as a combination with the highest diagnostic performance.
Further validation revealed that anti-RBD IgG1, IgG3, IgM, and IgA1
levels were significantly elevated in convalescent plasma, while IgG2,
IgG4, and IgA2 were not informative. Anti-RBD IgG1 levels in convalescent
(2138 ng/mL) vs negative (95 ng/mL) plasma revealed 385 ng/mL as a
cutoff to detect COVID-19 convalescent plasma. Immunoprecipitation-targeted
proteomic assays will facilitate improvement and standardization of
the existing serological tests, enable rational design of novel tests,
and offer tools for the comprehensive investigation of immunoglobulin
subclass cooperation in immune response.
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Affiliation(s)
- Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Delaram Dara
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Dana Jackson
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
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176
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Pająk B, Zieliński R, Manning JT, Matejin S, Paessler S, Fokt I, Emmett MR, Priebe W. The Antiviral Effects of 2-Deoxy-D-glucose (2-DG), a Dual D-Glucose and D-Mannose Mimetic, against SARS-CoV-2 and Other Highly Pathogenic Viruses. Molecules 2022; 27:molecules27185928. [PMID: 36144664 PMCID: PMC9503362 DOI: 10.3390/molecules27185928] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 12/15/2022] Open
Abstract
Viral infection almost invariably causes metabolic changes in the infected cell and several types of host cells that respond to the infection. Among metabolic changes, the most prominent is the upregulated glycolysis process as the main pathway of glucose utilization. Glycolysis activation is a common mechanism of cell adaptation to several viral infections, including noroviruses, rhinoviruses, influenza virus, Zika virus, cytomegalovirus, coronaviruses and others. Such metabolic changes provide potential targets for therapeutic approaches that could reduce the impact of infection. Glycolysis inhibitors, especially 2-deoxy-D-glucose (2-DG), have been intensively studied as antiviral agents. However, 2-DG’s poor pharmacokinetic properties limit its wide clinical application. Herein, we discuss the potential of 2-DG and its novel analogs as potent promising antiviral drugs with special emphasis on targeted intracellular processes.
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Affiliation(s)
- Beata Pająk
- Independent Laboratory of Genetics and Molecular Biology, Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland
- WPD Pharmaceuticals, Zwirki i Wigury 101, 01-163 Warsaw, Poland
- Correspondence: (B.P.); (W.P.)
| | - Rafał Zieliński
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA
| | - John Tyler Manning
- Department of Pathology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
| | - Stanislava Matejin
- Department of Advanced Cardiopulmonary Therapies and Transplantation, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Slobodan Paessler
- Department of Pathology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
| | - Izabela Fokt
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA
| | - Mark R. Emmett
- Department of Pathology, The University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
| | - Waldemar Priebe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA
- Correspondence: (B.P.); (W.P.)
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177
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Proteomic Analysis Identifies Molecular Players and Biological Processes Specific to SARS-CoV-2 Exposure in Endothelial Cells. Int J Mol Sci 2022; 23:ijms231810452. [PMID: 36142365 PMCID: PMC9500950 DOI: 10.3390/ijms231810452] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the severe pandemic of acute respiratory disease, coronavirus disease 2019 (COVID-19), experienced in the 21st century. The clinical manifestations range from mild symptoms to abnormal blood coagulation and severe respiratory failure. In severe cases, COVID-19 manifests as a thromboinflammatory disease. Damage to the vascular compartment caused by SARS-CoV-2 has been linked to thrombosis, triggered by an enhanced immune response. The molecular mechanisms underlying endothelial activation have not been fully elucidated. We aimed to identify the proteins correlated to the molecular response of human umbilical vein endothelial cells (HUVECs) after exposure to SARS-CoV-2, which might help to unravel the molecular mechanisms of endothelium activation in COVID-19. In this direction, we exposed HUVECs to SARS-CoV-2 and analyzed the expression of specific cellular receptors, and changes in the proteome of HUVECs at different time points. We identified that HUVECs exhibit non-productive infection without cytopathic effects, in addition to the lack of expression of specific cell receptors known to be essential for SARS-CoV-2 entry into cells. We highlighted the enrichment of the protein SUMOylation pathway and the increase in SUMO2, which was confirmed by orthogonal assays. In conclusion, proteomic analysis revealed that the exposure to SARS-CoV-2 induced oxidative stress and changes in protein abundance and pathways enrichment that resembled endothelial dysfunction.
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178
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Plavec Z, Domanska A, Liu X, Laine P, Paulin L, Varjosalo M, Auvinen P, Wolf SG, Anastasina M, Butcher SJ. SARS-CoV-2 Production, Purification Methods and UV Inactivation for Proteomics and Structural Studies. Viruses 2022; 14:v14091989. [PMID: 36146795 PMCID: PMC9505060 DOI: 10.3390/v14091989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 is the causative agent of COVID-19. During the pandemic of 2019–2022, at least 500 million have been infected and over 6.3 million people have died from COVID-19. The virus is pleomorphic, and due to its pathogenicity is often handled in very restrictive biosafety containments laboratories. We developed two effective and rapid purification methods followed by UV inactivation that allow easy downstream handling of the virus. We monitored the purification through titering, sequencing, mass spectrometry and electron cryogenic microscopy. Although pelleting through a sucrose cushion, followed by gentle resuspension overnight gave the best particle recovery, infectivity decreased, and the purity was significantly worse than if using the size exclusion resin Capto Core. Capto Core can be used in batch mode, and was seven times faster than the pelleting method, obviating the need for ultracentrifugation in the containment laboratory, but resulting in a dilute virus. UV inactivation was readily optimized to allow handling of the inactivated samples under standard operating conditions. When containment laboratory space is limited, we recommend the use of Capto Core for purification and UV for inactivation as a simple, rapid workflow prior, for instance, to electron cryogenic microscopy or cell activation experiments.
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Affiliation(s)
- Zlatka Plavec
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Aušra Domanska
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Pia Laine
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Sharon G. Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maria Anastasina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (M.A.); (S.J.B.); Tel.: +358-5044-84629 (M.A.); +358-5041-55492 (S.J.B.)
| | - Sarah J. Butcher
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (M.A.); (S.J.B.); Tel.: +358-5044-84629 (M.A.); +358-5041-55492 (S.J.B.)
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179
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Xu G, Wu Y, Xiao T, Qi F, Fan L, Zhang S, Zhou J, He Y, Gao X, Zeng H, Li Y, Zhang Z. Multiomics approach reveals the ubiquitination-specific processes hijacked by SARS-CoV-2. Signal Transduct Target Ther 2022; 7:312. [PMID: 36071039 PMCID: PMC9449932 DOI: 10.1038/s41392-022-01156-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/21/2022] [Accepted: 08/04/2022] [Indexed: 11/09/2022] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a global pandemic that seriously threatens health and socioeconomic development, but the existed antiviral drugs and vaccines still cannot yet halt the spread of the epidemic. Therefore, a comprehensive and profound understanding of the pathogenesis of SARS-CoV-2 is urgently needed to explore effective therapeutic targets. Here, we conducted a multiomics study of SARS-CoV-2-infected lung epithelial cells, including transcriptomic, proteomic, and ubiquitinomic. Multiomics analysis showed that SARS-CoV-2-infected lung epithelial cells activated strong innate immune response, including interferon and inflammatory responses. Ubiquitinomic further reveals the underlying mechanism of SARS-CoV-2 disrupting the host innate immune response. In addition, SARS-CoV-2 proteins were found to be ubiquitinated during infection despite the fact that SARS-CoV-2 itself didn't code any E3 ligase, and that ubiquitination at three sites on the Spike protein could significantly enhance viral infection. Further screening of the E3 ubiquitin ligases and deubiquitinating enzymes (DUBs) library revealed four E3 ligases influencing SARS-CoV-2 infection, thus providing several new antiviral targets. This multiomics combined with high-throughput screening study reveals that SARS-CoV-2 not only modulates innate immunity, but also promotes viral infection, by hijacking ubiquitination-specific processes, highlighting potential antiviral and anti-inflammation targets.
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Affiliation(s)
- Gang Xu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China
| | - Yezi Wu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China
| | - Tongyang Xiao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China
| | - Furong Qi
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China
| | - Lujie Fan
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Shengyuan Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China
| | - Jian Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China
| | - Yanhua He
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, 200433, Shanghai, China
| | - Xiang Gao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China
| | - Hongxiang Zeng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China
| | - Yunfei Li
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong Province, China. .,Guangdong Key laboratory for anti-infection Drug Quality Evaluation, 518112, Shenzhen, Guangdong Province, China. .,Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, Guangdong Province, China.
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180
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Nepali K, Sharma R, Sharma S, Thakur A, Liou JP. Beyond the vaccines: a glance at the small molecule and peptide-based anti-COVID19 arsenal. J Biomed Sci 2022; 29:65. [PMID: 36064696 PMCID: PMC9444709 DOI: 10.1186/s12929-022-00847-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/16/2022] [Indexed: 02/08/2023] Open
Abstract
Unprecedented efforts of the researchers have been witnessed in the recent past towards the development of vaccine platforms for the control of the COVID-19 pandemic. Albeit, vaccination stands as a practical strategy to prevent SARS-CoV-2 infection, supplementing the anti-COVID19 arsenal with therapeutic options such as small molecules/peptides and antibodies is being conceived as a prudent strategy to tackle the emerging SARS-CoV-2 variants. Noteworthy to mention that collective efforts from numerous teams have led to the generation of a voluminous library composed of chemically and mechanistically diverse small molecules as anti-COVID19 scaffolds. This review article presents an overview of medicinal chemistry campaigns and drug repurposing programs that culminated in the identification of a plethora of small molecule-based anti-COVID19 drugs mediating their antiviral effects through inhibition of proteases, S protein, RdRp, ACE2, TMPRSS2, cathepsin and other targets. In light of the evidence ascertaining the potential of small molecule drugs to approach conserved proteins required for the viral replication of all coronaviruses, accelerated FDA approvals are anticipated for small molecules for the treatment of COVID19 shortly. Though the recent attempts invested in this direction in pursuit of enrichment of the anti-COVID-19 armoury (chemical tools) are praiseworthy, some strategies need to be implemented to extract conclusive benefits of the recently reported small molecule viz. (i) detailed preclinical investigation of the generated anti-COVID19 scaffolds (ii) in-vitro profiling of the inhibitors against the emerging SARS-CoV-2 variants (iii) development of assays enabling rapid screening of the libraries of anti-COVID19 scaffold (iv) leveraging the applications of machine learning based predictive models to expedite the anti-COVID19 drug discovery campaign (v) design of antibody-drug conjugates.
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Affiliation(s)
- Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, 11031, Taiwan
| | - Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Sachin Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan.
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, 11031, Taiwan.
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181
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Wolff DW, Bianchi-Smiraglia A, Nikiforov MA. Compartmentalization and regulation of GTP in control of cellular phenotypes. Trends Mol Med 2022; 28:758-769. [PMID: 35718686 PMCID: PMC9420775 DOI: 10.1016/j.molmed.2022.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
Genetic or pharmacological inhibition of enzymes involved in GTP biosynthesis has substantial biological effects, underlining the need to better understand the function of GTP levels in regulation of cellular processes and the significance of targeting GTP biosynthesis enzymes for therapeutic intervention. Our current understanding of spatiotemporal regulation of GTP metabolism and its role in physiological and pathological cellular processes is far from complete. Novel methodologies such as genetically encoded sensors of free GTP offered insights into intracellular distribution and function of GTP molecules. In the current Review, we provide analysis of recent discoveries in the field of GTP metabolism and evaluate the key enzymes as molecular targets.
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Affiliation(s)
- David W Wolff
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA.
| | - Anna Bianchi-Smiraglia
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Mikhail A Nikiforov
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA.
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182
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Crunfli F, Carregari VC, Veras FP, Silva LS, Nogueira MH, Antunes ASLM, Vendramini PH, Valença AGF, Brandão-Teles C, Zuccoli GDS, Reis-de-Oliveira G, Silva-Costa LC, Saia-Cereda VM, Smith BJ, Codo AC, de Souza GF, Muraro SP, Parise PL, Toledo-Teixeira DA, Santos de Castro ÍM, Melo BM, Almeida GM, Firmino EMS, Paiva IM, Silva BMS, Guimarães RM, Mendes ND, Ludwig RL, Ruiz GP, Knittel TL, Davanzo GG, Gerhardt JA, Rodrigues PB, Forato J, Amorim MR, Brunetti NS, Martini MC, Benatti MN, Batah SS, Siyuan L, João RB, Aventurato ÍK, Rabelo de Brito M, Mendes MJ, da Costa BA, Alvim MKM, da Silva Júnior JR, Damião LL, de Sousa IMP, da Rocha ED, Gonçalves SM, Lopes da Silva LH, Bettini V, Campos BM, Ludwig G, Tavares LA, Pontelli MC, Viana RMM, Martins RB, Vieira AS, Alves-Filho JC, Arruda E, Podolsky-Gondim GG, Santos MV, Neder L, Damasio A, Rehen S, Vinolo MAR, Munhoz CD, Louzada-Junior P, Oliveira RD, Cunha FQ, Nakaya HI, Mauad T, Duarte-Neto AN, Ferraz da Silva LF, Dolhnikoff M, Saldiva PHN, Farias AS, Cendes F, Moraes-Vieira PMM, Fabro AT, Sebollela A, Proença-Modena JL, Yasuda CL, Mori MA, Cunha TM, Martins-de-Souza D. Morphological, cellular, and molecular basis of brain infection in COVID-19 patients. Proc Natl Acad Sci U S A 2022. [DOI: 10.1073/pnas.2200960119 1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Although increasing evidence confirms neuropsychiatric manifestations associated mainly with severe COVID-19 infection, long-term neuropsychiatric dysfunction (recently characterized as part of “long COVID-19” syndrome) has been frequently observed after mild infection. We show the spectrum of cerebral impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, ranging from long-term alterations in mildly infected individuals (orbitofrontal cortical atrophy, neurocognitive impairment, excessive fatigue and anxiety symptoms) to severe acute damage confirmed in brain tissue samples extracted from the orbitofrontal region (via endonasal transethmoidal access) from individuals who died of COVID-19. In an independent cohort of 26 individuals who died of COVID-19, we used histopathological signs of brain damage as a guide for possible SARS-CoV-2 brain infection and found that among the 5 individuals who exhibited those signs, all of them had genetic material of the virus in the brain. Brain tissue samples from these five patients also exhibited foci of SARS-CoV-2 infection and replication, particularly in astrocytes. Supporting the hypothesis of astrocyte infection, neural stem cell–derived human astrocytes in vitro are susceptible to SARS-CoV-2 infection through a noncanonical mechanism that involves spike–NRP1 interaction. SARS-CoV-2–infected astrocytes manifested changes in energy metabolism and in key proteins and metabolites used to fuel neurons, as well as in the biogenesis of neurotransmitters. Moreover, human astrocyte infection elicits a secretory phenotype that reduces neuronal viability. Our data support the model in which SARS-CoV-2 reaches the brain, infects astrocytes, and consequently, leads to neuronal death or dysfunction. These deregulated processes could contribute to the structural and functional alterations seen in the brains of COVID-19 patients.
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Affiliation(s)
- Fernanda Crunfli
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Victor C. Carregari
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Flavio P. Veras
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Lucas S. Silva
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Mateus Henrique Nogueira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | | | - Pedro Henrique Vendramini
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | | | - Caroline Brandão-Teles
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Giuliana da Silva Zuccoli
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Guilherme Reis-de-Oliveira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Lícia C. Silva-Costa
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Verônica Monteiro Saia-Cereda
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Bradley J. Smith
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Ana Campos Codo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Gabriela F de Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Stéfanie P. Muraro
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Pierina Lorencini Parise
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Daniel A. Toledo-Teixeira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | | | - Bruno Marcel Melo
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Glaucia M. Almeida
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | | | - Isadora Marques Paiva
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | | | - Rafaela Mano Guimarães
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Niele D. Mendes
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Raíssa L. Ludwig
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Gabriel P. Ruiz
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Thiago L. Knittel
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Gustavo G. Davanzo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Jaqueline Aline Gerhardt
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Patrícia Brito Rodrigues
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Julia Forato
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Mariene Ribeiro Amorim
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Natália S. Brunetti
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Matheus Cavalheiro Martini
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Maíra Nilson Benatti
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Sabrina S. Batah
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Li Siyuan
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Rafael B. João
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Ítalo K. Aventurato
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Mariana Rabelo de Brito
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Maria J. Mendes
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Beatriz A. da Costa
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Marina K. M. Alvim
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - José Roberto da Silva Júnior
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Lívia L. Damião
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Iêda Maria P. de Sousa
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Elessandra D. da Rocha
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Solange M. Gonçalves
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Luiz H. Lopes da Silva
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Vanessa Bettini
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Brunno M. Campos
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Guilherme Ludwig
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Lucas Alves Tavares
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | | | | | - Ronaldo B. Martins
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Andre Schwambach Vieira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | | | - Eurico Arruda
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | | | - Marcelo Volpon Santos
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Luciano Neder
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Stevens Rehen
- D'Or Institute for Research and Education, 04502001, Brazil
- Institute of Biomedical Science, Federal University of Rio de Janeiro, Rio de Janeiro, 21941590, Brazil
| | - Marco Aurélio Ramirez Vinolo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | | | - Paulo Louzada-Junior
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Renê Donizeti Oliveira
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Fernando Q. Cunha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | | | - Thais Mauad
- University of São Paulo, São Paulo, 05508-220, Brazil
| | | | | | | | | | - Alessandro S. Farias
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Fernando Cendes
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Pedro Manoel M. Moraes-Vieira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Alexandre T. Fabro
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Adriano Sebollela
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - José L. Proença-Modena
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Clarissa L. Yasuda
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Marcelo A. Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
| | - Thiago M. Cunha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049900, Brazil
| | - Daniel Martins-de-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, 13083862, Brazil
- D'Or Institute for Research and Education, 04502001, Brazil
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183
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Abstract
Although increasing evidence confirms neuropsychiatric manifestations associated mainly with severe COVID-19 infection, long-term neuropsychiatric dysfunction (recently characterized as part of "long COVID-19" syndrome) has been frequently observed after mild infection. We show the spectrum of cerebral impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, ranging from long-term alterations in mildly infected individuals (orbitofrontal cortical atrophy, neurocognitive impairment, excessive fatigue and anxiety symptoms) to severe acute damage confirmed in brain tissue samples extracted from the orbitofrontal region (via endonasal transethmoidal access) from individuals who died of COVID-19. In an independent cohort of 26 individuals who died of COVID-19, we used histopathological signs of brain damage as a guide for possible SARS-CoV-2 brain infection and found that among the 5 individuals who exhibited those signs, all of them had genetic material of the virus in the brain. Brain tissue samples from these five patients also exhibited foci of SARS-CoV-2 infection and replication, particularly in astrocytes. Supporting the hypothesis of astrocyte infection, neural stem cell-derived human astrocytes in vitro are susceptible to SARS-CoV-2 infection through a noncanonical mechanism that involves spike-NRP1 interaction. SARS-CoV-2-infected astrocytes manifested changes in energy metabolism and in key proteins and metabolites used to fuel neurons, as well as in the biogenesis of neurotransmitters. Moreover, human astrocyte infection elicits a secretory phenotype that reduces neuronal viability. Our data support the model in which SARS-CoV-2 reaches the brain, infects astrocytes, and consequently, leads to neuronal death or dysfunction. These deregulated processes could contribute to the structural and functional alterations seen in the brains of COVID-19 patients.
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184
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Early Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater. Viruses 2022; 14:v14091876. [PMID: 36146683 PMCID: PMC9503272 DOI: 10.3390/v14091876] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. The Omicron sub-variants BA.4/BA.5 have spread globally, displacing the preceding variants. Due to the severe transmissibility and immune escape potential of BA.4/BA.5, early monitoring was required to assess and implement countermeasures in time. In this study, we monitored the prevalence of SARS-CoV-2 BA.4/BA.5 at six municipal wastewater treatment plants (WWTPs) in the Federal State of North Rhine-Westphalia (NRW, Germany) in May and June 2022. Initially, L452R-specific primers/probes originally designed for SARS-CoV-2 Delta detection were validated using inactivated authentic viruses and evaluated for their suitability for detecting BA.4/BA.5. Subsequently, the assay was used for RT-qPCR analysis of RNA purified from wastewater obtained twice a week at six WWTPs. The occurrence of L452R carrying RNA was detected in early May 2022, and the presence of BA.4/BA.5 was confirmed by variant-specific single nucleotide polymorphism PCR (SNP-PCR) targeting E484A/F486V and NGS sequencing. Finally, the mutant fractions were quantitatively monitored by digital PCR, confirming BA.4/BA.5 as the majority variant by 5 June 2022. In conclusion, the successive workflow using RT-qPCR, variant-specific SNP-PCR, and RT-dPCR demonstrates the strength of WBE as a versatile tool to rapidly monitor variants spreading independently of individual test capacities.
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185
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Upadhyai P, Shenoy PU, Banjan B, Albeshr MF, Mahboob S, Manzoor I, Das R. Exome-Wide Association Study Reveals Host Genetic Variants Likely Associated with the Severity of COVID-19 in Patients of European Ancestry. Life (Basel) 2022; 12:1300. [PMID: 36143338 PMCID: PMC9504138 DOI: 10.3390/life12091300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/03/2022] Open
Abstract
Host genetic variability plays a pivotal role in modulating COVID-19 clinical outcomes. Despite the functional relevance of protein-coding regions, rare variants located here are less likely to completely explain the considerable numbers of acutely affected COVID-19 patients worldwide. Using an exome-wide association approach, with individuals of European descent, we sought to identify common coding variants linked with variation in COVID-19 severity. Herein, cohort 1 compared non-hospitalized (controls) and hospitalized (cases) individuals, and in cohort 2, hospitalized subjects requiring respiratory support (cases) were compared to those not requiring it (controls). 229 and 111 variants differed significantly between cases and controls in cohorts 1 and 2, respectively. This included FBXO34, CNTN2, and TMCC2 previously linked with COVID-19 severity using association studies. Overall, we report SNPs in 26 known and 12 novel candidate genes with strong molecular evidence implicating them in the pathophysiology of life-threatening COVID-19 and post-recovery sequelae. Of these few notable known genes include, HLA-DQB1, AHSG, ALOX5AP, MUC5AC, SMPD1, SPG7, SPEG,GAS6, and SERPINA12. These results enhance our understanding of the pathomechanisms underlying the COVID-19 clinical spectrum and may be exploited to prioritize biomarkers for predicting disease severity, as well as to improve treatment strategies in individuals of European ancestry.
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Affiliation(s)
- Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Pooja U. Shenoy
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Bhavya Banjan
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Mohammed F. Albeshr
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Irfan Manzoor
- Department of Biology, The College of Arts and Sciences, Indiana University, Bloomington, IN 47405, USA
| | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
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186
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Pohler A, Abdelfatah S, Riedl M, Meesters C, Hildebrandt A, Efferth T. Potential Coronaviral Inhibitors of the Nucleocapsid Protein Identified In Silico and In Vitro from a Large Natural Product Library. Pharmaceuticals (Basel) 2022; 15:ph15091046. [PMID: 36145267 PMCID: PMC9503946 DOI: 10.3390/ph15091046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022] Open
Abstract
The nucleocapsid protein (NP) is one of the main proteins out of four structural proteins of coronaviruses including the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, discovered in 2019. NP packages the viral RNA during virus assembly and is, therefore, indispensable for virus reproduction. NP consists of two domains, i.e., the N- and C-terminal domains. RNA-binding is mainly performed by a binding pocket within the N-terminal domain (NTD). NP represents an important target for drug discovery to treat COVID-19. In this project, we used the Vina LC virtual drug screening software and a ZINC-based database with 210,541 natural and naturally derived compounds that specifically target the binding pocket of NTD of NP. Our aim was to identify coronaviral inhibitors that target NP not only of SARS-CoV-2 but also of other diverse human pathogenic coronaviruses. Virtual drug screening and molecular docking procedures resulted in 73 candidate compounds with a binding affinity below −9 kcal/mol with NP NTD of SARS-CoV-1, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-NL63, HoC-229E, and HCoV-HKU1. The top five compounds that met the applied drug-likeness criteria were then tested for their binding in vitro to the NTD of the full-length recombinant NP proteins using microscale thermophoresis. Compounds (1), (2), and (4), which belong to the same scaffold family of 4-oxo-substituted-6-[2-(4a-hydroxy-decahydroisoquinolin-2-yl)2H-chromen-2-ones and which are derivates of coumarin, were bound with good affinity to NP. Compounds (1) and (4) were bound to the full-length NP of SARS-CoV-2 (aa 1–419) with Kd values of 0.798 (±0.02) µM and 8.07 (±0.36) µM, respectively. Then, these coumarin derivatives were tested with the SARS-CoV-2 NP NTD (aa 48–174). Compounds (1) and (4) revealed Kd-values of 0.95 (±0.32) µM and 7.77 (±6.39) µM, respectively. Compounds (1) and (4) caused low toxicity in human A549 and MRC-5 cell lines. These compounds may represent possible drug candidates, which need further optimization to be used against COVID-19 and other coronaviral infections.
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Affiliation(s)
- Alexandra Pohler
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Sara Abdelfatah
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Max Riedl
- High Performance Computing Group, University of Mainz, 55131 Mainz, Germany
| | - Christian Meesters
- High Performance Computing Group, University of Mainz, 55131 Mainz, Germany
| | | | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
- Correspondence: ; Tel.: +49-6131-3925751; Fax: +49-6131-3923752
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Schloer S, Treuherz D, Faist A, Witt MD, Wunderlich K, Wiewrodt R, Wiebe K, Barth P, Wälzlein JH, Kummer S, Balkema-Buschmann A, Ludwig S, Brunotte L, Rescher U. 3D ex vivo tissue platforms to investigate the early phases of influenza A virus- and SARS-CoV-2-induced respiratory diseases. Emerg Microbes Infect 2022; 11:2160-2175. [PMID: 36000328 PMCID: PMC9518268 DOI: 10.1080/22221751.2022.2117101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pandemic outbreaks of viruses such as influenza virus or SARS-CoV-2 are associated with high morbidity and mortality and thus pose a massive threat to global health and economics. Physiologically relevant models are needed to study the viral life cycle, describe the pathophysiological consequences of viral infection, and explore possible drug targets and treatment options. While simple cell culture-based models do not reflect the tissue environment and systemic responses, animal models are linked with huge direct and indirect costs and ethical questions. Ex vivo platforms based on tissue explants have been introduced as suitable platforms to bridge the gap between cell culture and animal models. We established a murine lung tissue explant platform for two respiratory viruses, influenza A virus (IAV) and SARS-CoV-2. We observed efficient viral replication, associated with the release of inflammatory cytokines and the induction of an antiviral interferon response, comparable to ex vivo infection in human lung explants. Endolysosomal entry could be confirmed as a potential host target for pharmacological intervention, and the potential repurposing potentials of fluoxetine and interferons for host-directed therapy previously seen in vitro could be recapitulated in the ex vivo model.
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Affiliation(s)
- Sebastian Schloer
- Institute-Associated Research Group "Regulatory Mechanisms of Inflammation", Institute of Medical Biochemistry, Center for Molecular Biology of Inflammation, and "Cells in Motion" Interfaculty Center, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany.,Leibniz Institute of Virology, Martinistraße 52, 20251 Hamburg, Germany
| | - Daniel Treuherz
- Institute-Associated Research Group "Regulatory Mechanisms of Inflammation", Institute of Medical Biochemistry, Center for Molecular Biology of Inflammation, and "Cells in Motion" Interfaculty Center, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
| | - Aileen Faist
- Institute of Virology, Center for Molecular Biology of Inflammation, and "Cells in Motion" Interfaculty Center, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Marlous de Witt
- Institute of Virology, Center for Molecular Biology of Inflammation, and "Cells in Motion" Interfaculty Center, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Katharina Wunderlich
- Institute of Virology, Center for Molecular Biology of Inflammation, and "Cells in Motion" Interfaculty Center, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Rainer Wiewrodt
- Department of Medicine A, Hematology, Oncology and Respiratory Medicine, University Hospital Münster, Münster, Germany
| | - Karsten Wiebe
- Department of Thoracic Surgery, University Hospital Münster, Münster, Germany
| | - Peter Barth
- Gerhard-Domagk-Institute of Pathology, Westfälische Wilhelms-University, Münster, Germany
| | - Joo-Hee Wälzlein
- Center for Biological Threats and Special Pathogens, Robert Koch-Institute, Berlin, Germany
| | - Susann Kummer
- Center for Biological Threats and Special Pathogens, Robert Koch-Institute, Berlin, Germany
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institute, Institute of Novel and Emerging Infectious Diseases, Südufer 10, 17493 Greifswald, Germany
| | - Stephan Ludwig
- Institute of Virology, Center for Molecular Biology of Inflammation, and "Cells in Motion" Interfaculty Center, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Linda Brunotte
- Institute of Virology, Center for Molecular Biology of Inflammation, and "Cells in Motion" Interfaculty Center, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Ursula Rescher
- Institute-Associated Research Group "Regulatory Mechanisms of Inflammation", Institute of Medical Biochemistry, Center for Molecular Biology of Inflammation, and "Cells in Motion" Interfaculty Center, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
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188
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Patra SK, Szyf M. Epigenetic perspectives of COVID-19: Virus infection to disease progression and therapeutic control. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166527. [PMID: 36002132 PMCID: PMC9393109 DOI: 10.1016/j.bbadis.2022.166527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022]
Abstract
COVID-19 has caused numerous deaths as well as imposed social isolation and upheaval world-wide. Although, the genome and the composition of the virus, the entry process and replication mechanisms are well investigated from by several laboratories across the world, there are many unknown remaining questions. For example, what are the functions of membrane lipids during entry, packaging and exit of virus particles? Also, the metabolic aspects of the infected tissue cells are poorly understood. In the course of virus replication and formation of virus particles within the host cell, the enhanced metabolic activities of the host is directly proportional to viral loads. The epigenetic landscape of the host cells is also altered, particularly the expression/repression of genes associated with cellular metabolism as well as cellular processes that are antagonistic to the virus. Metabolic pathways are enzyme driven processes and the expression profile and mechanism of regulations of the respective genes encoding those enzymes during the course of pathogen invasion might be highly informative on the course of the disease. Recently, the metabolic profile of the patients' sera have been analysed from few patients. In view of this, and to gain further insights into the roles that epigenetic mechanisms might play in this scenario in regulation of metabolic pathways during the progression of COVID-19 are discussed and summarised in this contribution for ensuring best therapy.
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Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McIntyre Medical Sciences Building, McGill University, Montreal, QC H3G 1Y6, Canada
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189
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Zhong Y, Ashley CL, Steain M, Ataide SF. Assessing the suitability of long non-coding RNAs as therapeutic targets and biomarkers in SARS-CoV-2 infection. Front Mol Biosci 2022; 9:975322. [PMID: 36052163 PMCID: PMC9424846 DOI: 10.3389/fmolb.2022.975322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts that are over 200 nucleotides and rarely encode proteins or peptides. They regulate gene expression and protein activities and are heavily involved in many cellular processes such as cytokine secretion in respond to viral infection. In severe COVID-19 cases, hyperactivation of the immune system may cause an abnormally sharp increase in pro-inflammatory cytokines, known as cytokine release syndrome (CRS), which leads to severe tissue damage or even organ failure, raising COVID-19 mortality rate. In this review, we assessed the correlation between lncRNAs expression and cytokine release syndrome by comparing lncRNA profiles between COVID-19 patients and health controls, as well as between severe and non-severe cases. We also discussed the role of lncRNAs in CRS contributors and showed that the lncRNA profiles display consistency with patients’ clinic symptoms, thus suggesting the potential of lncRNAs as drug targets or biomarkers in COVID-19 treatment.
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Affiliation(s)
- Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Caroline L. Ashley
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Megan Steain
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Sandro Fernandes Ataide
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- *Correspondence: Sandro Fernandes Ataide,
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Reciprocal interplay between OTULIN-LUBAC determines genotoxic and inflammatory NF-κB signal responses. Proc Natl Acad Sci U S A 2022; 119:e2123097119. [PMID: 35939695 PMCID: PMC9388121 DOI: 10.1073/pnas.2123097119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Targeting nuclear factor-kappa B (NF-κB) represents a highly viable strategy against chemoresistance in cancers as well as cell death. Ubiquitination, including linear ubiquitination mediated by the linear ubiquitin chain assembly complex (LUBAC), is emerging as a crucial mechanism of overactivated NF-κB signaling. Ovarian tumor family deubiquitinase OTULIN is the only linear linkage-specific deubiquitinase; however, the molecular mechanisms of how it counteracts LUBAC-mediated NF-κB activation have been largely unknown. Here, we identify Lys64/66 of OTULIN for linear ubiquitination facilitated in a LUBAC-dependent manner as a necessary event required for OTULIN-LUBAC interaction under unstressed conditions, which becomes deubiquitinated by OTULIN itself in response to genotoxic stress. Furthermore, this self-deubiquitination of OTULIN occurs intermolecularly, mediated by OTULIN dimerization, resulting in the subsequent dissociation of OTULIN from the LUBAC complex and NF-κB overactivation. Oxidative stress induces OTULIN dimerization via cysteine-mediated covalent disulfide bonds. Our study reveals that the status of the physical interaction between OTULIN and LUBAC is a crucial determining factor for the genotoxic NF-κB signaling, as measured by cell survival and proliferation, while OTULIN loss of function resulting from its dimerization and deubiquitination leads to a dissociation of OTULIN from the LUBAC complex. Of note, similar molecular mechanisms apply to the inflammatory NF-κB signaling in response to tumor necrosis factor α. Hence, a fuller understanding of the detailed molecular mechanisms underlying the disruption of the OTULIN-LUBAC interaction will be instrumental for developing future therapeutic strategies against cancer chemoresistance and necroptotic processes pertinent to numerous human diseases.
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Okendo J, Musanabaganwa C, Mwangi P, Nyaga M, Onywera H. SARS-CoV-2-positive patients display considerable differences in proteome diversity in urine, nasopharyngeal, gargle solution and bronchoalveolar lavage fluid samples. PLoS One 2022; 17:e0271870. [PMID: 35939435 PMCID: PMC9359582 DOI: 10.1371/journal.pone.0271870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/09/2022] [Indexed: 11/18/2022] Open
Abstract
Proteome profile changes post-severe acute respiratory syndrome coronavirus 2 (post-SARS-CoV-2) infection in different body sites of humans remains an active scientific investigation whose solutions stand a chance of providing more information on what constitutes SARS-CoV-2 pathogenesis. While proteomics has been used to understand SARS-CoV-2 pathogenesis, there are limited data about the status of proteome profile in different human body sites infected by the SARS-CoV-2 virus. To bridge this gap, our study aims to characterize the proteins secreted in urine, bronchoalveolar lavage fluid (BALF), gargle solution, and nasopharyngeal samples and assess the proteome differences in these body samples collected from SARS-CoV-2-positive patients. We downloaded publicly available proteomic data from (https://www.ebi.ac.uk/pride/). The data we downloaded had the following identifiers: (i) PXD019423, n = 3 from Charles Tanford Protein Center in Germany. (ii) IPX0002166000, n = 15 from Beijing Proteome Research Centre, China. (iii) IPX0002429000, n = 5 from Huazhong University of Science and Technology, China, and (iv) PXD022889, n = 18 from Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA. MaxQuant was used for the human peptide spectral matching using human and SARS-CoV-2 proteome database which we downloaded from the UniProt database (access date 13th October 2021). The individuals infected with SARS-CoV-2 viruses displayed a different proteome diversity from the different body sites we investigated. Overally, we identified 1809 proteins across the four sample types we compared. Urine and BALF samples had significantly more abundant SARS-CoV-2 proteins than the other body sites we compared. Urine samples had 257(33.7%) unique proteins, followed by nasopharyngeal with 250(32.8%) unique proteins. Gargle solution and BALF had 38(5%) and 73(9.6%) unique proteins respectively. Urine, gargle solution, nasopharyngeal, and bronchoalveolar lavage fluid samples have different protein diversity in individuals infected with SARS-CoV-2. Moreover, our data also demonstrated that a given body site is characterized by a unique set of proteins in SARS-CoV-2 seropositive individuals.
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Affiliation(s)
- Javan Okendo
- Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | | | - Peter Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Martin Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Harris Onywera
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Microbiology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Research, Innovations and Academics Unit, Tunacare Services Health Providers Limited, Nairobi, Kenya
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192
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Bhatt AN, Shenoy S, Munjal S, Chinnadurai V, Agarwal A, Vinoth Kumar A, Shanavas A, Kanwar R, Chandna S. 2-deoxy-D-glucose as an adjunct to standard of care in the medical management of COVID-19: a proof-of-concept and dose-ranging randomised phase II clinical trial. BMC Infect Dis 2022; 22:669. [PMID: 35927676 PMCID: PMC9351257 DOI: 10.1186/s12879-022-07642-6] [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: 12/13/2021] [Accepted: 07/24/2022] [Indexed: 11/24/2022] Open
Abstract
Background At present, no single efficacious therapeutic exists for acute COVID-19 management and a multimodal approach may be necessary. 2-deoxy-d-glucose (2-DG) is a metabolic inhibitor that has been shown to limit multiplication of SARS-CoV-2 in-vitro. We evaluated the efficacy and safety of 2-DG as adjunct to standard care in the treatment of moderate to severe COVID-19 patients. Methods We conducted a randomized, open-label, phase II, clinical study to evaluate the efficacy, safety, and tolerability of 2-DG administered as adjunct to standard of care (SOC). A total of 110 patients between the ages of 18 and 65 years with moderate to severe COVID-19 were included. Patients were randomized to receive 63, 90, or 126 mg/kg/day 2-DG in addition to SOC or SOC only. Times to maintaining SpO2 ≥ 94% on room air, discharge, clinical recovery, vital signs normalisation, improvement by 1 and 2 points on WHO clinical progression scale, negative conversion on RT-PCR, requirement for intensive care, and mortality were analyzed to assess the efficacy. Results Patients treated with 90 mg/kg/day 2-DG plus SOC showed better outcomes. Time to maintaining SpO2 ≥ 94% was significantly shorter in the 2-DG 90 mg compared to SOC (median 2.5 days vs. 5 days, Hazard ratio [95% confidence interval] = 2.3 [1.14, 4.64], p = 0.0201). Times to discharge from isolation ward, to clinical recovery, and to vital signs normalization were significantly shorter for the 2-DG 90 mg group. All three doses of 2-DG were well tolerated. Thirty-three (30.3%) patients reported 65 adverse events and were mostly (86%) mild. Conclusions 2-DG 90 mg/kg/day as adjunct to SOC showed clinical benefit over SOC alone in the treatment of moderate to severe COVID-19. The promising trends observed in current phase II study is encouraging for confirmatory evaluation of the efficacy and safety of 2-DG in a larger phase III trial. Trial registration: CTRI, CTRI/2020/06/025664. Registered 5th June 2020, http://ctri.nic.in/Clinicaltrials/pdf_generate.php?trialid=44369&EncHid=&modid=&compid=%27,%2744369det%27. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07642-6.
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Affiliation(s)
- Anant Narayan Bhatt
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Timarpur, Delhi, 110054, India.
| | - Srinivas Shenoy
- Dr Reddy's Laboratories Limited, 8-2-337, Road No. 3, Banjara Hills, 500 034, Hyderabad, India.
| | - Sagar Munjal
- Dr Reddy's Laboratories Limited, 8-2-337, Road No. 3, Banjara Hills, 500 034, Hyderabad, India
| | - Vijayakumar Chinnadurai
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Timarpur, Delhi, 110054, India
| | - Apurva Agarwal
- Department of Anaesthesia, Critical Care and Pain Medicine, RMC, GSVM Medical College, Jalaun, Kanpur, India
| | - A Vinoth Kumar
- Department of Pharmacology, Chengalpattu Medical College, Chengalpattu, 603001, India
| | - A Shanavas
- Dr Reddy's Laboratories Limited, 8-2-337, Road No. 3, Banjara Hills, 500 034, Hyderabad, India
| | - Ratnesh Kanwar
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Timarpur, Delhi, 110054, India
| | - Sudhir Chandna
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Timarpur, Delhi, 110054, India
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193
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The global succinylation of SARS-CoV-2–infected host cells reveals drug targets. Proc Natl Acad Sci U S A 2022; 119:e2123065119. [PMID: 35858407 PMCID: PMC9335334 DOI: 10.1073/pnas.2123065119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The continued rapid evolution of SARS-CoV-2 and the emergence of immune-evading variants pose significant challenges to COVID-19 prevention and control, highlighting the urgent need for development of novel antiviral therapies. Our study found that SARS-CoV-2 infection promotes host succinylation and inhibits several key enzymes of the TCA, a crucial metabolic pathway that connects carbohydrate, fat, and protein metabolism, as well as regulating cellular energy. Additionally, viral NSP14 is capable to participate in succinylation through interacting with host SIRT5, a cellular desuccinylase. It is noteworthy that succinylation inhibitors can significantly reduce the viral replication, as a potential guide for the treatment of COVID-19. SARS-CoV-2, the causative agent of the COVID-19 pandemic, undergoes continuous evolution, highlighting an urgent need for development of novel antiviral therapies. Here we show a quantitative mass spectrometry-based succinylproteomics analysis of SARS-CoV-2 infection in Caco-2 cells, revealing dramatic reshape of succinylation on host and viral proteins. SARS-CoV-2 infection promotes succinylation of several key enzymes in the TCA, leading to inhibition of cellular metabolic pathways. We demonstrated that host protein succinylation is regulated by viral nonstructural protein (NSP14) through interaction with sirtuin 5 (SIRT5); overexpressed SIRT5 can effectively inhibit virus replication. We found succinylation inhibitors possess significant antiviral effects. We also found that SARS-CoV-2 nucleocapsid and membrane proteins underwent succinylation modification, which was conserved in SARS-CoV-2 and its variants. Collectively, our results uncover a regulatory mechanism of host protein posttranslational modification and cellular pathways mediated by SARS-CoV-2, which may become antiviral drug targets against COVID-19.
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194
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Grikscheit K, Rabenau HF, Ghodratian Z, Widera M, Wilhelm A, Toptan Grabmair T, Hoehl S, Layer E, Helfritz F, Ciesek S. Characterization of the Antibody and Interferon-Gamma Release Response after a Second COVID-19 Booster Vaccination. Vaccines (Basel) 2022; 10:vaccines10071163. [PMID: 35891326 PMCID: PMC9323888 DOI: 10.3390/vaccines10071163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/28/2022] [Accepted: 07/14/2022] [Indexed: 11/26/2022] Open
Abstract
The emergence of SARS-CoV-2 Omicron subvariants prompted countries to call for accelerated booster vaccinations to limit disease and transmission. Here, we characterized correlates of protection over time after the second booster or after Omicron BA.1 infection comparing variants of concern (VOCs). Sera from subjects before and two and seven weeks after the second booster or after Omicron infection were examined for the level of Spike receptor-binding-domain (RBD)-specific antibodies. Furthermore, neutralizing antibodies (nABs) were characterized in in vitro neutralization assays comparing the variants of concern Alpha, Beta, Delta, and Omicron BA.1 and BA.2 against the ancestral strain B.1. Here, the second booster resulted in an increase in anti-RBD-IgG-antibodies, remaining nearly constant over time, accompanied by an increase in nABs against B.1 and the VOCs Alpha, Beta, Delta, and Omicron BA.1 and BA.2. However, compared to B.1, the neutralizing capacity against the Omicron subvariants remained low and was limited after the second booster vaccination. This indicates that antibody-mediated protection against infection with this VOC is unlikely, as evidenced by the fact that three individuals of our study cohort became infected with Omicron BA.1 after the second booster. T cell activation was measured by interferon-gamma release assays in a subgroup of subjects and was increased in all subjects tested after the second booster vaccination, correlating with the amount of Spike-specific antibodies. In subjects with Omicron BA.1 breakthrough infection, a significant increase in nABs to all VOCs studied was observed independently of booster vaccinations. Taken together, our data indicate that a second booster or Omicron BA.1 infection mediate a substantial increase in anti-Spike IgG antibodies; however, infection with Omicron BA.1 induced a stronger increase in neutralizing antibodies against the different VOCs
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Affiliation(s)
- Katharina Grikscheit
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt, Germany; (K.G.); (H.F.R.); (Z.G.); (M.W.); (A.W.); (T.T.G.); (S.H.)
| | - Holger F. Rabenau
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt, Germany; (K.G.); (H.F.R.); (Z.G.); (M.W.); (A.W.); (T.T.G.); (S.H.)
| | - Zahra Ghodratian
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt, Germany; (K.G.); (H.F.R.); (Z.G.); (M.W.); (A.W.); (T.T.G.); (S.H.)
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt, Germany; (K.G.); (H.F.R.); (Z.G.); (M.W.); (A.W.); (T.T.G.); (S.H.)
| | - Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt, Germany; (K.G.); (H.F.R.); (Z.G.); (M.W.); (A.W.); (T.T.G.); (S.H.)
| | - Tuna Toptan Grabmair
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt, Germany; (K.G.); (H.F.R.); (Z.G.); (M.W.); (A.W.); (T.T.G.); (S.H.)
| | - Sebastian Hoehl
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt, Germany; (K.G.); (H.F.R.); (Z.G.); (M.W.); (A.W.); (T.T.G.); (S.H.)
| | - Emily Layer
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany;
| | - Fabian Helfritz
- Bürgerhospital Frankfurt, Nibelungenallee 37-41, 60318 Frankfurt am Main, Germany;
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt, Germany; (K.G.); (H.F.R.); (Z.G.); (M.W.); (A.W.); (T.T.G.); (S.H.)
- German Centre for Infection Research (DZIF), Partner Site Frankfurt, 60596 Frankfurt, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch Translational Medicine and Pharmcology, 60596 Frankfurt am Main, Germany
- Correspondence:
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195
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Wang GQ, Gu Y, Wang C, Wang F, Hsu ACY. A Game of Infection - Song of Respiratory Viruses and Interferons. Front Cell Infect Microbiol 2022; 12:937460. [PMID: 35846766 PMCID: PMC9277140 DOI: 10.3389/fcimb.2022.937460] [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: 05/06/2022] [Accepted: 05/25/2022] [Indexed: 12/15/2022] Open
Abstract
Humanity has experienced four major pandemics since the twentieth century, with the 1918 Spanish flu, the 2002 severe acute respiratory syndrome (SARS), the 2009 swine flu, and the 2019 coronavirus disease (COVID)-19 pandemics having the most important impact in human health. The 1918 Spanish flu caused unprecedented catastrophes in the recorded human history, with an estimated death toll between 50 – 100 million. While the 2002 SARS and 2009 swine flu pandemics caused approximately 780 and 280,000 deaths, respectively, the current COVID-19 pandemic has resulted in > 6 million deaths globally at the time of writing. COVID-19, instigated by the SARS – coronavirus-2 (SARS-CoV-2), causes unprecedented challenges in all facets of our lives, and never before brought scientists of all fields together to focus on this singular topic. While for the past 50 years research have been heavily focused on viruses themselves, we now understand that the host immune responses are just as important in determining the pathogenesis and outcomes of infection. Research in innate immune mechanisms is crucial in understanding all aspects of host antiviral programmes and the mechanisms underpinning virus-host interactions, which can be translated to the development of effective therapeutic avenues. This review summarizes what is known and what remains to be explored in the innate immune responses to influenza viruses and SARS-CoVs, and virus-host interactions in driving disease pathogenesis. This hopefully will encourage discussions and research on the unanswered questions, new paradigms, and antiviral strategies against these emerging infectious pathogens before the next pandemic occurs.
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Affiliation(s)
- Guo Qiang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Yinuo Gu
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Chao Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Fang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Alan Chen-Yu Hsu
- Signature Research Program in Emerging Infectious Diseases, Duke - National University of Singapore (NUS) Graduate Medical School, Singapore, Singapore.,School of Medicine and Public Health, The University of Newcastle, Newcastle, NSW, Australia.,Viruses, Infections/Immunity, Vaccines and Asthma, Hunter Medical Research Institute, Newcastle, NSW, Australia
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196
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Valipour M, Irannejad H, Emami S. Application of emetine in SARS-CoV-2 treatment: regulation of p38 MAPK signaling pathway for preventing emetine-induced cardiac complications. Cell Cycle 2022; 21:2379-2386. [DOI: 10.1080/15384101.2022.2100575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Mehdi Valipour
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hamid Irannejad
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Saeed Emami
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection. Commun Biol 2022; 5:714. [PMID: 35854100 PMCID: PMC9296638 DOI: 10.1038/s42003-022-03663-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/29/2022] [Indexed: 11/08/2022] Open
Abstract
SARS-CoV-2 hijacks the host cell transcriptional machinery to induce a phenotypic state amenable to its replication. Here we show that analysis of Master Regulator proteins representing mechanistic determinants of the gene expression signature induced by SARS-CoV-2 in infected cells revealed coordinated inactivation of Master Regulators enriched in physical interactions with SARS-CoV-2 proteins, suggesting their mechanistic role in maintaining a host cell state refractory to virus replication. To test their functional relevance, we measured SARS-CoV-2 replication in epithelial cells treated with drugs predicted to activate the entire repertoire of repressed Master Regulators, based on their experimentally elucidated, context-specific mechanism of action. Overall, 15 of the 18 drugs predicted to be effective by this methodology induced significant reduction of SARS-CoV-2 replication, without affecting cell viability. This model for host-directed pharmacological therapy is fully generalizable and can be deployed to identify drugs targeting host cell-based Master Regulator signatures induced by virtually any pathogen.
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Habeichi NJ, Tannous C, Yabluchanskiy A, Altara R, Mericskay M, Booz GW, Zouein FA. Insights into the modulation of the interferon response and NAD + in the context of COVID-19. Int Rev Immunol 2022; 41:464-474. [PMID: 34378474 DOI: 10.1080/08830185.2021.1961768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in dramatic worldwide mortality. Along with developing vaccines, the medical profession is exploring new strategies to curb this pandemic. A better understanding of the molecular consequences of SARS-CoV-2 cellular infection could lead to more effective and safer treatments. This review discusses the potential underlying impact of SARS-CoV-2 in modulating interferon (IFN) secretion and in causing mitochondrial NAD+ depletion that could be directly linked to COVID-19's deadly manifestations. What is known or surmised about an imbalanced innate immune response and mitochondrial dysfunction post-SARS-CoV-2 infection, and the potential benefits of well-timed IFN treatments and NAD+ boosting therapies in the context of the COVID-19 pandemic are discussed.
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Affiliation(s)
- Nada J Habeichi
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon.,Department of Signaling and Cardiovascular Pathophysiology, Université Paris-Saclay, Inserm, UMR-S 1180, Châtenay-Malabry, France
| | - Cynthia Tannous
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Andriy Yabluchanskiy
- Center for Geroscience and Healthy Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Raffaele Altara
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,KG Jebsen Center for Cardiac Research, Oslo, Norway.,Department of Pathology, School of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Mathias Mericskay
- Department of Signaling and Cardiovascular Pathophysiology, Université Paris-Saclay, Inserm, UMR-S 1180, Châtenay-Malabry, France
| | - George W Booz
- Department of Pharmacology and Toxicology, School of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Fouad A Zouein
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon
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Abstract
Retinoids, a group of compounds including vitamin A and its active metabolite all-
trans
retinoic acid (ATRA), regulate serial physiological activity in multiple organ systems, such as cell growth, differentiation, and apoptosis. The ATRA analogues reported to date include more than 4,000 natural and synthetic molecules that are structurally and/or functionally related to ATRA.
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Limited neutralisation of the SARS-CoV-2 Omicron subvariants BA.1 and BA.2 by convalescent and vaccine serum and monoclonal antibodies. EBioMedicine 2022; 82:104158. [PMID: 35834885 PMCID: PMC9271884 DOI: 10.1016/j.ebiom.2022.104158] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 12/22/2022] Open
Abstract
Background In recent months, Omicron variants of SARS-CoV-2 have become dominant in many regions of the world, and case numbers with Omicron subvariants BA.1 and BA.2 continue to increase. Due to numerous mutations in the spike protein, the efficacy of currently available vaccines, which are based on Wuhan-Hu 1 isolate of SARS-CoV-2, is reduced, leading to breakthrough infections. Efficacy of monoclonal antibody therapy is also likely impaired. Methods In our in vitro study using A549-AT cells constitutively expressing ACE2 and TMPRSS2, we determined and compared the neutralizing capacity of vaccine-elicited sera, convalescent sera and monoclonal antibodies against authentic SARS-CoV-2 Omicron BA.1 and BA.2 compared with Delta. Findings Almost no neutralisation of Omicron BA.1 and BA.2 was observed using sera from individuals vaccinated with two doses 6 months earlier, regardless of the type of vaccine taken. Shortly after the booster dose, most sera from triple BNT162b2-vaccinated individuals were able to neutralise both Omicron variants. In line with waning antibody levels three months after the booster, only weak residual neutralisation was observed for BA.1 (26%, n = 34, 0 median NT50) and BA.2 (44%, n = 34, 0 median NT50). In addition, BA.1 but not BA.2 was resistant to the neutralising monoclonal antibodies casirivimab/imdevimab, while BA.2 exhibited almost a complete evasion from the neutralisation induced by sotrovimab. Interpretation Both SARS-CoV-2 Omicron subvariants BA.1 and BA.2 escape antibody-mediated neutralisation elicited by vaccination, previous infection with SARS-CoV-2, and monoclonal antibodies. Waning immunity renders the majority of tested sera obtained three months after booster vaccination negative in BA.1 and BA.2 neutralisation. Omicron subvariant specific resistance to the monoclonal antibodies casirivimab/imdevimab and sotrovimab emphasizes the importance of genotype-surveillance and guided application. Funding This study was supported in part by the Goethe-Corona-Fund of the Goethe University Frankfurt (M.W.) and the Federal Ministry of Education and Research (COVIDready; grant 02WRS1621C (M.W.).
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