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Das R, Sinnarasan VSP, Paul D, Venkatesan A. A Machine Learning Approach to Identify Potential miRNA-Gene Regulatory Network Contributing to the Pathogenesis of SARS-CoV-2 Infection. Biochem Genet 2024; 62:987-1006. [PMID: 37515735 DOI: 10.1007/s10528-023-10458-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023]
Abstract
Worldwide, many lives have been lost in the recent outbreak of coronavirus disease. The pathogen responsible for this disease takes advantage of the host machinery to replicate itself and, in turn, causes pathogenesis in humans. Human miRNAs are seen to have a major role in the pathogenesis and progression of viral diseases. Hence, an in-silico approach has been used in this study to uncover the role of miRNAs and their target genes in coronavirus disease pathogenesis. This study attempts to perform the miRNA seq data analysis to identify the potential differentially expressed miRNAs. Considering only the experimentally proven interaction databases TarBase, miRTarBase, and miRecords, the target genes of the miRNAs have been identified from the mirNET analytics platform. The identified hub genes were subjected to gene ontology and pathway enrichment analysis using EnrichR. It is found that a total of 9 miRNAs are deregulated, out of which 2 were upregulated (hsa-mir-3614-5p and hsa-mir-3614-3p) and 7 were downregulated (hsa-mir-17-5p, hsa-mir-106a-5p, hsa-mir-17-3p, hsa-mir-181d-5p, hsa-mir-93-3p, hsa-mir-28-5p, and hsa-mir-100-5p). These miRNAs help us to classify the diseased and healthy control patients accurately. Moreover, it is also found that crucial target genes (UBC and UBB) of 4 signature miRNAs interact with viral replicase polyprotein 1ab of SARS-Coronavirus. As a result, it is noted that the virus hijacks key immune pathways like various cancer and virus infection pathways and molecular functions such as ubiquitin ligase binding and transcription corepressor and coregulator binding.
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Affiliation(s)
- Rajesh Das
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India
| | | | - Dahrii Paul
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India
| | - Amouda Venkatesan
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India.
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2
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Warren CJ, Barbachano-Guerrero A, Bauer VL, Stabell AC, Dirasantha O, Yang Q, Sawyer SL. Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.13.566830. [PMID: 38014262 PMCID: PMC10680607 DOI: 10.1101/2023.11.13.566830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Simian immunodeficiency viruses (SIVs) comprise a large group of primate lentiviruses that endemically infect African monkeys. HIV-1 spilled over to humans from this viral reservoir, but the spillover did not occur directly from monkeys to humans. Instead, a key event was the introduction of SIVs into great apes, which then set the stage for infection of humans. Here, we investigate the role of the lentiviral entry receptor, CD4, in this key and fateful event in the history of SIV/HIV emergence. First, we reconstructed and tested ancient forms of CD4 at two important nodes in ape speciation, both prior to the infection of chimpanzees and gorillas with these viruses. These ancestral CD4s fully supported entry of diverse SIV isolates related to the viruses that made this initial jump to apes. In stark contrast, modern chimpanzee and gorilla CD4 orthologs are more resistant to these viruses. To investigate how this resistance in CD4 was gained, we acquired CD4 gene sequences from 32 gorilla individuals of two species, and identified alleles that encode 8 unique CD4 protein variants. Functional testing of these identified variant-specific differences in susceptibility to virus entry. By engineering single point mutations from resistant gorilla CD4 variants into the permissive human CD4 receptor, we demonstrate that acquired substitutions in gorilla CD4 did convey resistance to virus entry. We provide a population genetic analysis to support the theory that selection is acting in favor of more and more resistant CD4 alleles in ape species harboring SIV endemically (gorillas and chimpanzees), but not in other ape species that lack SIV infections (bonobos and orangutans). Taken together, our results show that SIV has placed intense selective pressure on ape CD4, acting to propagate SIV-resistant alleles in chimpanzee and gorilla populations.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Vanessa L. Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Alex C. Stabell
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Obaiah Dirasantha
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Qing Yang
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
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3
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Lear TB, Boudreau ÁN, Lockwood KC, Chu E, Camarco DP, Cao Q, Nguyen M, Evankovich JW, Finkel T, Liu Y, Chen BB. E3 ubiquitin ligase ZBTB25 suppresses beta coronavirus infection through ubiquitination of the main viral protease MPro. J Biol Chem 2023; 299:105388. [PMID: 37890782 PMCID: PMC10679490 DOI: 10.1016/j.jbc.2023.105388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The main protease of severe acute respiratory syndrome coronavirus 2, Mpro, is a key viral protein essential for viral infection and replication. Mpro has been the target of many pharmacological efforts; however, the host-specific regulation of Mpro protein remains unclear. Here, we report the ubiquitin-proteasome-dependent degradation of Mpro protein in human cells, facilitated by the human E3 ubiquitin ligase ZBTB25. We demonstrate that Mpro has a short half-life that is prolonged via proteasomal inhibition, with its Lys-100 residue serving as a potential ubiquitin acceptor. Using in vitro binding assays, we observed ZBTB25 and Mpro bind to each other in vitro, and using progressive deletional mapping, we further uncovered the required domains for this interaction. Finally, we used an orthologous beta-coronavirus infection model and observed that genetic ablation of ZBTB25 resulted in a more highly infective virus, an effect lost upon reconstitution of ZBTB25 to deleted cells. In conclusion, these data suggest a new mechanism of Mpro protein regulation as well as identify ZBTB25 as an anticoronaviral E3 ubiquitin ligase.
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Affiliation(s)
- Travis B Lear
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Áine N Boudreau
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Karina C Lockwood
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Elise Chu
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Daniel P Camarco
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - Qing Cao
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Matthew Nguyen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA
| | - John W Evankovich
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Toren Finkel
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuan Liu
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bill B Chen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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4
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Zheng Y, Yang H, Zhang X, Gao C. Regulation of SARS-CoV-2 infection and antiviral innate immunity by ubiquitination and ubiquitin-like conjugation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194984. [PMID: 37717938 DOI: 10.1016/j.bbagrm.2023.194984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
A global pandemic COVID-19 resulting from SARS-CoV-2 has affected a significant portion of the human population. Antiviral innate immunity is critical for controlling and eliminating the viral infection. Ubiquitination is extensively involved in antiviral signaling, and recent studies suggest that ubiquitin-like proteins (Ubls) modifications also participate in innate antiviral pathways such as RLR and cGAS-STING pathways. Notably, virus infection harnesses ubiquitination and Ubls modifications to facilitate viral replication and counteract innate antiviral immunity. These observations indicate that ubiquitination and Ubls modifications are critical checkpoints for the tug-of-war between virus and host. This review discusses the current progress regarding the modulation of the SARS-CoV-2 life cycle and antiviral innate immune pathways by ubiquitination and Ubls modifications. This paper emphasizes the arising concept that ubiquitination and Ubls modifications are powerful modulators of virus and host interaction and potential drug targets for treating the infection of SARS-CoV-2.
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Affiliation(s)
- Yi Zheng
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
| | - Huiyu Yang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Xuejing Zhang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
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Stewart H, Lu Y, O’Keefe S, Valpadashi A, Cruz-Zaragoza LD, Michel HA, Nguyen SK, Carnell GW, Lukhovitskaya N, Milligan R, Adewusi Y, Jungreis I, Lulla V, Matthews DA, High S, Rehling P, Emmott E, Heeney JL, Davidson AD, Edgar JR, Smith GL, Firth AE. The SARS-CoV-2 protein ORF3c is a mitochondrial modulator of innate immunity. iScience 2023; 26:108080. [PMID: 37860693 PMCID: PMC10583119 DOI: 10.1016/j.isci.2023.108080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 08/06/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
The SARS-CoV-2 genome encodes a multitude of accessory proteins. Using comparative genomic approaches, an additional accessory protein, ORF3c, has been predicted to be encoded within the ORF3a sgmRNA. Expression of ORF3c during infection has been confirmed independently by ribosome profiling. Despite ORF3c also being present in the 2002-2003 SARS-CoV, its function has remained unexplored. Here we show that ORF3c localizes to mitochondria, where it inhibits innate immunity by restricting IFN-β production, but not NF-κB activation or JAK-STAT signaling downstream of type I IFN stimulation. We find that ORF3c is inhibitory after stimulation with cytoplasmic RNA helicases RIG-I or MDA5 or adaptor protein MAVS, but not after TRIF, TBK1 or phospho-IRF3 stimulation. ORF3c co-immunoprecipitates with the antiviral proteins MAVS and PGAM5 and induces MAVS cleavage by caspase-3. Together, these data provide insight into an uncharacterized mechanism of innate immune evasion by this important human pathogen.
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Affiliation(s)
- Hazel Stewart
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Yongxu Lu
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Sarah O’Keefe
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Anusha Valpadashi
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | | | | | - George W. Carnell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Rachel Milligan
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Yasmin Adewusi
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Valeria Lulla
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - David A. Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Stephen High
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Edward Emmott
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew D. Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - James R. Edgar
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
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Kakoulidis P, Vlachos IS, Thanos D, Blatch GL, Emiris IZ, Anastasiadou E. Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon. Commun Biol 2023; 6:752. [PMID: 37468602 PMCID: PMC10356814 DOI: 10.1038/s42003-023-05076-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 06/26/2023] [Indexed: 07/21/2023] Open
Abstract
Using protein structure to predict function, interactions, and evolutionary history is still an open challenge, with existing approaches relying extensively on protein homology and families. Here, we present Machaon, a data-driven method combining orientation invariant metrics on phi-psi angles, inter-residue contacts and surface complexity. It can be readily applied on whole structures or segments-such as domains and binding sites. Machaon was applied on SARS-CoV-2 Spike monomers of native, Delta and Omicron variants and identified correlations with a wide range of viral proteins from close to distant taxonomy ranks, as well as host proteins, such as ACE2 receptor. Machaon's meta-analysis of the results highlights structural, chemical and transcriptional similarities between the Spike monomer and human proteins, indicating a multi-level viral mimicry. This extended analysis also revealed relationships of the Spike protein with biological processes such as ubiquitination and angiogenesis and highlighted different patterns in virus attachment among the studied variants. Available at: https://machaonweb.com .
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Affiliation(s)
- Panos Kakoulidis
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Ilisia, 157 84, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St., 115 27, Athens, Greece
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Merkin Building, 415 Main St., Cambridge, MA, 02142, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Dana Building, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA
| | - Dimitris Thanos
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St., 115 27, Athens, Greece
| | - Gregory L Blatch
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, PO Box 94, Makhanda (Grahamstown) 6140, Eastern Cape, South Africa
- Biomedical and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, PO 25026, Sharjah, UAE
- Institute for Health and Sport, Victoria University, Melbourne, PO Box 14428, VIC 8001, Melbourne, Australia
- The Vice Chancellery, The University of Notre Dame Australia, PO Box 1225, WA 6959, Fremantle, Australia
| | - Ioannis Z Emiris
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Ilisia, 157 84, Athens, Greece
- ATHENA Research and Innovation Center, Artemidos 6 & Epidavrou 15125, Marousi, Greece
| | - Ema Anastasiadou
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St., 115 27, Athens, Greece.
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7
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Zhao M, Zhang M, Yang Z, Zhou Z, Huang J, Zhao B. Role of E3 ubiquitin ligases and deubiquitinating enzymes in SARS-CoV-2 infection. Front Cell Infect Microbiol 2023; 13:1217383. [PMID: 37360529 PMCID: PMC10288995 DOI: 10.3389/fcimb.2023.1217383] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Ever since its emergence in 2019, COVID-19 has rapidly disseminated worldwide, engendering a pervasive pandemic that has profoundly impacted healthcare systems and the socio-economic milieu. A plethora of studies has been conducted targeting its pathogenic virus, SARS-CoV-2, to find ways to combat COVID-19. The ubiquitin-proteasome system (UPS) is widely recognized as a crucial mechanism that regulates human biological activities by maintaining protein homeostasis. Within the UPS, the ubiquitination and deubiquitination, two reversible modifications, of substrate proteins have been extensively studied and implicated in the pathogenesis of SARS-CoV-2. The regulation of E3 ubiquitin ligases and DUBs(Deubiquitinating enzymes), which are key enzymes involved in the two modification processes, determines the fate of substrate proteins. Proteins associated with the pathogenesis of SARS-CoV-2 may be retained, degraded, or even activated, thus affecting the ultimate outcome of the confrontation between SARS-CoV-2 and the host. In other words, the clash between SARS-CoV-2 and the host can be viewed as a battle for dominance over E3 ubiquitin ligases and DUBs, from the standpoint of ubiquitin modification regulation. This review primarily aims to clarify the mechanisms by which the virus utilizes host E3 ubiquitin ligases and DUBs, along with its own viral proteins that have similar enzyme activities, to facilitate invasion, replication, escape, and inflammation. We believe that gaining a better understanding of the role of E3 ubiquitin ligases and DUBs in COVID-19 can offer novel and valuable insights for developing antiviral therapies.
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Affiliation(s)
- Mingjiu Zhao
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Mengdi Zhang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhou Yang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jiaqi Huang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Bin Zhao
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Furong Laboratory, Central South University, Changsha, China
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Park JW, Tyl MD, Cristea IM. Orchestration of Mitochondrial Function and Remodeling by Post-Translational Modifications Provide Insight into Mechanisms of Viral Infection. Biomolecules 2023; 13:biom13050869. [PMID: 37238738 DOI: 10.3390/biom13050869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The regulation of mitochondria structure and function is at the core of numerous viral infections. Acting in support of the host or of virus replication, mitochondria regulation facilitates control of energy metabolism, apoptosis, and immune signaling. Accumulating studies have pointed to post-translational modification (PTM) of mitochondrial proteins as a critical component of such regulatory mechanisms. Mitochondrial PTMs have been implicated in the pathology of several diseases and emerging evidence is starting to highlight essential roles in the context of viral infections. Here, we provide an overview of the growing arsenal of PTMs decorating mitochondrial proteins and their possible contribution to the infection-induced modulation of bioenergetics, apoptosis, and immune responses. We further consider links between PTM changes and mitochondrial structure remodeling, as well as the enzymatic and non-enzymatic mechanisms underlying mitochondrial PTM regulation. Finally, we highlight some of the methods, including mass spectrometry-based analyses, available for the identification, prioritization, and mechanistic interrogation of PTMs.
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Affiliation(s)
- Ji Woo Park
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Matthew D Tyl
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
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Tavakoli R, Rahimi P, Hamidi-Fard M, Eybpoosh S, Doroud D, Sadeghi SA, Zaheri Birgani M, Aghasadeghi M, Fateh A. Impact of TRIM5α and TRIM22 Genes Expression on the Clinical Course of Coronavirus Disease 2019. Arch Med Res 2023; 54:105-112. [PMID: 36621405 PMCID: PMC9794484 DOI: 10.1016/j.arcmed.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/30/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
OBJECTIVE The innate immune response in humans involves a wide variety of factors, including the tripartite motif-containing 5α (TRIM5α) and 22 (TRIM22) as a cluster of genes on chromosome 11 that have exhibited antiviral activity in several viral infections. We analyzed the correlation of the expression of TRIM5α and TRIM22 with the severity of Coronavirus Disease 2019 (COVID-19) in blood samples of 330 patients, divided into two groups of severe and mild disease, versus the healthy individuals who never had contact with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). METHODS The transcription level of TRIM5α and TRIM22 was determined by quantitative real-time polymerase chain reaction (qPCR). The laboratory values were collected from the patients' records. RESULTS The expression of both genes was significantly lower in the severe group containing the hospitalized patients than in both the mild group and the control group. However, in the mild group, TRIM22 expression was significantly higher (p <0.0001) than in the control group while TRIM5α expression was not significantly different between these two groups. We found a relationship between the cycle threshold (Ct) value of patients and the expression of the aforementioned genes. CONCLUSION The results of our study indicated that lower Ct values or higher RNA viral load might be associated with the downregulation of TRIM5α and TRIM22 and the severity of COVID-19. Additional studies are needed to confirm the results of this study.
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Affiliation(s)
- Rezvan Tavakoli
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran
| | - Pooneh Rahimi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran; Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Hamidi-Fard
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran; Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Delaram Doroud
- Quality Control Department, Production and Research Complex, Pasteur institute of Iran, Tehran, Iran
| | | | | | - Mohammadreza Aghasadeghi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran; Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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10
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Cheng N, Liu M, Li W, Sun B, Liu D, Wang G, Shi J, Li L. Protein post-translational modification in SARS-CoV-2 and host interaction. Front Immunol 2023; 13:1068449. [PMID: 36713387 PMCID: PMC9880545 DOI: 10.3389/fimmu.2022.1068449] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
SARS-CoV-2 can cause lung diseases, such as pneumonia and acute respiratory distress syndrome, and multi-system dysfunction. Post-translational modifications (PTMs) related to SARS-CoV-2 are conservative and pathogenic, and the common PTMs are glycosylation, phosphorylation, and acylation. The glycosylation of SARS-CoV-2 mainly occurs on spike (S) protein, which mediates the entry of the virus into cells through interaction with angiotensin-converting enzyme 2. SARS-CoV-2 utilizes glycans to cover its epitopes and evade the immune response through glycosylation of S protein. Phosphorylation of SARS-CoV-2 nucleocapsid (N) protein improves its selective binding to viral RNA and promotes viral replication and transcription, thereby increasing the load of the virus in the host. Succinylated N and membrane(M) proteins of SARS-CoV-2 synergistically affect virus particle assembly. N protein regulates its affinity for other proteins and the viral genome through acetylation. The acetylated envelope (E) protein of SARS-CoV-2 interacts with bromodomain-containing protein 2/4 to influence the host immune response. Both palmitoylation and myristoylation sites on S protein can affect the virus infectivity. Papain-like protease is a domain of NSP3 that dysregulates host inflammation by deubiquitination and impinges host IFN-I antiviral immune responses by deISGylation. Ubiquitination of ORF7a inhibits host IFN-α signaling by blocking STAT2 phosphorylation. The methylation of N protein can inhibit the formation of host stress granules and promote the binding of N protein to viral RNA, thereby promoting the production of virus particles. NSP3 macrodomain can reverse the ADP-ribosylation of host proteins, and inhibit the cascade immune response with IFN as the core, thereby promoting the intracellular replication of SARS-CoV-2. On the whole, PTMs have fundamental roles in virus entry, replication, particle assembly, and host immune response. Mutations in various SARS-CoV-2 variants, which lead to changes in PTMs at corresponding sites, cause different biological effects. In this paper, we mainly reviewed the effects of PTMs on SARS-CoV-2 and host cells, whose application is to inform the strategies for inhibiting viral infection and facilitating antiviral treatment and vaccine development for COVID-19.
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Affiliation(s)
- Nana Cheng
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
| | - Mingzhu Liu
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - Wanting Li
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - BingYue Sun
- First Affiliated Hospital of Jilin University, Changchun, China
| | - Dandan Liu
- First Affiliated Hospital of Jilin University, Changchun, China
| | - Guoqing Wang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis Research, Chinese Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Jingwei Shi
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
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11
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Che Y, Jiang D, Zhang Y, Zhang J, Xu T, Sun Y, Fan J, Wang J, Chang N, Wu Y, Yang S, Xu L, Ding J, Hu C, Huang Y, Zhang J, Yang K. Elevated ubiquitination contributes to protective immunity against severe SARS-CoV-2 infection. Clin Transl Med 2022; 12:e1103. [PMID: 36447039 PMCID: PMC9708907 DOI: 10.1002/ctm2.1103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The crosstalk between the ubiquitin-proteasome and the immune system plays an important role in the health and pathogenesis of viral infection. However, there have been few studies of ubiquitin activation in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. METHODS We investigated the effect of ubiquitination on SARS-CoV-2 infection and patient prognosis by integrating published coronavirus disease 2019 (COVID-19) multi-transcriptome data and bioinformatics methods. RESULTS The differential expression of COVID-19 samples revealed changed ubiquitination in most solid and hollow organs, and it was activated in lymphatic and other immune tissues. In addition, in the respiratory system of COVID-19 patients, the immune response was mainly focused on the alveoli, and the expression of ubiquitination reflected increasing immune infiltration. Ubiquitination stratification could significantly differentiate patients' prognosis and inflammation levels through the general transcriptional analysis of the peripheral blood of patients with COVID-19. Moreover, high ubiquitination levels were associated with a favourable prognosis, low inflammatory response, and reduced mechanical ventilation and intensive care unit. Moreover, high ubiquitination promoted a beneficial immune response while inhibiting immune damage. Finally, prognostic stratification and biomarker screening based on ubiquitination traits played an important role in clinical management and drug development. CONCLUSION Ubiquitination characteristics provides new ideas for clinical intervention and prognostic guidance for COVID-19 patients.
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Affiliation(s)
- Yinggang Che
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
- Department of Respiratory MedicineXijing HospitalAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Dongbo Jiang
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
- The Key Laboratory of Medicine for Bio‐Hazard Prevention and Treatment of People's Liberation ArmyBasic Medicine School, Air‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Yong Zhang
- Department of Respiratory MedicineXijing HospitalAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Junqi Zhang
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Tianqi Xu
- Department of Respiratory MedicineXijing HospitalAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Yuanjie Sun
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Jiangjiang Fan
- Department of Thoracic SurgeryTangdu HospitalAir‐Force Medical UniversityXi'anShaanxiChina
| | - Jiawei Wang
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Ning Chang
- Department of Respiratory MedicineXijing HospitalAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Yingtong Wu
- First Sanatorium of Air Force Healthcare Center for Special ServicesHangzhouZhejiangChina
| | - Shuya Yang
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Leidi Xu
- Department of Respiratory MedicineXijing HospitalAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Jiaqi Ding
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Chenchen Hu
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Yinan Huang
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Jian Zhang
- Department of Respiratory MedicineXijing HospitalAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
| | - Kun Yang
- Department of ImmunologyBasic Medicine SchoolAir‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
- The Key Laboratory of Medicine for Bio‐Hazard Prevention and Treatment of People's Liberation ArmyBasic Medicine School, Air‐Force Medical University (The Fourth Military Medical University)Xi'anShaanxiChina
- Department of Rheumatology and ImmunologyTangdu HospitalAir‐Force Medical UniversityXi'anShaanxiChina
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12
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Onisiforou A, Spyrou GM. Systems Bioinformatics Reveals Possible Relationship between COVID-19 and the Development of Neurological Diseases and Neuropsychiatric Disorders. Viruses 2022; 14:v14102270. [PMID: 36298824 PMCID: PMC9611753 DOI: 10.3390/v14102270] [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: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19) is associated with increased incidence of neurological diseases and neuropsychiatric disorders after infection, but how it contributes to their development remains under investigation. Here, we investigate the possible relationship between COVID-19 and the development of ten neurological disorders and three neuropsychiatric disorders by exploring two pathological mechanisms: (i) dysregulation of host biological processes via virus-host protein-protein interactions (PPIs), and (ii) autoreactivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epitopes with host "self" proteins via molecular mimicry. We also identify potential genetic risk factors which in combination with SARS-CoV-2 infection might lead to disease development. Our analysis indicated that neurodegenerative diseases (NDs) have a higher number of disease-associated biological processes that can be modulated by SARS-CoV-2 via virus-host PPIs than neuropsychiatric disorders. The sequence similarity analysis indicated the presence of several matching 5-mer and/or 6-mer linear motifs between SARS-CoV-2 epitopes with autoreactive epitopes found in Alzheimer's Disease (AD), Parkinson's Disease (PD), Myasthenia Gravis (MG) and Multiple Sclerosis (MS). The results include autoreactive epitopes that recognize amyloid-beta precursor protein (APP), microtubule-associated protein tau (MAPT), acetylcholine receptors, glial fibrillary acidic protein (GFAP), neurofilament light polypeptide (NfL) and major myelin proteins. Altogether, our results suggest that there might be an increased risk for the development of NDs after COVID-19 both via autoreactivity and virus-host PPIs.
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13
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Adams C, Boonen K, Laukens K, Bittremieux W. Open Modification Searching of SARS-CoV-2-Human Protein Interaction Data Reveals Novel Viral Modification Sites. Mol Cell Proteomics 2022; 21:100425. [PMID: 36241021 PMCID: PMC9554009 DOI: 10.1016/j.mcpro.2022.100425] [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: 03/16/2022] [Revised: 09/18/2022] [Accepted: 10/09/2022] [Indexed: 01/18/2023] Open
Abstract
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus 2019 disease, has led to an ongoing global pandemic since 2019. Mass spectrometry can be used to understand the molecular mechanisms of viral infection by SARS-CoV-2, for example, by determining virus-host protein-protein interactions through which SARS-CoV-2 hijacks its human hosts during infection, and to study the role of post-translational modifications. We have reanalyzed public affinity purification-mass spectrometry data using open modification searching to investigate the presence of post-translational modifications in the context of the SARS-CoV-2 virus-host protein-protein interaction network. Based on an over twofold increase in identified spectra, our detected protein interactions show a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. In addition, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. A detailed analysis of relevant modifications, including phosphorylation, ubiquitination, and S-nitrosylation, provides important hypotheses about the functional role of these modifications during viral infection by SARS-CoV-2.
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Affiliation(s)
- Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium,Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium,Sustainable Health Department, Flemish Institute for Technological Research (VITO), Antwerp, Belgium
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,For correspondence: Wout Bittremieux
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14
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Association between Mutations in Papain-like Protease (PLpro) of SARS-CoV-2 with COVID-19 Clinical Outcomes. Pathogens 2022; 11:pathogens11091008. [PMID: 36145442 PMCID: PMC9501953 DOI: 10.3390/pathogens11091008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 12/01/2022] Open
Abstract
Papain-like protease (PLpro) is important for the replication and transcription of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to reveal the PLpro mutations associated with the clinical outcomes of patients. Due to the importance of the S protein in the pathogenicity of SARS-CoV-2, the mutation of the S protein was also analyzed in this study. After downloading the data from the Global Initiative on Sharing Avian Influenza Data (GISAID) database, samples were divided into two groups on the basis of patient status, namely, recovered and dead groups. This study performed a univariate analysis and further explored the association of mutations with patient outcomes through multivariate logistic regression analysis. A total of 138,492 samples were used for analysis. The patients had a mean age of 43.66 ± 21.56 years, and 51.3% of them were female. Multivariate logistic regression results showed that, compared with men, women had a lower risk of dying from coronavirus disease 2019 (COVID-19) (OR = 0.687, 95%CI: 0.638–0.740). Compared with patients aged 17 years and younger, patients aged 18–64 years (OR = 2.864, 95%CI: 1.982–4.139) and patients over 65 years old (OR = 19.135, 95%CI: 13.280–27.572) had a higher risk of death after infection. Compared with the wild type, P78L (OR = 5.185, 95%CI: 2.763–9.730) and K233Q (OR = 5.154, 95%CI: 1.442–18.416) in PLpro were associated with an increased risk of death. A synergistic interaction existed between age and mutations A146D and P78L. The results of the multivariate logistic regression analysis of the data on vaccinated patients demonstrated that, compared with the wild type, the P78L (OR = 3.376, 95%CI: 2.040–5.585) mutation was associated with an increased risk of death. In conclusion, compared with the wild-type PLpro protein, the P78L and K233Q mutations may increase the risk of death in infected individuals. In addition, a synergistic effect existed between age and P78L and K233Q that increased the risk of death in older patients.
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15
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Nishitsuji H, Iwahori S, Ohmori M, Shimotohno K, Murata T. Ubiquitination of SARS-CoV-2 NSP6 and ORF7a Facilitates NF-κB Activation. mBio 2022; 13:e0097122. [PMID: 35856559 PMCID: PMC9426613 DOI: 10.1128/mbio.00971-22] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/01/2022] [Indexed: 11/20/2022] Open
Abstract
Patients with severe coronavirus disease 2019 tend to have high levels of proinflammatory cytokines, which eventually lead to cytokine storm and the development of acute respiratory distress syndrome. However, the detailed molecular mechanisms of proinflammatory cytokine production remain unknown. Here, we screened severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes and found that nonstructural protein 6 (NSP6) and open reading frame 7a (ORF7a) activated the NF-κB pathway. NSP6 and ORF7a interacted with transforming growth factor β-activated kinase 1 (TAK1), and knockout (KO) of TAK1 or NF-κB essential modulator (NEMO) abolished NF-κB activation by NSP6 and ORF7a. Interestingly, K61 of NSP6 was conjugated to K63-linked polyubiquitin chains by the E3 ubiquitin ligase tripartite motif-containing 13, and this polyubiquitination of NSP6 appeared crucial for recruitment of NEMO to the NSP6-TAK1 complex and NF-κB activation. On the other hand, ring finger protein 121 (RNF121) was required for the polyubiquitination of ORF7a. Knockdown of RNF121 significantly decreased ORF7a binding of TAK1 and NEMO, resulting in the suppression of NF-κB activation. Taken together, our results provide novel molecular insights into the pathogenesis of SARS-CoV-2 and the host immune response to SARS-CoV-2 infection. IMPORTANCE The detailed molecular basis of the induction of proinflammatory cytokines and chemokines by SARS-CoV-2 is unclear, although such induction is clearly related to the severity of COVID-19. Here, we show that SARS-CoV-2 NSP6 and ORF7a lead to NF-κB activation through associations with TAK1. K63-linked polyubiquitination of NSP6 and ORF7a by TRIM13 and RNF121, respectively, appears essential for NF-κB activation. These results suggest that inhibition of the NSP6 and ORF7a gene products may reduce the severity of COVID-19 symptoms by decreasing proinflammatory cytokine levels.
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Affiliation(s)
- Hironori Nishitsuji
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Aichi, Japan
| | - Satoko Iwahori
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Aichi, Japan
| | - Mariko Ohmori
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Aichi, Japan
| | - Kunitada Shimotohno
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Aichi, Japan
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16
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Hou L, Du J, Ren Q, Zhu L, Zhao X, Kong X, Gu W, Wang L, Meng Q. Ubiquitin-modified proteome analysis of Eriocheir sinensis hemocytes during Spiroplasma eriocheiris infection. FISH & SHELLFISH IMMUNOLOGY 2022; 125:109-119. [PMID: 35500876 DOI: 10.1016/j.fsi.2022.04.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Spiroplasma eriocheiris, the pathogen of Eriocheir sinensis tremor disease (TD), has bring a huge economic loss to China aquaculture. The hemocytes of crab as the first target cells of S. eriocheiris, but the interactive relationship between the E. sinensis and this pathogen not particularly clear. The present study is the first time to analysis the role of protein ubiquitination in the process of E. sinensis hemocytes response S. eriocheiris infection. By applying label-free quantitative liquid chromatography with tandem mass spectrometry proteomics, 950 lysine ubiquitination sites and 803 ubiquitination peptides on 458 proteins were identified, of which 48 ubiquitination sites on 40 proteins were quantified as significantly changed after the S. eriocheiris infection. Bioinformatics analysis of ubiquitination different proteins suggested many biological process and pathways were participated in the interaction between S. eriocheiris and host cell, such as ubiquitin system, endocytosis, prophenoloxidase system (proPO system), cell apoptosis, glycolysis. Our study can enhance our understanding of interaction between the crab and S. eriocheiris, and also provides basis to study the role of protein ubiquitination in other crustacean innate immune system.
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Affiliation(s)
- Libo Hou
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Jie Du
- Animal Husbandry and Veterinary College, Jiangsu Vocational College of Agriculture and Forestry, Jurong, Jiangsu, 212400, China
| | - Qiulin Ren
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Lei Zhu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xianliang Zhao
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xianghui Kong
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Wei Gu
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, 2 Xuelin Road, Nanjing, 210046, China
| | - Li Wang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China.
| | - Qingguo Meng
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, 2 Xuelin Road, Nanjing, 210046, China.
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17
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Israeli M, Finkel Y, Yahalom-Ronen Y, Paran N, Chitlaru T, Israeli O, Cohen-Gihon I, Aftalion M, Falach R, Rotem S, Elia U, Nemet I, Kliker L, Mandelboim M, Beth-Din A, Israely T, Cohen O, Stern-Ginossar N, Bercovich-Kinori A. Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2. Nat Commun 2022; 13:2237. [PMID: 35469023 PMCID: PMC9039069 DOI: 10.1038/s41467-022-29896-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
The global spread of SARS-CoV-2 led to major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SARS-CoV-2 can provide insights into the virus pathogenesis, and facilitate the development of novel therapeutics. Here, employing a genome-scale CRISPR screen, we provide a comprehensive data-set of cellular factors that are exploited by wild type SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. We identified several host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination, Heparan sulfate biogenesis and host phosphatidylglycerol biosynthesis. Comparative analysis of the different VOCs revealed the host factors KREMEN2 and SETDB1 as potential unique candidates required only to the Alpha variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential proviral gene for all variants inspected. We show that GATA6 directly regulates ACE2 transcription and accordingly, is critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals shows elevated levels of GATA6, suggesting a role in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 resulted in down-modulation of ACE2 and inhibition of viral infectivity. Overall, we show GATA6 may represent a target for the development of anti-SARS-CoV-2 therapeutic strategies and reaffirm the value of the CRISPR loss-of-function screens in providing a list of potential new targets for therapeutic interventions.
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Affiliation(s)
- Ma'ayan Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Theodor Chitlaru
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Moshe Aftalion
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Reut Falach
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shahar Rotem
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Uri Elia
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ital Nemet
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Limor Kliker
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofer Cohen
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Bercovich-Kinori
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
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18
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A BioID-Derived Proximity Interactome for SARS-CoV-2 Proteins. Viruses 2022; 14:v14030611. [PMID: 35337019 PMCID: PMC8951556 DOI: 10.3390/v14030611] [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] [Received: 02/10/2022] [Revised: 03/09/2022] [Accepted: 03/12/2022] [Indexed: 12/11/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 is responsible for the ongoing COVID-19 pandemic and has caused a major health and economic burden worldwide. Understanding how SARS-CoV-2 viral proteins behave in host cells can reveal underlying mechanisms of pathogenesis and assist in development of antiviral therapies. Here, the cellular impact of expressing SARS-CoV-2 viral proteins was studied by global proteomic analysis, and proximity biotinylation (BioID) was used to map the SARS-CoV-2 virus–host interactome in human lung cancer-derived cells. Functional enrichment analyses revealed previously reported and unreported cellular pathways that are associated with SARS-CoV-2 proteins. We have established a website to host the proteomic data to allow for public access and continued analysis of host–viral protein associations and whole-cell proteomes of cells expressing the viral–BioID fusion proteins. Furthermore, we identified 66 high-confidence interactions by comparing this study with previous reports, providing a strong foundation for future follow-up studies. Finally, we cross-referenced candidate interactors with the CLUE drug library to identify potential therapeutics for drug-repurposing efforts. Collectively, these studies provide a valuable resource to uncover novel SARS-CoV-2 biology and inform development of antivirals.
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19
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Cai C, Tang YD, Zheng C. When RING Finger Family Proteins meet SARS-CoV-2. J Med Virol 2022; 94:2977-2985. [PMID: 35257387 DOI: 10.1002/jmv.27701] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
Abstract
The pandemic coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently the most formidable challenge to humans. Understanding the complicated virus-host interplay is crucial for fighting against viral infection. A growing number of studies point to the critical roles of RING (really interesting new gene) finger (RNF) proteins during SARS-CoV-2 infection. RNF proteins exert direct antiviral activity by targeting genome and envelope glycoproteins of SARS-CoV-2. Additionally, some RNF members serve as potent regulators for antiviral innate immunity and antibody-dependent neutralization of SARS-CoV-2. Notably, SARS-CoV-2 also hijacks the RNF proteins-mediated ubiquitination process to evade host antiviral innate immunity and enhance viral replication. In this mini-review, we discuss the diverse antiviral mechanisms of RNF proteins and viral immune evasion in an RNF proteins-dependent manner. Understanding the crosstalk between RNF proteins and SARS-CoV-2 infection would help design potential novel targets for COVID-19 treatment. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chunmei Cai
- Research Center for High Altitude Medicine, School of Medical, Qinghai University, Xining, China.,Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province, Qinghai University, Xining, China
| | - Yan-Dong Tang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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20
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Vere G, Alam MR, Farrar S, Kealy R, Kessler BM, O’Brien DP, Pinto-Fernández A. Targeting the Ubiquitylation and ISGylation Machinery for the Treatment of COVID-19. Biomolecules 2022; 12:biom12020300. [PMID: 35204803 PMCID: PMC8869442 DOI: 10.3390/biom12020300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Ubiquitylation and ISGylation are protein post-translational modifications (PTMs) and two of the main events involved in the activation of pattern recognition receptor (PRRs) signals allowing the host defense response to viruses. As with similar viruses, SARS-CoV-2, the virus causing COVID-19, hijacks these pathways by removing ubiquitin and/or ISG15 from proteins using a protease called PLpro, but also by interacting with enzymes involved in ubiquitin/ISG15 machinery. These enable viral replication and avoidance of the host immune system. In this review, we highlight potential points of therapeutic intervention in ubiquitin/ISG15 pathways involved in key host-pathogen interactions, such as PLpro, USP18, TRIM25, CYLD, A20, and others that could be targeted for the treatment of COVID-19, and which may prove effective in combatting current and future vaccine-resistant variants of the disease.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Md Rashadul Alam
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Sam Farrar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Rachel Kealy
- Environmental Futures & Big Data Impact Lab, University of Exeter, Stocker Rd., Exeter EX4 4PY, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Darragh P. O’Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Correspondence: (D.P.O.); (A.P.-F.)
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (D.P.O.); (A.P.-F.)
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21
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From Drosophila to Human: Biological Function of E3 Ligase Godzilla and Its Role in Disease. Cells 2022; 11:cells11030380. [PMID: 35159190 PMCID: PMC8834447 DOI: 10.3390/cells11030380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/29/2022] Open
Abstract
The ubiquitin–proteasome system is of fundamental importance in all fields of biology due to its impact on proteostasis and in regulating cellular processes. Ubiquitination, a type of protein post-translational modification, involves complex enzymatic machinery, such as E3 ubiquitin ligases. The E3 ligases regulate the covalent attachment of ubiquitin to a target protein and are involved in various cellular mechanisms, including the cell cycle, cell division, endoplasmic reticulum stress, and neurotransmission. Because the E3 ligases regulate so many physiological events, they are also associated with pathologic conditions, such as cancer, neurological disorders, and immune-related diseases. This review focuses specifically on the protease-associated transmembrane-containing the Really Interesting New Gene (RING) subset of E3 ligases. We describe the structure, partners, and physiological functions of the Drosophila Godzilla E3 ligase and its human homologues, RNF13, RNF167, and ZNRF4. Also, we summarize the information that has emerged during the last decade regarding the association of these E3 ligases with pathophysiological conditions, such as cancer, asthma, and rare genetic disorders. We conclude by highlighting the limitations of the current knowledge and pinpointing the unresolved questions relevant to RNF13, RNF167, and ZNRF4 ubiquitin ligases.
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22
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Long S, Yang L, Dang W, Xin S, Jiang M, Zhang W, Li J, Wang Y, Zhang S, Lu J. Cellular Deubiquitylating Enzyme: A Regulatory Factor of Antiviral Innate Immunity. Front Microbiol 2021; 12:805223. [PMID: 34966378 PMCID: PMC8710732 DOI: 10.3389/fmicb.2021.805223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Deubiquitylating enzymes (DUBs) are proteases that crack the ubiquitin code from ubiquitylated substrates to reverse the fate of substrate proteins. Recently, DUBs have been found to mediate various cellular biological functions, including antiviral innate immune response mediated by pattern-recognition receptors (PRRs) and NLR Family pyrin domain containing 3 (NLRP3) inflammasomes. So far, many DUBs have been identified to exert a distinct function in fine-tuning antiviral innate immunity and are utilized by viruses for immune evasion. Here, the recent advances in the regulation of antiviral responses by DUBs are reviewed. We also discussed the DUBs-mediated interaction between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and antiviral innate immunity. The understanding of the mechanisms on antiviral innate immunity regulated by DUBs may provide therapeutic opportunities for viral infection.
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Affiliation(s)
- Sijing Long
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Li Yang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Wei Dang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Shuyu Xin
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Mingjuan Jiang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Wentao Zhang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Jing Li
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Yiwei Wang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Senmiao Zhang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Jianhong Lu
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
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23
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Cakir M, Obernier K, Forget A, Krogan NJ. Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. mSystems 2021; 6:e0038821. [PMID: 34519533 PMCID: PMC8547474 DOI: 10.1128/msystems.00388-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Current epidemics, such as AIDS or flu, and the emergence of new threatening pathogens, such as the one causing the current coronavirus disease 2019 (COVID-19) pandemic, represent major global health challenges. While vaccination is an important part of the arsenal to counter the spread of viral diseases, it presents limitations and needs to be complemented by efficient therapeutic solutions. Intricate knowledge of host-pathogen interactions is a powerful tool to identify host-dependent vulnerabilities that can be exploited to dampen viral replication. Such host-directed antiviral therapies are promising and are less prone to the development of drug-resistant viral strains. Here, we first describe proteomics-based strategies that allow the rapid characterization of host-pathogen interactions. We then discuss how such data can be exploited to help prioritize compounds with potential host-directed antiviral activity that can be tested in preclinical models.
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Affiliation(s)
- Merve Cakir
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
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24
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Reddy R, Efimenko I, Chertman W, Kohn T, Diaz P, Seetharam D, Khodamoradi K, Kresch E, Ramasamy R. Whole Exome Sequencing Identifies a Rare Mutation in NACAD as a Possible Cause of COVID Orchitis in Brothers. Urology 2021; 159:83-86. [PMID: 34678309 PMCID: PMC8526121 DOI: 10.1016/j.urology.2021.09.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/20/2021] [Accepted: 09/26/2021] [Indexed: 12/22/2022]
Abstract
COVID orchitis (testicular pain) is reported in 10-15% of men with long COVID. We identified 2 siblings with COVID orchitis and hypothesized that genetic mutations are associated with susceptibility. Blood samples from 5 COVID-19 (+) men, three of whom had orchitis were evaluated by whole-exome-sequencing. A rare deletion on chromosome 7 was found in NACAD among the 3 men with orchitis. Interestingly, circulating ACE2 levels was decreased in men with COVID orchitis. This pilot study generated the hypothesis that men who develop COVID orchitis could have underlying genetic variants and altered levels in circulating ACE2 that may increase their risk.
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Affiliation(s)
- Rohit Reddy
- Miller School of Medicine, University of Miami 1120 NW 14th Street, Miami, FL
| | - Iakov Efimenko
- Miller School of Medicine, University of Miami 1120 NW 14th Street, Miami, FL
| | - Willy Chertman
- Miller School of Medicine, University of Miami 1120 NW 14th Street, Miami, FL
| | - Taylor Kohn
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Parris Diaz
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL
| | - Deepa Seetharam
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL
| | - Kajal Khodamoradi
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL
| | - Eliyahu Kresch
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL
| | - Ranjith Ramasamy
- Department of Urology, University of Miami Miller School of Medicine, Miami, FL.
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25
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May DG, Martin-Sancho L, Anschau V, Liu S, Chrisopulos RJ, Scott KL, Halfmann CT, Peña RD, Pratt D, Campos AR, Roux KJ. A BioID-derived proximity interactome for SARS-CoV-2 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34580671 PMCID: PMC8475972 DOI: 10.1101/2021.09.17.460814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The novel coronavirus SARS-CoV-2 is responsible for the ongoing COVID-19 pandemic and has caused a major health and economic burden worldwide. Understanding how SARS-CoV-2 viral proteins behave in host cells can reveal underlying mechanisms of pathogenesis and assist in development of antiviral therapies. Here we use BioID to map the SARS-CoV-2 virus-host interactome using human lung cancer derived A549 cells expressing individual SARS-CoV-2 viral proteins. Functional enrichment analyses revealed previously reported and unreported cellular pathways that are in association with SARS-CoV-2 proteins. We have also established a website to host the proteomic data to allow for public access and continued analysis of host-viral protein associations and whole-cell proteomes of cells expressing the viral-BioID fusion proteins. Collectively, these studies provide a valuable resource to potentially uncover novel SARS-CoV-2 biology and inform development of antivirals.
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26
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Lee WS, Yousefi M, Yan B, Yong CL, Ooi YS. Know your enemy and know yourself - the case of SARS-CoV-2 host factors. Curr Opin Virol 2021; 50:159-170. [PMID: 34488003 PMCID: PMC8379091 DOI: 10.1016/j.coviro.2021.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/10/2021] [Accepted: 08/14/2021] [Indexed: 02/06/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent that causes Coronavirus Disease 2019 (COVID-19) pandemic, is a newly emerging respiratory RNA virus with exceptional transmissibility and pathogenicity. Numerous COVID-19 related studies have been fast-tracked, with the ultimate goal to end the pandemic. Here we review the major stages of SARS-CoV-2 infection cycle in cells, with specific emphasis on essential host factors. Insights into the cell biology of SARS-CoV-2 infection have accelerated the development of host-directed therapeutics, as shown by dozens of clinical trials evaluating COVID-19 treatments using host-targeting compounds.
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Affiliation(s)
- Wai Suet Lee
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Meisam Yousefi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Biaoguo Yan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Cythia Lingli Yong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Yaw Shin Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore.
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27
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Grossegesse M, Leupold P, Doellinger J, Schaade L, Nitsche A. Inactivation of Coronaviruses during Sample Preparation for Proteomics Experiments. J Proteome Res 2021; 20:4598-4602. [PMID: 34432478 PMCID: PMC8406924 DOI: 10.1021/acs.jproteome.1c00320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 12/24/2022]
Abstract
Mass spectrometry-based proteomics is applied in SARS-CoV-2 research and is, moreover, being discussed as a novel method for SARS-CoV-2 diagnostics. However, the safe inactivation of coronaviruses by proteomics lysis buffers has not been systematically analyzed yet. Hence, for safety reasons a heating step prior to sample preparation is often performed. This step could be omitted once the safe inactivation with the typical buffers is proven. Here we test five different proteomics lysis buffers-4% SDS, 1% SDC, TFA, 6 M GdmCl, and 8 M urea-for their inactivation capacity of coronaviruses. Two representative human coronaviruses, namely HCoV-229E and HCoV-OC43, were used as surrogate for SARS-CoV-2. Lysis was performed at room temperature and at 95 °C for 5 min. Inactivation was confirmed by the absence of a cytopathic effect in MRC-5 cells, and equivocal results were further confirmed by serial passaging and quantitative real-time PCR. While at room temperature SDS, SDC, and TFA inactivated both coronaviruses, and GdmCl and urea resulted in partially incomplete inactivation. This demonstrates that care should be taken when choosing lysis buffers for proteomics analysis of coronaviruses, because some buffers do not ensure inactivation and, hence, biosafety during the further sample preparation.
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Affiliation(s)
- Marica Grossegesse
- Robert
Koch Institute, Centre for Biological
Threats and Special Pathogens, ZBS 1: Highly Pathogenic Viruses, Seestr. 10, 13353, Berlin, Germany
| | - Paula Leupold
- Robert
Koch Institute, Centre for Biological
Threats and Special Pathogens, ZBS 1: Highly Pathogenic Viruses, Seestr. 10, 13353, Berlin, Germany
| | - Joerg Doellinger
- Robert
Koch Institute, Centre for Biological
Threats and Special Pathogens, ZBS 1: Highly Pathogenic Viruses, Seestr. 10, 13353, Berlin, Germany
- Robert
Koch Institute, Centre for Biological
Threats and Special Pathogens, ZBS 6: Proteomics and Spectroscopy, Seestr. 10, 13353, Berlin, Germany
| | - Lars Schaade
- Robert
Koch Institute, Centre for Biological Threats and Special Pathogens, Seestr. 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Robert
Koch Institute, Centre for Biological
Threats and Special Pathogens, ZBS 1: Highly Pathogenic Viruses, Seestr. 10, 13353, Berlin, Germany
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28
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Yang J, Yan Y, Zhong W. Application of omics technology to combat the COVID-19 pandemic. MedComm (Beijing) 2021; 2:381-401. [PMID: 34766152 PMCID: PMC8554664 DOI: 10.1002/mco2.90] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
As of August 27, 2021, the ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to over 220 countries, areas, and territories. Thus far, 214,468,601 confirmed cases, including 4,470,969 deaths, have been reported to the World Health Organization. To combat the COVID-19 pandemic, multiomics-based strategies, including genomics, transcriptomics, proteomics, and metabolomics, have been used to study the diagnosis methods, pathogenesis, prognosis, and potential drug targets of COVID-19. In order to help researchers and clinicians to keep up with the knowledge of COVID-19, we summarized the most recent progresses reported in omics-based research papers. This review discusses omics-based approaches for studying COVID-19, summarizing newly emerged SARS-CoV-2 variants as well as potential diagnostic methods, risk factors, and pathological features of COVID-19. This review can help researchers and clinicians gain insight into COVID-19 features, providing direction for future drug development and guidance for clinical treatment, so that patients can receive appropriate treatment as soon as possible to reduce the risk of disease progression.
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Affiliation(s)
- Jingjing Yang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
- School of Pharmaceutical SciencesHainan UniversityHaikouHainanChina
| | - Yunzheng Yan
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Wu Zhong
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
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29
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Tovo PA, Garazzino S, Daprà V, Pruccoli G, Calvi C, Mignone F, Alliaudi C, Denina M, Scolfaro C, Zoppo M, Licciardi F, Ramenghi U, Galliano I, Bergallo M. COVID-19 in Children: Expressions of Type I/II/III Interferons, TRIM28, SETDB1, and Endogenous Retroviruses in Mild and Severe Cases. Int J Mol Sci 2021; 22:7481. [PMID: 34299101 PMCID: PMC8303145 DOI: 10.3390/ijms22147481] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/07/2021] [Accepted: 07/10/2021] [Indexed: 02/07/2023] Open
Abstract
Children with the new coronavirus disease 2019 (COVID-19) have milder symptoms and a better prognosis than adult patients. Several investigations assessed type I, II, and III interferon (IFN) signatures in SARS-CoV-2 infected adults, however no data are available for pediatric patients. TRIM28 and SETDB1 regulate the transcription of multiple genes involved in the immune response as well as of human endogenous retroviruses (HERVs). Exogenous viral infections can trigger the activation of HERVs, which in turn can induce inflammatory and immune reactions. Despite the potential cross-talks between SARS-CoV-2 infection and TRIM28, SETDB1, and HERVs, information on their expressions in COVID-19 patients is lacking. We assessed, through a PCR real time Taqman amplification assay, the transcription levels of six IFN-I stimulated genes, IFN-II and three of its sensitive genes, three IFN-lIIs, as well as of TRIM28, SETDB1, pol genes of HERV-H, -K, and -W families, and of env genes of Syncytin (SYN)1, SYN2, and multiple sclerosis-associated retrovirus (MRSV) in peripheral blood from COVID-19 children and in control uninfected subjects. Higher expression levels of IFN-I and IFN-II inducible genes were observed in 36 COVID-19 children with mild or moderate disease as compared to uninfected controls, whereas their concentrations decreased in 17 children with severe disease and in 11 with multisystem inflammatory syndrome (MIS-C). Similar findings were found for the expression of TRIM-28, SETDB1, and every HERV gene. Positive correlations emerged between the transcriptional levels of type I and II IFNs, TRIM28, SETDB1, and HERVs in COVID-19 patients. IFN-III expressions were comparable in each group of subjects. This preserved induction of IFN-λs could contribute to the better control of the infection in children as compared to adults, in whom IFN-III deficiency has been reported. The upregulation of IFN-I, IFN-II, TRIM28, SETDB1, and HERVs in children with mild symptoms, their declines in severe cases or with MIS-C, and the positive correlations of their transcription in SARS-CoV-2-infected children suggest that they may play important roles in conditioning the evolution of the infection.
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Affiliation(s)
- Pier-Angelo Tovo
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Silvia Garazzino
- Infectious Diseases Unit, Department of Pediatrics, Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy; (S.G.); (F.M.); (C.S.); (M.Z.)
| | - Valentina Daprà
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
| | - Giulia Pruccoli
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Cristina Calvi
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
| | - Federica Mignone
- Infectious Diseases Unit, Department of Pediatrics, Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy; (S.G.); (F.M.); (C.S.); (M.Z.)
| | - Carla Alliaudi
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
| | - Marco Denina
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Carlo Scolfaro
- Infectious Diseases Unit, Department of Pediatrics, Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy; (S.G.); (F.M.); (C.S.); (M.Z.)
| | - Marisa Zoppo
- Infectious Diseases Unit, Department of Pediatrics, Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy; (S.G.); (F.M.); (C.S.); (M.Z.)
| | - Francesco Licciardi
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Ugo Ramenghi
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Ilaria Galliano
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
| | - Massimiliano Bergallo
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
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Kumar S, Shanker OR, Kumari N, Tripathi M, Chandra PS, Dixit AB, Banerjee J. Neuromodulatory effects of SARS-CoV2 infection: Possible therapeutic targets. Expert Opin Ther Targets 2021; 25:509-519. [PMID: 34232801 PMCID: PMC8330012 DOI: 10.1080/14728222.2021.1953475] [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: 05/27/2021] [Accepted: 07/06/2021] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Although SARS-CoV-2 primarily manifests in the form of respiratory symptoms, emerging evidence suggests that the disease is associated with numerous neurological complications, such as stroke and Guillain-Barre syndrome. Hence, further research is necessary to seek possible therapeutic targets in the CNS for effective management of these complications. AREAS COVERED This review examines the neurological complications associated with SARS-CoV-2 infections and the possible routes of infection. It progresses to illuminate the possible therapeutic targets for effective management of these neuromodulatory effects and the repurposing of drugs that could serve this purpose. To this end, literature from the year 1998-2021 was derived from PubMed. EXPERT OPINION The neurological manifestations associated with COVID-19 may be related to poor prognosis and higher comorbidity. Identification of the key molecular targets in the brain that are potential indicators of the observed neuropathology, such as inflammatory mediators and chromatin modifiers, is key. The repurposing of existing drugs to target potential candidates could reduce the mortality attributed to these associated neurological complications.
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Affiliation(s)
- Sonali Kumar
- Dr. B.R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, New Delhi, India
| | - Ozasvi R Shanker
- Dr. B.R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, New Delhi, India
| | - Neeraj Kumari
- Department of Neurosurgery, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Manjari Tripathi
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - P Sarat Chandra
- Department of Neurosurgery, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Aparna Banerjee Dixit
- Dr. B.R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, New Delhi, India
| | - Jyotirmoy Banerjee
- Department of Biophysics All India Institute of Medical Sciences (AIIMS), New Delhi, India
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