1
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Wang J, Ye X, Wang Y. Anshen Shumai Decoction inhibits post-infarction inflammation and myocardial remodeling through suppression of the p38 MAPK/c-FOS/EGR1 pathway. J Mol Histol 2024; 55:437-454. [PMID: 38874870 DOI: 10.1007/s10735-024-10214-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Anshen Shumai Decoction (ASSMD) is traditionally employed to manage coronary artery disease arrhythmias. Its protective efficacy against myocardial infarction remains to be elucidated. This investigation employed a rat model of myocardial infarction, achieved through the ligation of the left anterior descending (LAD) coronary artery, followed by a 28-day administration of ASSMD. The study observed the decoction's mitigative impact on myocardial injury, with gene regulation effects discerned through transcriptomic analysis. Furthermore, ASSMD's influence on cardiomyocyte apoptosis and fibrotic protein secretion was assessed using an embryonic rat cardiomyocyte cell line (H9c2) under hypoxic conditions and rat cardiac fibroblasts subjected to normoxic culture conditions with TGF-β. A functional rescue assay involving overexpression of FOS and Early Growth Response Factor 1 (EGR1), combined with inhibition of the p38 Mitogen-activated Protein Kinase (MAPK) pathway, was conducted. Results indicated that ASSMD significantly curtailed cardiomyocyte apoptosis and myocardial fibrosis in infarcted rats, primarily by downregulating FOS and EGR1 gene expression and inhibiting the upstream p38 MAPK pathway. These actions of ASSMD culminated in reduced expression of pro-apoptotic, collagen, and fibrosis-associated proteins, conferring myocardial protection and anti-fibrotic effects on cardiac fibroblasts.
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Affiliation(s)
- Jianfeng Wang
- Department of Cardiology, Chun'an County Traditional Chinese Medicine Hospital, No. 1 Xin'an West Road, Qiandaohu Town, Chun'an County, Hangzhou, 311700, P. R. China
| | - Xiaolei Ye
- School of Medicine, Ningbo University, Ningbo, 315211, P. R. China
| | - Yanqin Wang
- Department of Cardiology, Chun'an County Traditional Chinese Medicine Hospital, No. 1 Xin'an West Road, Qiandaohu Town, Chun'an County, Hangzhou, 311700, P. R. China.
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2
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Zawieja SD, Pea GA, Broyhill SE, Bromert KH, Norton CE, Kim HJ, Li M, Castorena-Gonzalez JA, Drumm BT, Davis MJ. Lymphatic muscle cells are the innate pacemaker cells regulating mouse lymphatic collecting vessel contractions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554619. [PMID: 37662284 PMCID: PMC10473772 DOI: 10.1101/2023.08.24.554619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Collecting lymphatic vessels (cLVs) exhibit spontaneous contractions with a pressure-dependent frequency, but the identity of the lymphatic pacemaker cell is still debated. By analogy to pacemakers in the GI and lower urinary tracts, proposed cLV pacemaker cells include interstitial cells of Cajal like cells (ICLC), pericytes, as well as the lymphatic muscle (LMCs) cells themselves. Here we tested the extent to which these cell types are invested into the mouse cLV wall and if any cell type exhibited morphological and functional processes characteristic of pacemaker cells: a contiguous network; spontaneous Ca2+ transients; and depolarization-induced propagated contractions. We employed inducible Cre (iCre) mouse models routinely used to target these specific cell populations including: c-kitCreERT2 to target ICLC; PdgfrβCreERT2 to target pericytes; PdgfrαCreER™ to target CD34+ adventitial fibroblast-like cells or ICLC; and Myh11CreERT2 to target LMCs. These specific inducible Cre lines were crossed to the fluorescent reporter ROSA26mT/mG, the genetically encoded Ca2+ sensor GCaMP6f, and the light-activated cation channel rhodopsin2 (ChR2). c-KitCreERT2 labeled both a sparse population of LECs and round adventitial cells that responded to the mast cell activator compound 48-80. PdgfrβCreERT2 drove recombination in both adventitial cells and LMCs, limiting its power to discriminate a pericyte specific population. PdgfrαCreER™ labeled a large population of interconnected, oak leaf-shaped cells primarily along the adventitial surface of the vessel. Titrated induction of the smooth muscle-specific Myh11CreERT2 revealed a LMC population with heterogeneous morphology. Only LMCs consistently, but heterogeneously, displayed spontaneous Ca2+ events during the diastolic period of the contraction cycle, and whose frequency was modulated in a pressure-dependent manner. Optogenetic depolarization through the expression of ChR2 by Myh11CreERT2, but not PdgfrαCreER™ or c-KitCreERT2, resulted in a propagated contraction. These findings support the conclusion that LMCs, or a subset of LMCs, are responsible for mouse cLV pacemaking.
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Affiliation(s)
- S D Zawieja
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - G A Pea
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - S E Broyhill
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - K H Bromert
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - C E Norton
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - H J Kim
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | - M Li
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
| | | | - B T Drumm
- Smooth Muscle Research Centre, Dundalk Institute of Technology, Dundalk, Co. Louth, A91 K584, Ireland
| | - M J Davis
- Dept. of Medical Pharmacology & Physiology, University of Missouri, Columbia, Missouri
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3
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Saul S, Karim M, Ghita L, Huang PT, Chiu W, Durán V, Lo CW, Kumar S, Bhalla N, Leyssen P, Alem F, Boghdeh NA, Tran DH, Cohen CA, Brown JA, Huie KE, Tindle C, Sibai M, Ye C, Khalil AM, Chiem K, Martinez-Sobrido L, Dye JM, Pinsky BA, Ghosh P, Das S, Solow-Cordero DE, Jin J, Wikswo JP, Jochmans D, Neyts J, De Jonghe S, Narayanan A, Einav S. Anticancer pan-ErbB inhibitors reduce inflammation and tissue injury and exert broad-spectrum antiviral effects. J Clin Invest 2023; 133:e169510. [PMID: 37581931 PMCID: PMC10541190 DOI: 10.1172/jci169510] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023] Open
Abstract
Targeting host factors exploited by multiple viruses could offer broad-spectrum solutions for pandemic preparedness. Seventeen candidates targeting diverse functions emerged in a screen of 4,413 compounds for SARS-CoV-2 inhibitors. We demonstrated that lapatinib and other approved inhibitors of the ErbB family of receptor tyrosine kinases suppress replication of SARS-CoV-2, Venezuelan equine encephalitis virus (VEEV), and other emerging viruses with a high barrier to resistance. Lapatinib suppressed SARS-CoV-2 entry and later stages of the viral life cycle and showed synergistic effect with the direct-acting antiviral nirmatrelvir. We discovered that ErbB1, ErbB2, and ErbB4 bind SARS-CoV-2 S1 protein and regulate viral and ACE2 internalization, and they are required for VEEV infection. In human lung organoids, lapatinib protected from SARS-CoV-2-induced activation of ErbB-regulated pathways implicated in non-infectious lung injury, proinflammatory cytokine production, and epithelial barrier injury. Lapatinib suppressed VEEV replication, cytokine production, and disruption of blood-brain barrier integrity in microfluidics-based human neurovascular units, and reduced mortality in a lethal infection murine model. We validated lapatinib-mediated inhibition of ErbB activity as an important mechanism of antiviral action. These findings reveal regulation of viral replication, inflammation, and tissue injury via ErbBs and establish a proof of principle for a repurposed, ErbB-targeted approach to combat emerging viruses.
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Affiliation(s)
- Sirle Saul
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Marwah Karim
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Luca Ghita
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Pei-Tzu Huang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Verónica Durán
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Chieh-Wen Lo
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Sathish Kumar
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Nishank Bhalla
- National Center for Biodefense and Infectious Disease, Biomedical Research Laboratory, and
| | - Pieter Leyssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Farhang Alem
- Institute for Biohealth Innovation, George Mason University, Manassas, Virginia, USA
| | - Niloufar A. Boghdeh
- Institute for Biohealth Innovation, George Mason University, Manassas, Virginia, USA
| | - Do H.N. Tran
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Courtney A. Cohen
- US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, Maryland, USA
| | - Jacquelyn A. Brown
- Department of Physics and Astronomy, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee, USA
| | - Kathleen E. Huie
- US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, Maryland, USA
| | - Courtney Tindle
- Department of Cellular and Molecular Medicine and
- HUMANOID Center of Research Excellence, UCSD, San Diego, California, USA
| | - Mamdouh Sibai
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Chengjin Ye
- Disease Prevention and Intervention, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Ahmed Magdy Khalil
- Disease Prevention and Intervention, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Kevin Chiem
- Disease Prevention and Intervention, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Luis Martinez-Sobrido
- Disease Prevention and Intervention, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - John M. Dye
- US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, Maryland, USA
| | - Benjamin A. Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine and
- HUMANOID Center of Research Excellence, UCSD, San Diego, California, USA
- Department of Medicine and
| | - Soumita Das
- HUMANOID Center of Research Excellence, UCSD, San Diego, California, USA
- Department of Pathology, UCSD, San Diego, California, USA
| | | | - Jing Jin
- Vitalant Research Institute, San Francisco, California, USA
| | - John P. Wikswo
- Department of Biomedical Engineering, Department of Molecular Physiology and Biophysics, and Department of Physics and Astronomy, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee, USA
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Disease, Biomedical Research Laboratory, and
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
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4
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555625. [PMID: 37693555 PMCID: PMC10491142 DOI: 10.1101/2023.08.31.555625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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5
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Saul S, Karim M, Ghita L, Huang PT, Chiu W, Durán V, Lo CW, Kumar S, Bhalla N, Leyssen P, Alem F, Boghdeh NA, Tran DH, Cohen CA, Brown JA, Huie KE, Tindle C, Sibai M, Ye C, Khalil AM, Martinez-Sobrido L, Dye JM, Pinsky BA, Ghosh P, Das S, Solow-Cordero DE, Jin J, Wikswo JP, Jochmans D, Neyts J, Jonghe SD, Narayanan A, Einav S. Anticancer pan-ErbB inhibitors reduce inflammation and tissue injury and exert broad-spectrum antiviral effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2021.05.15.444128. [PMID: 34159337 PMCID: PMC8219101 DOI: 10.1101/2021.05.15.444128] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Targeting host factors exploited by multiple viruses could offer broad-spectrum solutions for pandemic preparedness. Seventeen candidates targeting diverse functions emerged in a screen of 4,413 compounds for SARS-CoV-2 inhibitors. We demonstrated that lapatinib and other approved inhibitors of the ErbB family receptor tyrosine kinases suppress replication of SARS-CoV-2, Venezuelan equine encephalitis virus (VEEV), and other emerging viruses with a high barrier to resistance. Lapatinib suppressed SARS-CoV-2 entry and later stages of the viral life cycle and showed synergistic effect with the direct-acting antiviral nirmatrelvir. We discovered that ErbB1, 2 and 4 bind SARS-CoV-2 S1 protein and regulate viral and ACE2 internalization, and they are required for VEEV infection. In human lung organoids, lapatinib protected from SARS-CoV-2-induced activation of ErbB-regulated pathways implicated in non-infectious lung injury, pro-inflammatory cytokine production, and epithelial barrier injury. Lapatinib suppressed VEEV replication, cytokine production and disruption of the blood-brain barrier integrity in microfluidic-based human neurovascular units, and reduced mortality in a lethal infection murine model. We validated lapatinib-mediated inhibition of ErbB activity as an important mechanism of antiviral action. These findings reveal regulation of viral replication, inflammation, and tissue injury via ErbBs and establish a proof-of-principle for a repurposed, ErbB-targeted approach to combat emerging viruses.
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6
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Kozak RA, Salvant E, Chang V, Oikonomou A, Biondi MJ, Feld JJ, Armstrong S, Wasif S, Mubareka S, Nirmalarajah K, Seth A, Amemiya Y, Wang C, Tsui H. Host Expression Profiling From Diagnostic Coronavirus Disease 2019 Swabs Associates Upper Respiratory Tract Immune Responses With Radiologic Lung Pathology and Clinical Severity. Open Forum Infect Dis 2023; 10:ofad190. [PMID: 37180592 PMCID: PMC10173546 DOI: 10.1093/ofid/ofad190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Background COVID-19 presents with a breadth of symptomatology including a spectrum of clinical severity requiring intensive care unit (ICU) admission. We investigated the mucosal host gene response at the time of gold standard COVID-19 diagnosis using clinical surplus RNA from upper respiratory tract swabs. Methods Host response was evaluated by RNA-sequencing, and transcriptomic profiles of 44 unvaccinated patients including outpatients and in-patients with varying levels of oxygen supplementation were included. Additionally, chest X-rays were reviewed and scored for patients in each group. Results Host transcriptomics revealed significant changes in the immune and inflammatory response. Patients destined for the ICU were distinguished by the significant upregulation of immune response pathways and inflammatory chemokines, including cxcl2 which has been linked to monocyte subsets associated with COVID-19 related lung damage. In order to temporally associate gene expression profiles in the upper respiratory tract at diagnosis of COVID-19 with lower respiratory tract sequalae, we correlated our findings with chest radiography scoring, showing nasopharygeal or mid-turbinate sampling can be a relevant surrogate for downstream COVID-19 pneumonia/ICU severity. Conclusions This study demonstrates the potential and relevance for ongoing study of the mucosal site of infection of SARS-CoV-2 using a single sampling that remains standard of care in hospital settings. We highlight also the archival value of high quality clinical surplus specimens, especially with rapidly evolving COVID-19 variants and changing public health/vaccination measures.
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Affiliation(s)
- Robert A Kozak
- Correspondence: Hubert Tsui, MD, PhD, FRCPC, Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada (); Robert A. Kozak, PhD, FCCM, Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada ()
| | - Elsa Salvant
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Veronica Chang
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Anastasia Oikonomou
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Mia J Biondi
- School of Nursing, York University, Toronto, Ontario, Canada
- Toronto Centre for Liver Disease, University Health Network, Toronto, Ontario, Canada
| | - Jordan J Feld
- Toronto Centre for Liver Disease, University Health Network, Toronto, Ontario, Canada
| | - Susan Armstrong
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Sumaiyah Wasif
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Samira Mubareka
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Kuganya Nirmalarajah
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Arun Seth
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Precision Diagnostics and Therapeutics Program, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yutaka Amemiya
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Chao Wang
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Hubert Tsui
- Correspondence: Hubert Tsui, MD, PhD, FRCPC, Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada (); Robert A. Kozak, PhD, FCCM, Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada ()
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7
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Wydorski PM, Osipiuk J, Lanham BT, Tesar C, Endres M, Engle E, Jedrzejczak R, Mullapudi V, Michalska K, Fidelis K, Fushman D, Joachimiak A, Joachimiak LA. Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. Nat Commun 2023; 14:2366. [PMID: 37185902 PMCID: PMC10126577 DOI: 10.1038/s41467-023-38031-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub2) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.
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Affiliation(s)
- Pawel M Wydorski
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jerzy Osipiuk
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Benjamin T Lanham
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Christine Tesar
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Elizabeth Engle
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Robert Jedrzejczak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Vishruth Mullapudi
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Karolina Michalska
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Krzysztof Fidelis
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, CA, 95616, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA.
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA.
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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8
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Preparation and characterization of nanobodies targeting SARS-CoV-2 papain-like protease. Protein Expr Purif 2023; 207:106267. [PMID: 37030644 PMCID: PMC10076250 DOI: 10.1016/j.pep.2023.106267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 04/09/2023]
Abstract
Coronavirus Papain-like protease (PLpro) mediates the cleavage of viral polyproteins and assists the virus escaping from innate immune response. Thus, PLpro is an attractive target for the development of broad-spectrum drugs as it has a conserved structure across different coronaviruses. In this study, we purified SARS-CoV-2 PLpro as an immune antigen, constructed a nanobody phage display library, and identified a set of nanobodies with high affinity for SARS-CoV-2. In addition, enzyme activity experiments demonstrated that two nanobodies had a significant inhibitory effect on the PLpro. These nanobodies should therefore be investigated as candidates for the treatment of coronaviruses.
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9
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Sameni M, Mirmotalebisohi SA, Dehghan Z, Abooshahab R, Khazaei-Poul Y, Mozafar M, Zali H. Deciphering molecular mechanisms of SARS-CoV-2 pathogenesis and drug repurposing through GRN motifs: a comprehensive systems biology study. 3 Biotech 2023; 13:117. [PMID: 37070032 PMCID: PMC10090260 DOI: 10.1007/s13205-023-03518-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/13/2023] [Indexed: 03/28/2023] Open
Abstract
The world has recently been plagued by a new coronavirus infection called SARS-CoV-2. This virus may lead to severe acute respiratory syndrome followed by multiple organ failure. SARS-CoV-2 has approximately 80-90% genetic similarity to SARS-CoV. Given the limited omics data available for host response to the viruses (more limited data for SARS-CoV-2), we attempted to unveil the crucial molecular mechanisms underlying the SARS-CoV-2 pathogenesis by comparing its regulatory network motifs with SARS-CoV. We also attempted to identify the non-shared crucial molecules and their functions to predict the specific mechanisms for each infection and the processes responsible for their different manifestations. Deciphering the crucial shared and non-shared mechanisms at the molecular level and signaling pathways underlying both diseases may help shed light on their pathogenesis and pave the way for other new drug repurposing against COVID-19. We constructed the GRNs for host response to SARS-CoV and SARS-CoV-2 pathogens (in vitro) and identified the significant 3-node regulatory motifs by analyzing them topologically and functionally. We attempted to identify the shared and non-shared regulatory elements and signaling pathways between their host responses. Interestingly, our findings indicated that NFKB1, JUN, STAT1, FOS, KLF4, and EGR1 were the critical shared TFs between motif-related subnetworks in both SARS and COVID-1, which are considered genes with specific functions in the immune response. Enrichment analysis revealed that the NOD-like receptor signaling, TNF signaling, and influenza A pathway were among the first significant pathways shared between SARS and COVID-19 up-regulated DEGs networks, and the term "metabolic pathways" (hsa01100) among the down-regulated DEGs networks. WEE1, PMAIP1, and TSC22D2 were identified as the top three hubs specific to SARS. However, MYPN, SPRY4, and APOL6 were the tops specific to COVID-19 in vitro. The term "Complement and coagulation cascades" pathway was identified as the first top non-shared pathway for COVID-19 and the MAPK signaling pathway for SARS. We used the identified crucial DEGs to construct a drug-gene interaction network to propose some drug candidates. Zinc chloride, Fostamatinib, Copper, Tirofiban, Tretinoin, and Levocarnitine were the six drugs with higher scores in our drug-gene network analysis. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03518-x.
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Affiliation(s)
- Marzieh Sameni
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Amir Mirmotalebisohi
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Dehghan
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Yalda Khazaei-Poul
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Mozafar
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Hakimeh Zali
- Proteomics Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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10
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Amano K, Okabe M, Yoshida T, Oba J, Yoshida S, Wakasugi M, Usui A, Nakata Y, Okudera H. Hyperdry Human Amniotic Membrane as a Protective Dressing for Open Wounds With Exposed Bowel in Mice. J Surg Res 2023; 283:898-913. [PMID: 36915018 DOI: 10.1016/j.jss.2022.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/28/2022] [Accepted: 09/15/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION An enteroatmospheric fistula forms when the exposed bowel is perforated with chronic enteric fistula formation. Currently, there is no established preventative method for this condition. Hyperdry (HD) amniotic membrane (AM) can promote early granulation tissue formation on the exposed viscera and is suitable for dressing intractable wounds as it possesses anti-inflammatory, antibacterial, and immunomodulatory properties. This study investigated whether HD-AM promotes early formation of blood vessel-containing granulation tissue for enteroatmospheric fistula treatment. METHODS An experimental animal model of an open wound with exposed bowel was developed. A 15 × 20 mm wound was prepared on the abdomen of Institute of Cancer Research mice, and the HD-AM was placed. The mice were assigned to one of the following groups: HD-AM group, in which the stromal layer of the HD-AM was placed in contact with the exposed bowel; HD-AM UD group, in which the epithelial layer of the HD-AM was placed in contact with the exposed bowel; and the HD-AM (-) or control group, in which the HD-AM was not used. RESULTS On postoperative days 7 and 14, granulation tissue thickness significantly increased in the HD-AM and HD-AM UD groups compared with that in the HD-AM (-) group. Macrophages accumulated in the HD-AM epithelium only in the HD-AM group. During HD-AM contact, a subset of invading macrophages switched from M1 to M2 phenotype. CONCLUSIONS HD-AM is a practical wound dressing with its scaffolding function, regulation of TGF β-1 and C-X-C motif chemokine 5 (CXCL-5), and ability to induce M1-to-M2 macrophage conversion.
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Affiliation(s)
- Koji Amano
- Department of Emergency Surgery, Sakai City Medical Center, Sakai, Osaka, Japan
| | - Motonori Okabe
- Department of Regenerative Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Toyama, Japan
| | - Toshiko Yoshida
- Department of Clinical Biomaterial Application, Medical, University of Toyama, Toyama, Japan.
| | - Jiro Oba
- Department of Emergency & Disaster Medicine, Juntendo University School of Medicine/Graduate School of Medicine, Tokyo, Japan
| | - Satoshi Yoshida
- Department of Regenerative Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Toyama, Japan
| | - Masahiro Wakasugi
- Department of Emergency and Disaster Medicine, University of Toyama, Toyama, Toyama, Japan
| | - Akihiro Usui
- Department of Emergency Surgery, Sakai City Medical Center, Sakai, Osaka, Japan
| | - Yasuki Nakata
- Department of Emergency Surgery, Sakai City Medical Center, Sakai, Osaka, Japan
| | - Hiroshi Okudera
- Department of Emergency and Disaster Medicine, University of Toyama, Toyama, Toyama, Japan
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11
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Islam MS, Wang Z, Abdel-Mohsen M, Chen X, Montaner LJ. Tissue injury and leukocyte changes in post-acute sequelae of SARS-CoV-2: review of 2833 post-acute patient outcomes per immune dysregulation and microbial translocation in long COVID. J Leukoc Biol 2023; 113:236-254. [PMID: 36807444 DOI: 10.1093/jleuko/qiac001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Indexed: 01/18/2023] Open
Abstract
A significant number of persons with coronavirus disease 2019 (COVID-19) experience persistent, recurrent, or new symptoms several months after the acute stage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. This phenomenon, termed post-acute sequelae of SARS-CoV-2 (PASC) or long COVID, is associated with high viral titers during acute infection, a persistently hyperactivated immune system, tissue injury by NETosis-induced micro-thrombofibrosis (NETinjury), microbial translocation, complement deposition, fibrotic macrophages, the presence of autoantibodies, and lymphopenic immune environments. Here, we review the current literature on the immunological imbalances that occur during PASC. Specifically, we focus on data supporting common immunopathogenesis and tissue injury mechanisms shared across this highly heterogenous disorder, including NETosis, coagulopathy, and fibrosis. Mechanisms include changes in leukocyte subsets/functions, fibroblast activation, cytokine imbalances, lower cortisol, autoantibodies, co-pathogen reactivation, and residual immune activation driven by persistent viral antigens and/or microbial translocation. Taken together, we develop the premise that SARS-CoV-2 infection results in PASC as a consequence of acute and/or persistent single or multiple organ injury mediated by PASC determinants to include the degree of host responses (inflammation, NETinjury), residual viral antigen (persistent antigen), and exogenous factors (microbial translocation). Determinants of PASC may be amplified by comorbidities, age, and sex.
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Affiliation(s)
- Md Sahidul Islam
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, Avenida da Universidade, Taipa 999078, University of Macau, Macau S.A.R., China
| | - Zhaoxiong Wang
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, Avenida da Universidade, Taipa 999078, University of Macau, Macau S.A.R., China
| | - Mohamed Abdel-Mohsen
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, United States
| | - Xin Chen
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, Avenida da Universidade, Taipa 999078, University of Macau, Macau S.A.R., China.,Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa 999078, Macau S.A.R., China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Avenida da Universidade, Taipa 999078, Macau S.A.R., China.,Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Research Building N22, University of Macau, Avenida da Universidade, Taipa 999078, Macau S.A.R., China
| | - Luis J Montaner
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, United States
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12
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Wydorski PM, Osipiuk J, Lanham BT, Tesar C, Endres M, Engle E, Jedrzejczak R, Mullapudi V, Michalska K, Fidelis K, Fushman D, Joachimiak A, Joachimiak LA. Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2021.09.15.460543. [PMID: 35547846 PMCID: PMC9094096 DOI: 10.1101/2021.09.15.460543] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub 2 ) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub 2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub 2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub 2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.
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Affiliation(s)
- Pawel M. Wydorski
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Jerzy Osipiuk
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667 USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439 USA
| | - Benjamin T. Lanham
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742 USA
| | - Christine Tesar
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667 USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439 USA
| | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667 USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439 USA
| | - Elizabeth Engle
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742 USA
| | - Robert Jedrzejczak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667 USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439 USA
| | - Vishruth Mullapudi
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Karolina Michalska
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667 USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439 USA
| | - Krzysztof Fidelis
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, CA, 95616 USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742 USA
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667 USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439 USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367 USA
| | - Lukasz A. Joachimiak
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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13
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Arguinchona LM, Zagona-Prizio C, Joyce ME, Chan ED, Maloney JP. Microvascular significance of TGF-β axis activation in COVID-19. Front Cardiovasc Med 2023; 9:1054690. [PMID: 36684608 PMCID: PMC9852847 DOI: 10.3389/fcvm.2022.1054690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/09/2022] [Indexed: 01/09/2023] Open
Abstract
As 2023 approaches, the COVID-19 pandemic has killed millions. While vaccines have been a crucial intervention, only a few effective medications exist for prevention and treatment of COVID-19 in breakthrough cases or in unvaccinated or immunocompromised patients. SARS-CoV-2 displays early and unusual features of micro-thrombosis and immune dysregulation that target endothelial beds of the lungs, skin, and other organs. Notably, anticoagulation improves outcomes in some COVID-19 patients. The protein transforming growth factor-beta (TGF-β1) has constitutive roles in maintaining a healthy microvasculature through its roles in regulating inflammation, clotting, and wound healing. However, after infection (including viral infection) TGF-β1 activation may augment coagulation, cause immune dysregulation, and direct a path toward tissue fibrosis. Dysregulation of TGF-β signaling in immune cells and its localization in areas of microvascular injury are now well-described in COVID-19, and such events may contribute to the acute respiratory distress syndrome and skin micro-thrombosis outcomes frequently seen in severe COVID-19. The high concentration of TGF-β in platelets and in other cells within microvascular thrombi, its ability to activate the clotting cascade and dysregulate immune pathways, and its pro-fibrotic properties all contribute to a unique milieu in the COVID-19 microvasculature. This unique environment allows for propagation of microvascular clotting and immune dysregulation. In this review we summarize the physiological functions of TGF-β and detail the evidence for its effects on the microvasculature in COVID-19. In addition, we explore the potential role of existing TGF-β inhibitors for the prevention and treatment of COVID-19 associated microvascular thrombosis and immune dysregulation.
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Affiliation(s)
- Lauren M. Arguinchona
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Caterina Zagona-Prizio
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Megan E. Joyce
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Edward D. Chan
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States,National Jewish Health, Denver, CO, United States
| | - James P. Maloney
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,*Correspondence: James P. Maloney,
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14
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Brock S, Jackson DB, Soldatos TG, Hornischer K, Schäfer A, Diella F, Emmert MY, Hoerstrup SP. Whole patient knowledge modeling of COVID-19 symptomatology reveals common molecular mechanisms. FRONTIERS IN MOLECULAR MEDICINE 2023; 2:1035290. [PMID: 39086962 PMCID: PMC11285600 DOI: 10.3389/fmmed.2022.1035290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/12/2022] [Indexed: 08/02/2024]
Abstract
Infection with SARS-CoV-2 coronavirus causes systemic, multi-faceted COVID-19 disease. However, knowledge connecting its intricate clinical manifestations with molecular mechanisms remains fragmented. Deciphering the molecular basis of COVID-19 at the whole-patient level is paramount to the development of effective therapeutic approaches. With this goal in mind, we followed an iterative, expert-driven process to compile data published prior to and during the early stages of the pandemic into a comprehensive COVID-19 knowledge model. Recent updates to this model have also validated multiple earlier predictions, suggesting the importance of such knowledge frameworks in hypothesis generation and testing. Overall, our findings suggest that SARS-CoV-2 perturbs several specific mechanisms, unleashing a pathogenesis spectrum, ranging from "a perfect storm" triggered by acute hyper-inflammation, to accelerated aging in protracted "long COVID-19" syndromes. In this work, we shortly report on these findings that we share with the community via 1) a synopsis of key evidence associating COVID-19 symptoms and plausible mechanisms, with details presented within 2) the accompanying "COVID-19 Explorer" webserver, developed specifically for this purpose (found at https://covid19.molecularhealth.com). We anticipate that our model will continue to facilitate clinico-molecular insights across organ systems together with hypothesis generation for the testing of potential repurposing drug candidates, new pharmacological targets and clinically relevant biomarkers. Our work suggests that whole patient knowledge models of human disease can potentially expedite the development of new therapeutic strategies and support evidence-driven clinical hypothesis generation and decision making.
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Affiliation(s)
| | | | - Theodoros G. Soldatos
- Molecular Health GmbH, Heidelberg, Germany
- SRH Hochschule, University of Applied Science, Heidelberg, Germany
| | | | | | | | - Maximilian Y. Emmert
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
- Wyss Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
- Department of Cardiothoracic and Vascular Surgery, German Heart Institute Berlin, Berlin, Germany
- Department of Cardiovascular Surgery, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Simon P. Hoerstrup
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
- Wyss Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
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15
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Tian H, Xu F, Zhao F, Pan N, Lu S, Jia X, Zhou Y. Early-immediate gene Egr1 is associated with TGFβ1 regulation of epigenetic reader Bromodomain-containing protein 4 via the canonical Smad3 signaling in hepatic stellate cells in vitro and in vivo. FASEB J 2022; 36:e22605. [PMID: 36250963 DOI: 10.1096/fj.202201263r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/17/2022] [Accepted: 09/29/2022] [Indexed: 12/31/2022]
Abstract
Upon chronic damage to the liver, multiple cytokines stimulate hepatic stellate cells (HSCs), causing the alterations of gene expression profiles and thus leading to HSC activation, a key step in liver fibrogenesis. Activated HSCs are the dominant contributors to liver fibrosis. Bromodomain containing protein 4 (BrD4), an important epigenetic reader, was demonstrated to concentrate on hundreds of enhancers associated with genes involved in multiple profibrotic pathways, thereby directing HSC activation and the fibrotic responses. The present studies were designed to examine the effect of transforming growth factor beta-1 (TGFβ1), the most potent pro-fibrotic cytokine, on BrD4 expression in HSCs and, if so, elucidated the underlying mechanisms in vitro and in vivo. The experiments employed the heterogeneous TGFβ1 knockout (TGFβ1+/- ) mice, gene knockdown in vivo, and a model of thioacetamide (TAA)-induced liver injury. The results revealed that TGFβ1 enhanced BrD4 expression in HSCs, which was mediated, at least, by Smad3 signaling and early-immediate gene Egr1 (early growth response-1). TGFβ1-induced Smad3 signaling increased Egr1 expression and promoted Egr1 binding to BrD4 promoter at a site around -111 bp, promoting BrD4 expression. Egr1 knockdown reduced BrD4 expression in HSCs in a mouse model of TAA-induced liver injury and lessened liver fibrosis. Double fluorescence staining demonstrated a strong increase in BrD4 expression in activated HSCs in fibrotic areas of the human livers, paralleling the upregulation of p-Smad3 and Egr1. This research suggested novel molecular events underlying the roles of the master pro-fibrotic cytokine TGFβ1 in HSC activation and liver fibrogenesis.
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Affiliation(s)
- Haimeng Tian
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Nantong, China
| | - Feifan Xu
- Department of Clinical Laboratory, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Nantong, China
| | - Feifei Zhao
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Nantong, China
| | - Nachuan Pan
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Sidan Lu
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Nantong, China
| | - Xin Jia
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Nantong, China
| | - Yajun Zhou
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Nantong, China
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16
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Woodson CM, Kehn-Hall K. Examining the role of EGR1 during viral infections. Front Microbiol 2022; 13:1020220. [PMID: 36338037 PMCID: PMC9634628 DOI: 10.3389/fmicb.2022.1020220] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/26/2022] [Indexed: 09/06/2023] Open
Abstract
Early growth response 1 (EGR1) is a multifunctional mammalian transcription factor capable of both enhancing and/or inhibiting gene expression. EGR1 can be activated by a wide array of stimuli such as exposure to growth factors, cytokines, apoptosis, and various cellular stress states including viral infections by both DNA and RNA viruses. Following induction, EGR1 functions as a convergence point for numerous specialized signaling cascades and couples short-term extracellular signals to influence transcriptional regulation of genes required to initiate the appropriate biological response. The role of EGR1 has been extensively studied in both physiological and pathological conditions of the adult nervous system where it is readily expressed in various regions of the brain and is critical for neuronal plasticity and the formation of memories. In addition to its involvement in neuropsychiatric disorders, EGR1 has also been widely examined in the field of cancer where it plays paradoxical roles as a tumor suppressor gene or oncogene. EGR1 is also associated with multiple viral infections such as Venezuelan equine encephalitis virus (VEEV), Kaposi's sarcoma-associated herpesvirus (KSHV), herpes simplex virus 1 (HSV-1), human polyomavirus JC virus (JCV), human immunodeficiency virus (HIV), and Epstein-Barr virus (EBV). In this review, we examine EGR1 and its role(s) during viral infections. First, we provide an overview of EGR1 in terms of its structure, other family members, and a brief overview of its roles in non-viral disease states. We also review upstream regulators of EGR1 and downstream factors impacted by EGR1. Then, we extensively examine EGR1 and its roles, both direct and indirect, in regulating replication of DNA and RNA viruses.
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Affiliation(s)
- Caitlin M. Woodson
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kylene Kehn-Hall
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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17
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Qin D, Liu P, Zhou H, Jin J, Gong W, Liu K, Chen S, Huang J, Fan W, Tao Z, Xu Y. TIM-4 in macrophages contributes to nasal polyp formation through the TGF-β1–mediated epithelial to mesenchymal transition in nasal epithelial cells. Front Immunol 2022; 13:941608. [PMID: 35990621 PMCID: PMC9389014 DOI: 10.3389/fimmu.2022.941608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/13/2022] [Indexed: 12/02/2022] Open
Abstract
Chronic rhinosinusitis with nasal polyps (CRSwNP) is caused by prolonged inflammation of the paranasal sinus mucosa. The epithelial to mesenchymal transition (EMT) is involved in the occurrence and development of CRSwNP. The T-cell immunoglobulin domain and the mucin domain 4 (TIM-4) is closely related to chronic inflammation, but its mechanism in CRSwNP is poorly understood. In our study, we found that TIM-4 was increased in the sinonasal mucosa of CRSwNP patients and, especially, in macrophages. TIM-4 was positively correlated with α-SMA but negatively correlated with E-cadherin in CRS. Moreover, we confirmed that TIM-4 was positively correlated with the clinical parameters of the Lund-Mackay and Lund-Kennedy scores. In the NP mouse model, administration of TIM-4 neutralizing antibody significantly reduced the polypoid lesions and inhibited the EMT process. TIM-4 activation by stimulating with tissue extracts of CRSwNP led to a significant increase of TGF-β1 expression in macrophages in vitro. Furthermore, coculture of macrophages and human nasal epithelial cells (hNECs) results suggested that the overexpression of TIM-4 in macrophages made a contribution to the EMT process in hNECs. Mechanistically, TIM-4 upregulated TGF-β1 expression in macrophages via the ROS/p38 MAPK/Egr-1 pathway. In conclusion, TIM-4 contributes to the EMT process and aggravates the development of CRSwNP by facilitating the production of TGF-β1 in macrophages. Inhibition of TIM-4 expression suppresses nasal polyp formation, which might provide a new therapeutic approach for CRSwNP.
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Affiliation(s)
- Danxue Qin
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Peiqiang Liu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Huiqin Zhou
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jing Jin
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wanyang Gong
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Kunyu Liu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Siyuan Chen
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jingyu Huang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenjun Fan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zezhang Tao
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yu Xu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Yu Xu,
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18
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Keskinidou C, Vassiliou AG, Dimopoulou I, Kotanidou A, Orfanos SE. Mechanistic Understanding of Lung Inflammation: Recent Advances and Emerging Techniques. J Inflamm Res 2022; 15:3501-3546. [PMID: 35734098 PMCID: PMC9207257 DOI: 10.2147/jir.s282695] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/04/2022] [Indexed: 12/12/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a life-threatening lung injury characterized by an acute inflammatory response in the lung parenchyma. Hence, it is considered as the most appropriate clinical syndrome to study pathogenic mechanisms of lung inflammation. ARDS is associated with increased morbidity and mortality in the intensive care unit (ICU), while no effective pharmacological treatment exists. It is very important therefore to fully characterize the underlying pathobiology and the related mechanisms, in order to develop novel therapeutic approaches. In vivo and in vitro models are important pre-clinical tools in biological and medical research in the mechanistic and pathological understanding of the majority of diseases. In this review, we will present data from selected experimental models of lung injury/acute lung inflammation, which have been based on clinical disorders that can lead to the development of ARDS and related inflammatory lung processes in humans, including ventilation-induced lung injury (VILI), sepsis, ischemia/reperfusion, smoke, acid aspiration, radiation, transfusion-related acute lung injury (TRALI), influenza, Streptococcus (S.) pneumoniae and coronaviruses infection. Data from the corresponding clinical conditions will also be presented. The mechanisms related to lung inflammation that will be covered are oxidative stress, neutrophil extracellular traps, mitogen-activated protein kinase (MAPK) pathways, surfactant, and water and ion channels. Finally, we will present a brief overview of emerging techniques in the field of omics research that have been applied to ARDS research, encompassing genomics, transcriptomics, proteomics, and metabolomics, which may recognize factors to help stratify ICU patients at risk, predict their prognosis, and possibly, serve as more specific therapeutic targets.
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Affiliation(s)
- Chrysi Keskinidou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Alice G Vassiliou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Ioanna Dimopoulou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Anastasia Kotanidou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Stylianos E Orfanos
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
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19
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Ramírez-Martínez G, Jiménez-Álvarez LA, Cruz-Lagunas A, Ignacio-Cortés S, Gómez-García IA, Rodríguez-Reyna TS, Choreño-Parra JA, Zúñiga J. Possible Role of Matrix Metalloproteinases and TGF-β in COVID-19 Severity and Sequelae. J Interferon Cytokine Res 2022; 42:352-368. [PMID: 35647937 PMCID: PMC9422783 DOI: 10.1089/jir.2021.0222] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The costs of coronavirus disease 2019 (COVID-19) are devastating. With millions of deaths worldwide, specific serological biomarkers, antiviral agents, and novel therapies are urgently required to reduce the disease burden. For these purposes, a profound understanding of the pathobiology of COVID-19 is mandatory. Notably, the study of immunity against other respiratory infections has generated reference knowledge to comprehend the paradox of the COVID-19 pathogenesis. Past studies point to a complex interplay between cytokines and other factors mediating wound healing and extracellular matrix (ECM) remodeling that results in exacerbated inflammation, tissue injury, severe manifestations, and a sequela of respiratory infections. This review provides an overview of the immunological process elicited after severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Also, we analyzed available data about the participation of matrix metalloproteinases (MMPs) and transforming growth factor-beta (TGF-β) in immune responses of the lungs. Furthermore, we discuss their possible implications in severe COVID-19 and sequela, including pulmonary fibrosis, and remark on the potential of these molecules as biomarkers for diagnosis, prognosis, and treatment of convalescent COVID-19 patients. Our review provides a theoretical framework for future research aimed to discover molecular hallmarks that, combined with clinical features, could serve as therapeutic targets and reliable biomarkers of the different clinical forms of COVID-19, including convalescence.
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Affiliation(s)
- Gustavo Ramírez-Martínez
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas," Mexico City, Mexico
| | - Luis Armando Jiménez-Álvarez
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas," Mexico City, Mexico
| | - Alfredo Cruz-Lagunas
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas," Mexico City, Mexico
| | - Sergio Ignacio-Cortés
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas," Mexico City, Mexico.,Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Mexico City, Mexico
| | - Itzel Alejandra Gómez-García
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas," Mexico City, Mexico.,Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Mexico City, Mexico
| | - Tatiana Sofia Rodríguez-Reyna
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - José Alberto Choreño-Parra
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas," Mexico City, Mexico.,Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Mexico City, Mexico
| | - Joaquín Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas," Mexico City, Mexico.,Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Mexico City, Mexico
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20
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Abstract
Analysis of the SARS-CoV-2 sequence revealed a multibasic furin cleavage site at the S1/S2 boundary of the spike protein distinguishing this virus from SARS-CoV. Furin, the best-characterized member of the mammalian proprotein convertases, is an ubiquitously expressed single pass type 1 transmembrane protein. Cleavage of SARS-CoV-2 spike protein by furin promotes viral entry into lung cells. While furin knockout is embryonically lethal, its knockout in differentiated somatic cells is not, thus furin provides an exciting therapeutic target for viral pathogens including SARS-CoV-2 and bacterial infections. Several peptide-based and small-molecule inhibitors of furin have been recently reported, and select cocrystal structures have been solved, paving the way for further optimization and selection of clinical candidates. This perspective highlights furin structure, substrates, recent inhibitors, and crystal structures with emphasis on furin's role in SARS-CoV-2 infection, where the current data strongly suggest its inhibition as a promising therapeutic intervention for SARS-CoV-2.
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Affiliation(s)
- Essam
Eldin A. Osman
- Department
of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Alnawaz Rehemtulla
- Department
of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nouri Neamati
- Department
of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
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21
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Suprewicz Ł, Swoger M, Gupta S, Piktel E, Byfield FJ, Iwamoto DV, Germann D, Reszeć J, Marcińczyk N, Carroll RJ, Janmey PA, Schwarz JM, Bucki R, Patteson AE. Extracellular Vimentin as a Target Against SARS-CoV-2 Host Cell Invasion. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105640. [PMID: 34866333 PMCID: PMC9252327 DOI: 10.1002/smll.202105640] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/29/2021] [Indexed: 05/07/2023]
Abstract
Infection of human cells by pathogens, including SARS-CoV-2, typically proceeds by cell surface binding to a crucial receptor. The primary receptor for SARS-CoV-2 is the angiotensin-converting enzyme 2 (ACE2), yet new studies reveal the importance of additional extracellular co-receptors that mediate binding and host cell invasion by SARS-CoV-2. Vimentin is an intermediate filament protein that is increasingly recognized as being present on the extracellular surface of a subset of cell types, where it can bind to and facilitate pathogens' cellular uptake. Biophysical and cell infection studies are done to determine whether vimentin might bind SARS-CoV-2 and facilitate its uptake. Dynamic light scattering shows that vimentin binds to pseudovirus coated with the SARS-CoV-2 spike protein, and antibodies against vimentin block in vitro SARS-CoV-2 pseudovirus infection of ACE2-expressing cells. The results are consistent with a model in which extracellular vimentin acts as a co-receptor for SARS-CoV-2 spike protein with a binding affinity less than that of the spike protein with ACE2. Extracellular vimentin may thus serve as a critical component of the SARS-CoV-2 spike protein-ACE2 complex in mediating SARS-CoV-2 cell entry, and vimentin-targeting agents may yield new therapeutic strategies for preventing and slowing SARS-CoV-2 infection.
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Affiliation(s)
- Łukasz Suprewicz
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
| | - Maxx Swoger
- Physics Department and BioInspired Institute, Syracuse University
| | - Sarthak Gupta
- Physics Department and BioInspired Institute, Syracuse University
| | - Ewelina Piktel
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
| | - Fitzroy J. Byfield
- Institute for Medicine and Engineering and Department of Physiology, University of Pennsylvania
| | - Daniel V. Iwamoto
- Institute for Medicine and Engineering and Department of Physiology, University of Pennsylvania
| | - Danielle Germann
- Physics Department and BioInspired Institute, Syracuse University
| | - Joanna Reszeć
- Department of Medical Pathomorphology, Medical University of Białystok, PL-15269 Białystok, Poland
| | - Natalia Marcińczyk
- Department of Biopharmacy, Medical University of Białystok, Białystok, Poland
| | | | - Paul A. Janmey
- Institute for Medicine and Engineering and Department of Physiology, University of Pennsylvania
| | - J. M. Schwarz
- Physics Department and BioInspired Institute, Syracuse University
- Indian Creek Farm, Ithaca, NY
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
- Institute for Medicine and Engineering and Department of Physiology, University of Pennsylvania
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22
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Abstract
Abstract
Viruses completely rely on the energy and metabolic systems of host cells for life activities. Viral infections usually lead to cytopathic effects and host diseases. To date, there are still no specific clinical vaccines or drugs against most viral infections. Therefore, understanding the molecular and cellular mechanisms of viral infections is of great significance to prevent and treat viral diseases. A variety of viral infections are related to the p38 MAPK signalling pathway, and p38 is an important host factor in virus-infected cells. Here, we introduce the different signalling pathways of p38 activation and then summarise how different viruses induce p38 phosphorylation. Finally, we provide a general summary of the effect of p38 activation on virus replication. Our review provides integrated data on p38 activation and viral infections and describes the potential application of targeting p38 as an antiviral strategy.
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23
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Parthasarathi KTS, Munjal NS, Dey G, Kumar A, Pandey A, Balakrishnan L, Sharma J. A pathway map of signaling events triggered upon SARS-CoV infection. J Cell Commun Signal 2021; 15:595-600. [PMID: 34487344 PMCID: PMC8419830 DOI: 10.1007/s12079-021-00642-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 08/15/2021] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronaviruses (SARS-CoVs) caused worldwide epidemics over the past few decades. Extensive studies on various strains of coronaviruses provided a basic understanding of the pathogenesis of the disease. Presently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is leading a global pandemic with unprecedented challenges. This is the third coronavirus outbreak of this century. A signaling pathway map of signaling events induced by SARS-CoV infection is not yet available. In this study, we present a literature-annotated signaling pathway map of reactions induced by SARS-CoV infected cells. Multiple signaling modules were found to be orchestrated including PI3K-AKT, Ras-MAPK, JAK-STAT, Type 1 IFN and NFκB. The signaling pathway map of SARS-CoV consists of 110 molecules and 101 reactions mediated by SARS-CoV proteins. The pathway reaction data are available in various community standard data exchange formats including Systems Biology Graphical Notation (SBGN). The pathway map is publicly available through the GitHub repository and data in various formats can be freely downloadable.
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Affiliation(s)
| | - Nupur S Munjal
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Akhilesh Pandey
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Lavanya Balakrishnan
- Mazumdar Shaw Center for Translational Research, Narayana Hrudayalaya Health City, Bangalore, India.
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
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24
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Xie P, Fang Y, Shen Z, Shao Y, Ma Q, Yang Z, Zhao J, Li H, Li R, Dong S, Wen W, Xia X. Broad antiviral and anti-inflammatory activity of Qingwenjiere mixture against SARS-CoV-2 and other human coronavirus infections. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 93:153808. [PMID: 34753027 PMCID: PMC8522682 DOI: 10.1016/j.phymed.2021.153808] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 10/07/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Qingwenjiere Mixture (QJM) is a traditional Chinese medicine (TCM) that has been shown to have remarkable clinical efficacy against COVID-19. However, little is known about the antiviral and anti-inflammatory activities of QJM against a wider range of human coronavirus (HCoV) strains. PURPOSE The study aims to investigate the antiviral and anti-inflammatory activities of QJM, as well as the underlying mechanisms against HCoV infections. METHODS The chemical compositions from QJM were analyzed by LC-MS. The inhibitory effect of QJM on infections of HCoV-OC43, HCoV-229E, HCoV-NL63, and SARS-CoV-2 was evaluated in HRT-18 cells, Huh7 cells, LLC-MK2 cells, and Vero-E6 cells, respectively, by using cytopathic effect (CPE) inhibition assay or RT-qPCR detection of viral n, s, or RdRp/Hel genes. The expression of pro-inflammatory cytokines induced by HCoV-OC43, HCoV-229E, and SARS-CoV-2, as well as the host ace2 gene was also determined by RT-qPCR assay. Furthermore, the expression of key molecules in the NF-κB/MAPKs signaling pathways was determined by western blot. RESULTS In alcohol-extraction groups of QJM and reference decoction pieces, 53 similar ion peaks were identified, the majority of which were phenylpropanoids, iridoids, and flavonoids. In addition, QJM reduced CPE caused by HCoVs and the expression of viral n genes or N protein. Pretreatment with QJM also exerted inhibitory effect on viral n gene expression. QJM also inhibited the expression of RdRp/Hel and s genes of SARS-CoV-2, as well as the host ace2 gene. Besides, QJM markedly reduced virus-induced mRNA expression of a panel of pro-inflammatory cytokines, such as IL-6, CXCL-8/IL-8, CXCL-10/IP-10, CCL-5/RANTES, TNF-α, IFN-α, CCL-2/MCP-1, CXCL-9/MIG, and IL1-α. We further showed that QJM inhibited the phosphorylation of NF-κB p65, and JNK, ERK 1/2, and p38 MAPKs in HCoV-OC43-infected HRT-18 cells. CONCLUSIONS QJM has broad antiviral and anti-inflammatory activity against both common and newly emerged HCoVs possibly by inhibiting the activation of key components in NF-κB/MAPKs signaling pathway. QJM also has a prevention effect against HCoV infections and inhibits the host receptor required for virus entry. These results indicate that QJM may have the therapeutic potential in the treatment of diseases caused by a broad range of HCoVs.
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Affiliation(s)
- Peifang Xie
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yue Fang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Zhili Shen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yulan Shao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Qinhai Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Hongmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Rongtao Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Shuwei Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Weibo Wen
- Chinese medicine hospitals in Yunnan Province, Yunnan University of Chinese medicine, Kunming, Yunnan 650500, China.
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
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25
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Abstract
Early growth response‐1 (Egr‐1) is a master regulator and transcriptional sensor in vascular dysfunction and disease. This article reviews recent developments in our understanding of the regulatory roles this zinc finger protein and product of an immediate‐early gene plays in a range of cardiovascular and inflammatory disorders. Egr‐1 can amplify pathologic signals from the extracellular environment by serving as a molecular conduit in the inducible expression of proliferative, migratory and proinflammatory genes driving disease progression. Strategies targeting Egr‐1 may provide therapeutic benefit in cardiovascular and inflammatory disorders.
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Affiliation(s)
- Levon M Khachigian
- Vascular Biology and Translational Research School of Medical Sciences Faculty of Medicine and Health University of New South Wales Sydney NSW Australia
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26
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Abstract
Transforming Growth Factor-β is a potent regulator of the immune system, acting at every stage from thymic differentiation, population of the periphery, control of responsiveness, tissue repair and generation of memory. It is therefore a central player in the immune response to infectious pathogens, but its contribution is often clouded by multiple roles acting on different cells in time and space. Hence, context is all-important in understanding when TGF-β is beneficial or detrimental to the outcome of infection. In this review, a full range of infectious agents from viruses to helminth parasites are explored within this framework, drawing contrasts and general conclusions about the importance of TGF-β in these diseases.
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Affiliation(s)
- Rick M Maizels
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.
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27
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Lee JJ, Alzamil J, Rehman S, Pan W, Dimke H, Alexander RT. Activation of the calcium sensing receptor increases claudin-14 expression via a PLC -p38-Sp1 pathway. FASEB J 2021; 35:e21982. [PMID: 34694654 PMCID: PMC9297942 DOI: 10.1096/fj.202002137rrr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022]
Abstract
Activation of the basolateral calcium sensing receptor (CaSR) in the renal tubular thick ascending limb (TAL) increases claudin‐14 expression, which reduces paracellular calcium (Ca2+) permeability, thus increasing urinary Ca2+ excretion. However, the upstream signaling pathway contributing to altered CLDN14 gene expression is unknown. To delineate this pathway, we identified and then cloned the CaSR responsive region including the promoter of mouse Cldn14 into a luciferase reporter vector. This 1500 bp sequence upstream of the 5′ UTR of Cldn14 variant 1, conferred increased reporter activity in the presence of high extracellular Ca2+ (5 mM) relative to a lower (0.5 mM) concentration. Assessment of Cldn14 reporter activity in response to increased extracellular Ca2+ in the presence or absence of specific inhibitors confirmed signaling through PLC and p38, but not JNK. Overexpression of SP1 attenuated Cldn14 reporter activity in response to CasR signaling. SP1 is expressed in the TAL and phosphorylation was attenuated by CaSR signaling. Finally, activating mutations in the CaSR increased Cldn14 reporter activity while a dominant negative mutation in the CaSR inhibited it. Together, these studies suggest that basolateral activation of the CASR leads to increased Cldn14 expression via a PLC‐ stimulated p38 pathway that prevents Sp1 mediated repression.
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Affiliation(s)
- Justin J Lee
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada.,The Women's & Children's Health Research Institute, Edmonton, Alberta, Canada
| | - Jawad Alzamil
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Saba Rehman
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Wanling Pan
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Henrik Dimke
- Department of Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Nephrology, Odense University Hospital, Odense, Denmark
| | - R Todd Alexander
- Department of Physiology, University of Alberta, Edmonton, Alberta, Canada.,The Women's & Children's Health Research Institute, Edmonton, Alberta, Canada.,Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
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28
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Castle RD, Williams MA, Bushell WC, Rindfleisch JA, Peterson CT, Marzolf J, Brouwer K, Mills PJ. Implications for Systemic Approaches to COVID-19: Effect Sizes of Remdesivir, Tocilizumab, Melatonin, Vitamin D3, and Meditation. J Inflamm Res 2021; 14:4859-4876. [PMID: 34588793 PMCID: PMC8473718 DOI: 10.2147/jir.s323356] [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: 06/12/2021] [Accepted: 08/28/2021] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION COVID-19 poses a chronic threat to inflammatory systems, reinforcing the need for efficient anti-inflammatory strategies. The purpose of this review and analysis was to determine the efficacy of various interventions upon the inflammatory markers most affected by COVID-19. The focus was on the markers associated with COVID-19, not the etiology of the virus itself. METHODS Based on 27 reviewed papers, information was extracted on the effects of COVID-19 upon inflammatory markers, then the effects of standard treatments (Remdesivir, Tocilizumab) and adjunctive interventions (vitamin D3, melatonin, and meditation) were extracted for those markers. These data were used to approximate effect sizes for the disease or interventions via standardized mean differences (SMD). RESULTS The data that were available indicated that adjunctive interventions affected 68.4% of the inflammatory markers impacted by COVID-19, while standard pharmaceutical medication affected 26.3%. DISCUSSION Nonstandard adjunctive care appeared to have comparable or superior effects in comparison to Remdesivir and Tocilizumab on the inflammatory markers most impacted by COVID-19. Alongside standards of care, melatonin, vitamin D3, and meditation should be considered for treatment of SARS-COV-2 infection and COVID-19 disease.
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Affiliation(s)
- Ryan D Castle
- Science Division, Whole Health Institute, Bentonville, AR, USA
| | - Michelle A Williams
- Harvard T.H. Chan School of Public Health, Department of Global Health and Population, Harvard University, Boston, MA, USA
| | | | - J Adam Rindfleisch
- Education Department, Whole Health School of Medicine and Health Sciences, Bentonville, AR, USA
| | - Christine Tara Peterson
- Center of Excellence for Research and Training in Integrative Health, Department of Family Medicine, School of Medicine, University of California, San Diego, CA, USA
| | - James Marzolf
- Health Sector Finance & Policy, Whole Health Institute, Bentonville, AR, USA
| | - Kimberly Brouwer
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, CA, USA
| | - Paul J Mills
- Herbert Wertheim School of Public Health and Human Longevity Science, Center of Excellence for Research and Training in Integrative Health, University of California, San Diego, CA, USA
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29
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Resveratrol as an Adjunctive Therapy for Excessive Oxidative Stress in Aging COVID-19 Patients. Antioxidants (Basel) 2021; 10:antiox10091440. [PMID: 34573071 PMCID: PMC8471532 DOI: 10.3390/antiox10091440] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/17/2021] [Accepted: 09/06/2021] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic continues to burden healthcare systems worldwide. COVID-19 symptoms are highly heterogeneous, and the patient may be asymptomatic or may present with mild to severe or fatal symptoms. Factors, such as age, sex, and comorbidities, are key determinants of illness severity and progression. Aging is accompanied by multiple deficiencies in interferon production by dendritic cells or macrophages in response to viral infections, resulting in dysregulation of inflammatory immune responses and excess oxidative stress. Age-related dysregulation of immune function may cause a more obvious pathophysiological response to SARS-CoV-2 infection in elderly patients and may accelerate the risk of biological aging, even after recovery. For more favorable treatment outcomes, inhibiting viral replication and dampening inflammatory and oxidative responses before induction of an overt cytokine storm is crucial. Resveratrol is a potent antioxidant with antiviral activity. Herein, we describe the reasons for impaired interferon production, owing to aging, and the impact of aging on innate and adaptive immune responses to infection, which leads to inflammation distress and immunosuppression, thereby causing fulminant disease. Additionally, the molecular mechanism by which resveratrol could reverse a state of excessive basal inflammatory and oxidative stress and low antiviral immunity is discussed.
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30
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Ford MJ, Harwalkar K, Pacis AS, Maunsell H, Wang YC, Badescu D, Teng K, Yamanaka N, Bouchard M, Ragoussis J, Yamanaka Y. Oviduct epithelial cells constitute two developmentally distinct lineages that are spatially separated along the distal-proximal axis. Cell Rep 2021; 36:109677. [PMID: 34496237 DOI: 10.1016/j.celrep.2021.109677] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 05/25/2021] [Accepted: 08/17/2021] [Indexed: 01/02/2023] Open
Abstract
Owing to technical advances in single-cell biology, the appreciation of cellular heterogeneity has increased, which has aided our understanding of organ function, homeostasis, and disease progression. The oviduct (also known as the fallopian tube) is the distalmost portion of the female reproductive tract. It is essential for reproduction and the proposed origin of high-grade serous ovarian carcinoma (HGSOC). In mammals, the oviduct is morphologically segmented along the ovary-uterus axis into four evolutionally conserved regions. It is unclear, however, if there is a diversification of epithelial cell characteristics between these regions. In this study, we identify transcriptionally distinct populations of secretory and multiciliated cells restricted to the distal and proximal regions of the oviduct. We demonstrate that distal and proximal populations are distinct lineages specified early in Müllerian duct development and are maintained separately. These results aid our understanding of epithelial development, homeostasis, and initiation of disease from the oviduct.
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Affiliation(s)
- Matthew J Ford
- Rosalind and Morris Goodman Cancer Research Institute, Department of Human Genetics, McGill University, Montreal, QC H3A 1A3, Canada
| | - Keerthana Harwalkar
- Rosalind and Morris Goodman Cancer Research Institute, Department of Human Genetics, McGill University, Montreal, QC H3A 1A3, Canada
| | - Alain S Pacis
- Canadian Centre for Computational Genomics (C3G), Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A 1A4, Canada
| | - Helen Maunsell
- Rosalind and Morris Goodman Cancer Research Institute, Department of Human Genetics, McGill University, Montreal, QC H3A 1A3, Canada
| | - Yu Chang Wang
- Department of Human Genetics, McGill University, Montreal, QC H3A OC7, Canada; McGill University and Genome Centre, Montreal, QC H3A 1A4, Canada
| | - Dunarel Badescu
- Department of Human Genetics, McGill University, Montreal, QC H3A OC7, Canada; McGill University and Genome Centre, Montreal, QC H3A 1A4, Canada
| | - Katie Teng
- Rosalind and Morris Goodman Cancer Research Institute, Department of Human Genetics, McGill University, Montreal, QC H3A 1A3, Canada
| | - Nobuko Yamanaka
- Rosalind and Morris Goodman Cancer Research Institute, Department of Human Genetics, McGill University, Montreal, QC H3A 1A3, Canada
| | - Maxime Bouchard
- Rosalind and Morris Goodman Cancer Research Institute and Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A OC7, Canada; McGill University and Genome Centre, Montreal, QC H3A 1A4, Canada; Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada
| | - Yojiro Yamanaka
- Rosalind and Morris Goodman Cancer Research Institute, Department of Human Genetics, McGill University, Montreal, QC H3A 1A3, Canada.
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31
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Zhang H, Chen H, Zhang J, Chen X, Guo B, Zhi P, Li Z, Liu G, Yang B, Chi X, Wang Y, Cao F, Ren J, Lu X. Bioinformatics analysis of SARS-CoV-2 infection-associated immune injury and therapeutic prediction for COVID-19. EMERGENCY AND CRITICAL CARE MEDICINE 2021; 1:20-28. [PMID: 38630100 PMCID: PMC8447736 DOI: 10.1097/ec9.0000000000000005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/19/2021] [Indexed: 11/26/2022]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 is a highly contagious viral infection, without any available targeted therapies. The high mortality rate of COVID-19 is speculated to be related to immune damage. Methods In this study, clinical bioinformatics analysis was conducted on transcriptome data of coronavirus infection. Results Bioinformatics analysis revealed that the complex immune injury induced by coronavirus infection provoked dysfunction of numerous immune-related molecules and signaling pathways, including immune cells and toll-like receptor cascades. Production of numerous cytokines through the Th17 signaling pathway led to elevation in plasma levels of cytokines (including IL6, NF-κB, and TNF-α) followed by concurrent inflammatory storm, which mediates the autoimmune response. Several novel medications seemed to display therapeutic effects on immune damage associated with coronavirus infection. Conclusions This study provided insights for further large-scale studies on the target therapy on reconciliation of immunological damage associated with COVID-19.
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Affiliation(s)
- Haomin Zhang
- Department of Hematology, the Second Medical Center of the China PLA General Hospital & National Center for Clinical Medicine of Geriatric Diseases, Beijing, China
| | - Haoran Chen
- Management School, Shanxi Medical University, Taiyuan, China
| | - Jundong Zhang
- Department of Hematology, the Second Medical Center of the China PLA General Hospital & National Center for Clinical Medicine of Geriatric Diseases, Beijing, China
| | - Ximeng Chen
- Chinese Journal of Hepatobiliary Surgery, Beijing, China
| | - Bin Guo
- Department of Personnel, Cardiovascular Disease Hospital of Shanxi Province, Taiyuan, China
| | - Peng Zhi
- Department of Hematology, the Second Medical Center of the China PLA General Hospital & National Center for Clinical Medicine of Geriatric Diseases, Beijing, China
- Management School, Shanxi Medical University, Taiyuan, China
| | - Zhuoyang Li
- Management School, Shanxi Medical University, Taiyuan, China
| | - Geliang Liu
- Management School, Shanxi Medical University, Taiyuan, China
| | - Bo Yang
- Department of Hematology, the Second Medical Center of the China PLA General Hospital & National Center for Clinical Medicine of Geriatric Diseases, Beijing, China
| | - Xiaohua Chi
- Department of Pharmacy, China PLA Special Medical Center, Beijing, China
| | - Yixing Wang
- Department of Internal Medicine of Traditional Chinese Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Cao
- Department of Cardiology, the Second Medical Center of the China PLA General Hospital, Beijing, China
| | - Jun Ren
- School of Pharmacy, University of Wyoming College of Health Sciences, Laramie, WY, USA
| | - Xuechun Lu
- Department of Hematology, the Second Medical Center of the China PLA General Hospital & National Center for Clinical Medicine of Geriatric Diseases, Beijing, China
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32
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EGR1 suppresses porcine epidemic diarrhea virus replication by regulating IRAV to degrade viral nucleocapsid protein. J Virol 2021; 95:e0064521. [PMID: 34287043 DOI: 10.1128/jvi.00645-21] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a globally distributed alphacoronavirus that has re-emerged lately, resulting in large economic losses. During viral infection, interferon (IFN-I) plays a vital role in the antiviral innate immunity. However, PEDV has evolved strategies to limit IFN-I production. To suppress virus replication, the host must activate the IFN-stimulated genes and some host restriction factors to circumvent viral replication. This study observed that PEDV infection-induced early growth response gene 1 (EGR1) expression in PEDV-permissive cells. EGR1 overexpression remarkably suppressed PEDV replication. In contrast, depletion of EGR1 led to a significant increase in viral replication. EGR1 suppressed PEDV replication by directly binding to the IFN-regulated antiviral (IRAV) promoter and upregulating IRAV expression. A detailed analysis revealed that IRAV interacts and colocalizes with the PEDV nucleocapsid (N) protein, inducing N protein degradation via E3 ubiquitin ligase MARCH8 to catalyze N protein ubiquitination. Knockdown of endogenous MARCH8 significantly reversed IRAV-mediated N protein degradation. The collective findings demonstrate a new mechanism of EGR1-mediated viral restriction, in which EGR1 upregulates the expression of IRAV to degrade PEDV N protein through MARCH8. IMPORTANCE PEDV is a highly contagious enteric coronavirus that has rapidly emerged worldwide and caused severe economic losses. No currently available drugs or vaccines could effectively control PEDV. PEDV has evolved many strategies to limit IFN-1 production. We identified EGR1 as a novel host restriction factor and demonstrated that EGR1 suppresses PEDV replication by directly binding to the IRAV promoter and upregulating the expression of IRAV, which interacts and degrades the PEDV N protein via E3 ubiquitin ligase MARCH8 to catalyze nucleocapsid protein ubiquitination, which adds another layer of complexity to innate antiviral immunity of this newly identified restriction factor. A better understanding of the innate immune response to PEDV infection will aid the development of novel therapeutic targets and more effective vaccines against virus infection.
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33
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Cárdenas-Rodríguez N, Bandala C, Vanoye-Carlo A, Ignacio-Mejía I, Gómez-Manzo S, Hernández-Cruz EY, Pedraza-Chaverri J, Carmona-Aparicio L, Hernández-Ochoa B. Use of Antioxidants for the Neuro-Therapeutic Management of COVID-19. Antioxidants (Basel) 2021; 10:971. [PMID: 34204362 PMCID: PMC8235474 DOI: 10.3390/antiox10060971] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is an emergent infectious disease that has caused millions of deaths throughout the world. COVID-19 infection's main symptoms are fever, cough, fatigue, and neurological manifestations such as headache, myalgias, anosmia, ageusia, impaired consciousness, seizures, and even neuromuscular junctions' disorders. In addition, it is known that this disease causes a series of systemic complications such as adverse respiratory distress syndrome, cardiac injury, acute kidney injury, and liver dysfunction. Due to the neurological symptoms associated with COVID-19, damage in the central nervous system has been suggested as well as the neuroinvasive potential of SARS-CoV-2. It is known that CoV infections are associated with an inflammation process related to the imbalance of the antioxidant system; cellular changes caused by oxidative stress contribute to brain tissue damage. Although anti-COVID-19 vaccines are under development, there is no specific treatment for COVID-19 and its clinical manifestations and complications; only supportive treatments with immunomodulators, anti-vascular endothelial growth factors, modulating drugs, statins, or nutritional supplements have been used. In the present work, we analyzed the potential of antioxidants as adjuvants for the treatment of COVID-19 and specifically their possible role in preventing or decreasing the neurological manifestations and neurological complications present in the disease.
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Affiliation(s)
- Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Cindy Bandala
- Division de Neurociencias, Instituto Nacional de Rehabilitación, Secretaría de Salud, Ciudad de México 14389, Mexico;
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - América Vanoye-Carlo
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Iván Ignacio-Mejía
- Laboratorio de Medicina Traslacional, Escuela Militar de Graduados de Sanidad, SEDENA, Ciudad de México 11200, Mexico;
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico;
| | | | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, UNAM, Ciudad de México 04150, Mexico; (E.Y.H.-C.); (J.P.-C.)
| | - Liliana Carmona-Aparicio
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de México 06720, Mexico;
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Amendola A, Garoffolo G, Songia P, Nardacci R, Ferrari S, Bernava G, Canzano P, Myasoedova V, Colavita F, Castilletti C, Sberna G, Capobianchi MR, Piacentini M, Agrifoglio M, Colombo GI, Poggio P, Pesce M. Human cardiosphere-derived stromal cells exposed to SARS-CoV-2 evolve into hyper-inflammatory/pro-fibrotic phenotype and produce infective viral particles depending on the levels of ACE2 receptor expression. Cardiovasc Res 2021; 117:1557-1566. [PMID: 33705542 PMCID: PMC7989620 DOI: 10.1093/cvr/cvab082] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/08/2021] [Indexed: 12/17/2022] Open
Abstract
Aims Patients with severe respiratory syndrome caused by SARS-CoV-2 undergo cardiac complications due to hyper-inflammatory conditions. Although the presence of the virus has been detected in the myocardium of infected patients, and infection of induced pluripotent cells-derived cardiomyocytes has been demonstrated, the reported expression of ACE2 in cardiac stromal cells suggests that SARS-CoV-2 may determine cardiac injury by sustaining productive infection and increasing inflammation. Methods and Results We analyzed expression of ACE2 receptor in primary human cardiac stromal cells derived from cardiospheres, using proteomics and transcriptomics before exposing them to SARS-CoV-2 in vitro. Using conventional and high sensitivity PCR methods, we measured virus release in the cellular supernatants and monitored the intracellular viral bioprocessing. We performed high-resolution imaging to show the sites of intracellular viral production and demonstrated the presence of viral particles in the cells with electron microscopy. We finally used RT-qPCR assays to detect genes linked to innate immunity and fibrotic pathways coherently regulated in cells after exposure to the virus. Conclusions Our findings indicate that cardiac stromal cells are susceptible to SARS-CoV-2 infection and produce variable viral yields depending on the extent of cellular ACE2 receptor expression. Interestingly, these cells also evolved toward hyper-inflammatory/pro-fibrotic phenotypes independently of ACE2 levels. Thus, SARS-CoV-2 infection of myocardial stromal cells could be involved in cardiac injury, and explain the high number of complications observed in severe cases of COVID-19. Translational Perspective In the present investigation, we provide evidence that human cardiac stromal cells, a major component of the non-contractile cellular fraction in the heart can be infected by SARS-CoV-2 in vitro, in direct relationship to the extent of ACE2 receptor expression. Our work also suggests that these cells, when exposed to the virus, can evolve toward inflammatory and fibrotic phenotypes independently of ACE2. In addition to describing a novel cellular target of SARS-CoV-2 in the human heart, our study generates new hypothesis on potential mechanisms underlying cardiac complications observed in COVID-19 patients.
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Affiliation(s)
- Alessandra Amendola
- Istituto Nazionale per le Malattie Infettive, Lazzaro Spallanzani, IRCCS, Rome, Italy
| | - Gloria Garoffolo
- Centro Cardiologico Monzino, IRCCS, Via C. Parea, 4, Milan, Italy.,DIMET Ph.D. program, Università di Milano-Bicocca, Italy
| | - Paola Songia
- Centro Cardiologico Monzino, IRCCS, Via C. Parea, 4, Milan, Italy
| | - Roberta Nardacci
- Istituto Nazionale per le Malattie Infettive, Lazzaro Spallanzani, IRCCS, Rome, Italy
| | - Silvia Ferrari
- Centro Cardiologico Monzino, IRCCS, Via C. Parea, 4, Milan, Italy.,Ph.D. program in Translational Medicine, Università degli studi di Pavia, Italy
| | - Giacomo Bernava
- Centro Cardiologico Monzino, IRCCS, Via C. Parea, 4, Milan, Italy
| | - Paola Canzano
- Centro Cardiologico Monzino, IRCCS, Via C. Parea, 4, Milan, Italy
| | | | - Francesca Colavita
- Istituto Nazionale per le Malattie Infettive, Lazzaro Spallanzani, IRCCS, Rome, Italy
| | - Concetta Castilletti
- Istituto Nazionale per le Malattie Infettive, Lazzaro Spallanzani, IRCCS, Rome, Italy
| | - Giuseppe Sberna
- Istituto Nazionale per le Malattie Infettive, Lazzaro Spallanzani, IRCCS, Rome, Italy
| | | | | | - Marco Agrifoglio
- Centro Cardiologico Monzino, IRCCS, Via C. Parea, 4, Milan, Italy.,Università degli studi di Milano, Milan, Italy
| | | | - Paolo Poggio
- Centro Cardiologico Monzino, IRCCS, Via C. Parea, 4, Milan, Italy
| | - Maurizio Pesce
- Centro Cardiologico Monzino, IRCCS, Via C. Parea, 4, Milan, Italy
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Jafarzadeh A, Nemati M, Jafarzadeh S. Contribution of STAT3 to the pathogenesis of COVID-19. Microb Pathog 2021; 154:104836. [PMID: 33691172 PMCID: PMC7937040 DOI: 10.1016/j.micpath.2021.104836] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/13/2021] [Accepted: 02/21/2021] [Indexed: 02/07/2023]
Abstract
Hyper-inflammatory responses, lymphopenia, unbalanced immune responses, cytokine storm, large viral replication and massive cell death play fundamental roles in the pathogenesis of COVID-19. Extreme production of many kinds of pro-inflammatory cytokines and chemokines occur in severe COVID-19 that called cytokine storm. Signal transducer and activator of transcription-3 (STAT-3) present in the cytoplasm in an inactive form and can be stimulated by a vast range of cytokines, chemokines and growth factors. Thus, STAT-3 can participate in the induction of inflammatory responses during coronavirus infections. STAT-3 can also suppress anti-virus interferon response and induce unbalanced anti-virus adaptive immune response, through influencing Th17-, Th1-, Treg-, and B cell-mediated functions. Furthermore, STAT-3 can contribute to the M2 macrophage polarization, lung fibrosis and thrombosis. Moreover, STAT-3 may be directly targeted by some virus-derived protein and operate as a pro-viral or anti-viral element in a virus-specific process. Here, the possible contribution of STAT-3 to the pathogenesis of COVID-19 was explained, while providing potential approaches to target this transcription factor in an attempt for COVID-19 treatment.
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Affiliation(s)
- Abdollah Jafarzadeh
- Department of Immunology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran; Department of Immunology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.
| | - Maryam Nemati
- Immunology of Infectious Diseases Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Hematology and Laboratory Sciences, School of Para-Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Sara Jafarzadeh
- Student Research Committee, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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Sharma A, Shah M, Lakshmi S, Sane H, Captain J, Gokulchandran N, Khubchandani P, Pradeep MK, Gote P, Tuppekar B, Kulkarni P, Paranjape A, Pradhan R, Varghese R, Kasekar S, Nair V, Khanbande U. A pilot study for treatment of COVID-19 patients in moderate stage using intravenous administration of ozonized saline as an adjuvant treatment-registered clinical trial. Int Immunopharmacol 2021; 96:107743. [PMID: 33984718 PMCID: PMC8084612 DOI: 10.1016/j.intimp.2021.107743] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 04/27/2021] [Indexed: 12/27/2022]
Abstract
Objective Ozone therapy has tremendous therapeutic potential owing to its antiviral, anti-inflammatory and antioxidant properties, and potential to improve oxygenation. A pilot clinical trial was conducted to evaluate the safety and efficacy of intravenous ozonised saline treatment in patients with moderate COVID-19 pneumonia. Patients and Methods 10 patients were administered 200 ml freshly prepared ozonised saline intravenously over 1 h once a day for 8 days along with standard medical treatment. Clinical symptoms were monitored everyday and laboratory biomarkers, radiological findings at 1,3,6,10 days. Telephonic follow up was done for all after discharge till Day 14. 7 out of 10 patients required oxygen supplementation at recruitment. Results There was severe adverse event recorded in the study group. All patients improved from moderate to mild category in average 8 days and were discharged in average 9.7 days. None deteriorated to severe stage. All clinical symptoms resolved within 6 days and oxygen supplementation requirement reduced to none within 4.1 days. There was statistically significant reduction in CRP (p = 0.003), D-Dimer (p = 0.049), IL6 (p = 0.002) and statistically significant improvement (p = 0.001) in SpO2/FiO2 ratio. Change in LDH was borderline statistically not significant (p = 0.058). All patients showed significant resolution of bilateral interstitial infiltrates at the end of 10 days. Conclusion Resolved clinical symptoms, improved oxygenation, clearance of infiltrates on Chest X-ray and improvement in biomarkers in a short period with non-progression of the disease showed that IV ozonised saline therapy was safe and effective to prevent disease progression in COVID-19, making it an effective novel therapeutic tool.
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Affiliation(s)
- Alok Sharma
- Department of Medical Services and Clinical Research, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | - Mili Shah
- Training and Education, Ozone Forum of India, Mumbai, India
| | - Satya Lakshmi
- National Institute of Naturopathy, Ministry of AYUSH, Pune, India
| | - Hemangi Sane
- Department of Research & Development, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | | | - Nandini Gokulchandran
- Department of Medical Services and Clinical Research, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | - Pallavi Khubchandani
- Department of Medical Services and Clinical Research, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | | | - Prakash Gote
- Department of Medical Services and Clinical Research, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | - Balaji Tuppekar
- Department of Medical Services and Clinical Research, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | - Pooja Kulkarni
- Department of Research & Development, NeuroGen Brain & Spine Institute, Navi Mumbai, India.
| | - Amruta Paranjape
- Department of Research & Development, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | - Radhika Pradhan
- Department of Research & Development, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | - Ritu Varghese
- Department of Research & Development, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | - Sushil Kasekar
- Department of Medical Services and Clinical Research, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | - Vivek Nair
- Department of Medical Services and Clinical Research, NeuroGen Brain & Spine Institute, Navi Mumbai, India
| | - Ummeammara Khanbande
- Department of Medical Services and Clinical Research, NeuroGen Brain & Spine Institute, Navi Mumbai, India
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Role of pirfenidone in TGF-β pathways and other inflammatory pathways in acute respiratory syndrome coronavirus 2 (SARS-Cov-2) infection: a theoretical perspective. Pharmacol Rep 2021; 73:712-727. [PMID: 33880743 PMCID: PMC8057922 DOI: 10.1007/s43440-021-00255-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/14/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes pulmonary injury or multiple-organ injury by various pathological pathways. Transforming growth factor-beta (TGF-β) is a key factor that is released during SARS-CoV-2 infection. TGF-β, by internalization of the epithelial sodium channel (ENaC), suppresses the anti-oxidant system, downregulates the cystic fibrosis transmembrane conductance regulator (CFTR), and activates the plasminogen activator inhibitor 1 (PAI-1) and nuclear factor-kappa-light-chain-enhancer of activated B cells (NF-kB). These changes cause inflammation and lung injury along with coagulopathy. Moreover, reactive oxygen species play a significant role in lung injury, which levels up during SARS-CoV-2 infection. Drug Suggestion Pirfenidone is an anti-fibrotic drug with an anti-oxidant activity that can prevent lung injury during SARS-CoV-2 infection by blocking the maturation process of transforming growth factor-beta (TGF-β) and enhancing the protective role of peroxisome proliferator-activated receptors (PPARs). Pirfenidone is a safe drug for patients with hypertension or diabetes and its side effect tolerated well. Conclusion The drug as a theoretical perspective may be an effective and safe choice for suppressing the inflammatory response during COVID-19. The recommendation would be a combination of pirfenidone and N-acetylcysteine to achieve maximum benefit during SARS-CoV-2 treatment.
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Mahmoudvand S, Shokri S. Interactions between SARS coronavirus 2 papain-like protease and immune system: A potential drug target for the treatment of COVID-19. Scand J Immunol 2021; 94:e13044. [PMID: 33872387 PMCID: PMC8250271 DOI: 10.1111/sji.13044] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/24/2021] [Accepted: 04/11/2021] [Indexed: 12/01/2022]
Abstract
Coronaviruses (CoVs) are a large family of respiratory viruses which can cause mild to moderate upper respiratory tract infections. Recently, new coronavirus named as Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been identified which is a major threat to public health. Innate immune responses play a vital role in a host's defence against viruses. Interestingly, CoVs have evolved elaborate strategies to evade the complex system of sensors and signalling molecules to suppress host immunity. SARS‐CoV‐2 papain‐like protease (PLpro), as an important coronavirus enzyme, regulates viral spread and innate immune responses. SCoV‐2 PLpro is multifunctional enzyme with deubiquitinating (DUB) and deISGylating activity. The PLpro can interact with key regulators in signalling pathways such as STING, NF‐κB, cytokine production, MAPK and TGF‐β and hijack those to block the immune responses. Therefore, the PLpro can be as an important target for the treatment of COVID‐19. Until now, several drugs or compounds have been identified that can inhibit PLpro activity. Here we discuss about the dysregulation effects of PLpro on immune system and drugs that have potential inhibitors for SCoV‐2 PLpro.
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Affiliation(s)
- Shahab Mahmoudvand
- Student Research CommitteeAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of VirologySchool of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Somayeh Shokri
- Student Research CommitteeAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of VirologySchool of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
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Chen J, Wang W, Tang Y, Huang XR, Yu X, Lan HY. Inflammatory stress in SARS-COV-2 associated Acute Kidney Injury. Int J Biol Sci 2021; 17:1497-1506. [PMID: 33907513 PMCID: PMC8071761 DOI: 10.7150/ijbs.58791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/01/2021] [Indexed: 01/08/2023] Open
Abstract
Increasing clinical evidence shows that acute kidney injury (AKI) is a common and severe complication in critically ill COVID-19 patients. The older age, the severity of COVID-19 infection, the ethnicity, and the history of smoking, diabetes, hypertension, and cardiovascular disease are the risk factor for AKI in COVID-19 patients. Of them, inflammation may be a key player in the pathogenesis of AKI in patients with COVID-19. It is highly possible that SARS-COV-2 infection may trigger the activation of multiple inflammatory pathways including angiotensin II, cytokine storm such as interleukin-6 (IL-6), C-reactive protein (CRP), TGF-β signaling, complement activation, and lung-kidney crosstalk to cause AKI. Thus, treatments by targeting these inflammatory molecules and pathways with a monoclonal antibody against IL-6 (Tocilizumab), C3 inhibitor AMY-101, anti-C5 antibody, anti-TGF-β OT-101, and the use of CRRT in critically ill patients may represent as novel and specific therapies for AKI in COVID-19 patients.
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Affiliation(s)
- Junzhe Chen
- Departments of Medicine & Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Department of Nephrology, The Third Affiliated hospital, Southern Medical university, Guangzhou, China
| | - Wenbiao Wang
- Departments of Medicine & Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Guangdong Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Ying Tang
- Department of Nephrology, The Third Affiliated hospital, Southern Medical university, Guangzhou, China
| | - Xiao-ru Huang
- Departments of Medicine & Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Guangdong-Hong Kong Joint Laboratory for Immunity and Genetics of Chronic Kidney Disease, Guangdong Academy of Medical Science, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory for Immunity and Genetics of Chronic Kidney Disease, Guangdong Academy of Medical Science, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Hui-Yao Lan
- Departments of Medicine & Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Guangdong-Hong Kong Joint Laboratory for Immunity and Genetics of Chronic Kidney Disease, The Chinese University of Hong Kong, Hong Kong, China
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Nain Z, Rana HK, Liò P, Islam SMS, Summers MA, Moni MA. Pathogenetic profiling of COVID-19 and SARS-like viruses. Brief Bioinform 2021; 22:1175-1196. [PMID: 32778874 PMCID: PMC7454314 DOI: 10.1093/bib/bbaa173] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/23/2020] [Accepted: 07/08/2020] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus (2019-nCoV) has recently emerged, causing COVID-19 outbreaks and significant societal/global disruption. Importantly, COVID-19 infection resembles SARS-like complications. However, the lack of knowledge about the underlying genetic mechanisms of COVID-19 warrants the development of prospective control measures. In this study, we employed whole-genome alignment and digital DNA-DNA hybridization analyses to assess genomic linkage between 2019-nCoV and other coronaviruses. To understand the pathogenetic behavior of 2019-nCoV, we compared gene expression datasets of viral infections closest to 2019-nCoV with four COVID-19 clinical presentations followed by functional enrichment of shared dysregulated genes. Potential chemical antagonists were also identified using protein-chemical interaction analysis. Based on phylogram analysis, the 2019-nCoV was found genetically closest to SARS-CoVs. In addition, we identified 562 upregulated and 738 downregulated genes (adj. P ≤ 0.05) with SARS-CoV infection. Among the dysregulated genes, SARS-CoV shared ≤19 upregulated and ≤22 downregulated genes with each of different COVID-19 complications. Notably, upregulation of BCL6 and PFKFB3 genes was common to SARS-CoV, pneumonia and severe acute respiratory syndrome, while they shared CRIP2, NSG1 and TNFRSF21 genes in downregulation. Besides, 14 genes were common to different SARS-CoV comorbidities that might influence COVID-19 disease. We also observed similarities in pathways that can lead to COVID-19 and SARS-CoV diseases. Finally, protein-chemical interactions suggest cyclosporine, resveratrol and quercetin as promising drug candidates against COVID-19 as well as other SARS-like viral infections. The pathogenetic analyses, along with identified biomarkers, signaling pathways and chemical antagonists, could prove useful for novel drug development in the fight against the current global 2019-nCoV pandemic.
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Affiliation(s)
- Zulkar Nain
- Department of Genetic Engineering and Biotechnology, East West University, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh
| | - Pietro Liò
- Artificial Intelligence Group at the University of Cambridge
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Luo X, Deng Q, Xue Y, Zhang T, Wu Z, Peng H, Xuan L, Pan G. Anti-Fibrosis Effects of Magnesium Lithospermate B in Experimental Pulmonary Fibrosis: By Inhibiting TGF-βRI/Smad Signaling. Molecules 2021; 26:molecules26061715. [PMID: 33808650 PMCID: PMC8003516 DOI: 10.3390/molecules26061715] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 02/06/2023] Open
Abstract
Pulmonary fibrosis is a severe and irreversible interstitial pulmonary disease with high mortality and few treatments. Magnesium lithospermate B (MLB) is a hydrosoluble component of Salvia miltiorrhiza and has been reported to have antifibrotic effects in other forms of tissue fibrosis. In this research, we studied the effects of MLB on pulmonary fibrosis and the underlying mechanisms. Our results indicated that MLB treatment (50 mg/kg) for seven days could attenuate bleomycin (BLM)-induced pulmonary fibrosis by reducing the alveolar structure disruption and collagen deposition in the C57 mouse model. MLB was also found to inhibit transforming growth factor-beta (TGF-β)-stimulated myofibroblastic transdifferentiation of human lung fibroblast cell line (MRC-5) cells and collagen production by human type II alveolar epithelial cell line (A549) cells, mainly by decreasing the expression of TGF-β receptor I (TGF-βRI) and regulating the TGF-β/Smad pathway. Further studies confirmed that the molecular mechanisms of MLB in BLM-induced pulmonary fibrosis mice were similar to those observed in vitro. In summary, our results demonstrated that MLB could alleviate experimental pulmonary fibrosis both in vivo and in vitro, suggesting that MLB has great potential for pulmonary fibrosis treatment.
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Affiliation(s)
- Xin Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 501 Haike Road, Shanghai 201203, China; (X.L.); (Q.D.); (Y.X.); (T.Z.); (H.P.)
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiangqiang Deng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 501 Haike Road, Shanghai 201203, China; (X.L.); (Q.D.); (Y.X.); (T.Z.); (H.P.)
| | - Yaru Xue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 501 Haike Road, Shanghai 201203, China; (X.L.); (Q.D.); (Y.X.); (T.Z.); (H.P.)
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianwei Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 501 Haike Road, Shanghai 201203, China; (X.L.); (Q.D.); (Y.X.); (T.Z.); (H.P.)
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhitao Wu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210033, China;
| | - Huige Peng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 501 Haike Road, Shanghai 201203, China; (X.L.); (Q.D.); (Y.X.); (T.Z.); (H.P.)
| | - Lijiang Xuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 501 Haike Road, Shanghai 201203, China; (X.L.); (Q.D.); (Y.X.); (T.Z.); (H.P.)
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (L.X.); (G.P.)
| | - Guoyu Pan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 501 Haike Road, Shanghai 201203, China; (X.L.); (Q.D.); (Y.X.); (T.Z.); (H.P.)
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (L.X.); (G.P.)
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42
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Uckun FM, Saund S, Windlass H, Trieu V. Repurposing Anti-Malaria Phytomedicine Artemisinin as a COVID-19 Drug. Front Pharmacol 2021; 12:649532. [PMID: 33815126 PMCID: PMC8017220 DOI: 10.3389/fphar.2021.649532] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Artemisinin is an anti-inflammatory phytomedicine with broad-spectrum antiviral activity. Artemisinin and its antimalarial properties were discovered by the Chinese scientist Tu Youyu, who became one of the laureates of the 2015 Nobel Prize in Physiology or Medicine for this breakthrough in tropical medicine. It is a commonly used anti-malaria drug. Artemisinin has recently been repurposed as a potential COVID-19 drug. Its documented anti-SARS-CoV-2 activity has been attributed to its ability to inhibit spike-protein mediated and TGF-β-dependent early steps in the infection process as well as its ability to disrupt the post-entry intracellular events of the SARS-CoV-2 infection cycle required for viral replication. In addition, Artemisinin has anti-inflammatory activity and reduces the systemic levels of inflammatory cytokines that contribute to cytokine storm and inflammatory organ injury in high-risk COVID-19 patients. We postulate that Artemisinin may prevent the worsening of the health condition of patients with mild-moderate COVID-19 when administered early in the course of their disease.
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Affiliation(s)
| | - Saran Saund
- Oncotelic Inc., Agoura Hills, CA, United States
| | | | - Vuong Trieu
- Oncotelic Inc., Agoura Hills, CA, United States
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Suprewicz Ł, Swoger M, Gupta S, Piktel E, Byfield FJ, Iwamoto DV, Germann D, Reszeć J, Marcińczyk N, Carroll RJ, Lenart M, Pyre K, Janmey P, Schwarz JM, Bucki R, Patteson A. Extracellular vimentin as a target against SARS-CoV-2 host cell invasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.08.425793. [PMID: 33442680 PMCID: PMC7805437 DOI: 10.1101/2021.01.08.425793] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Infection of human cells by pathogens, including SARS-CoV-2, typically proceeds by cell surface binding to a crucial receptor. In the case of SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2) has been identified as a necessary receptor, but not all ACE2-expressing cells are equally infected, suggesting that other extracellular factors are involved in host cell invasion by SARS-CoV-2. Vimentin is an intermediate filament protein that is increasingly recognized as being present on the extracellular surface of a subset of cell types, where it can bind to and facilitate pathogens' cellular uptake. Here, we present evidence that extracellular vimentin might act as a critical component of the SARS-CoV-2 spike protein-ACE2 complex in mediating SARS-CoV-2 cell entry. We demonstrate direct binding between vimentin and SARS-CoV-2 pseudovirus coated with the SARS-CoV-2 spike protein and show that antibodies against vimentin block in vitro SARS-CoV-2 pseudovirus infection of ACE2-expressing cells. Our results suggest new therapeutic strategies for preventing and slowing SARS-CoV-2 infection, focusing on targeting cell host surface vimentin.
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Affiliation(s)
- Łukasz Suprewicz
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
| | - Maxx Swoger
- Physics Department and BioInspired Institute, Syracuse University
| | - Sarthak Gupta
- Physics Department and BioInspired Institute, Syracuse University
| | - Ewelina Piktel
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
| | - Fitzroy J Byfield
- Institute for Medicine and Engineering and Department of Physiology, University of Pennsylvania
| | - Daniel V Iwamoto
- Institute for Medicine and Engineering and Department of Physiology, University of Pennsylvania
| | - Danielle Germann
- Physics Department and BioInspired Institute, Syracuse University
| | - Joanna Reszeć
- Department of Medical Pathomorphology, Medical University of Białystok, PL-15269 Białystok, Poland
| | - Natalia Marcińczyk
- Department of Biopharmacy, Medical University of Białystok, Białystok, Poland
| | - Robert J Carroll
- Physics Department and BioInspired Institute, Syracuse University
| | - Marzena Lenart
- Małopolska Centre of Biotechnology; Jagiellonian University; Kraków, Poland
| | - Krzysztof Pyre
- Małopolska Centre of Biotechnology; Jagiellonian University; Kraków, Poland
| | - Paul Janmey
- Institute for Medicine and Engineering and Department of Physiology, University of Pennsylvania
| | - J M Schwarz
- Physics Department and BioInspired Institute, Syracuse University
- Indian Creek Farm, Ithaca, NY
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
- Institute for Medicine and Engineering and Department of Physiology, University of Pennsylvania
| | - Alison Patteson
- Physics Department and BioInspired Institute, Syracuse University
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Hemmat N, Asadzadeh Z, Ahangar NK, Alemohammad H, Najafzadeh B, Derakhshani A, Baghbanzadeh A, Baghi HB, Javadrashid D, Najafi S, Ar Gouilh M, Baradaran B. The roles of signaling pathways in SARS-CoV-2 infection; lessons learned from SARS-CoV and MERS-CoV. Arch Virol 2021; 166:675-696. [PMID: 33462671 PMCID: PMC7812983 DOI: 10.1007/s00705-021-04958-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023]
Abstract
The number of descriptions of emerging viruses has grown at an unprecedented rate since the beginning of the 21st century. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), is the third highly pathogenic coronavirus that has introduced itself into the human population in the current era, after SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Molecular and cellular studies of the pathogenesis of this novel coronavirus are still in the early stages of research; however, based on similarities of SARS-CoV-2 to other coronaviruses, it can be hypothesized that the NF-κB, cytokine regulation, ERK, and TNF-α signaling pathways are the likely causes of inflammation at the onset of COVID-19. Several drugs have been prescribed and used to alleviate the adverse effects of these inflammatory cellular signaling pathways, and these might be beneficial for developing novel therapeutic modalities against COVID-19. In this review, we briefly summarize alterations of cellular signaling pathways that are associated with coronavirus infection, particularly SARS-CoV and MERS-CoV, and tabulate the therapeutic agents that are currently approved for treating other human diseases.
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Affiliation(s)
- Nima Hemmat
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
| | - Zahra Asadzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
| | - Noora Karim Ahangar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
| | - Hajar Alemohammad
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
| | - Basira Najafzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
| | - Afshin Derakhshani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
- IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Darya Javadrashid
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
| | - Souzan Najafi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran
| | - Meriadeg Ar Gouilh
- Groupe de Recherche sur l'Adaptation Microbienne, EA2656 Université de Caen Normandie, Caen, France.
- Virology Lab, Department of Biology, Centre Hospitalier Universitaire de Caen, 14000, Caen, France.
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166614731, Iran.
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat Commun 2021; 12:743. [PMID: 33531496 PMCID: PMC7854729 DOI: 10.1038/s41467-021-21060-3] [Citation(s) in RCA: 273] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
The pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to expand. Papain-like protease (PLpro) is one of two SARS-CoV-2 proteases potentially targetable with antivirals. PLpro is an attractive target because it plays an essential role in cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex, and disruption of host responses. We report a substantive body of structural, biochemical, and virus replication studies that identify several inhibitors of the SARS-CoV-2 enzyme. We determined the high resolution structure of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors. This collection of structures details inhibitors recognition and interactions providing fundamental molecular and mechanistic insight into PLpro. All compounds inhibit the peptidase activity of PLpro in vitro, some block SARS-CoV-2 replication in cell culture assays. These findings will accelerate structure-based drug design efforts targeting PLpro to identify high-affinity inhibitors of clinical value. The SARS-CoV-2 papain-like protease (PLpro) is of interest as an antiviral drug target. Here, the authors synthesize and characterise naphthalene-based inhibitors for PLpro and present the crystal structures of PLpro in its apo state and with the bound inhibitors, which is of interest for further structure-based drug design efforts.
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Vermani L, Kumar R, Senthil Kumar N. GAPDH and PUM1: Optimal Housekeeping Genes for Quantitative Polymerase Chain Reaction-Based Analysis of Cancer Stem Cells and Epithelial-Mesenchymal Transition Gene Expression in Rectal Tumors. Cureus 2020; 12:e12020. [PMID: 33457124 PMCID: PMC7797410 DOI: 10.7759/cureus.12020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background The overwhelming majority of published articles have taken colon and rectal cancer as a single group, i.e., colorectal cancer, when normalizing gene expression data with housekeeping genes (HKG) in quantitative polymerase chain reaction (qPCR) experiments though there are published reports that suggest the differential expression pattern of genes between the colon and rectal cancer groups and hence the current experiment was attempted to find out the optimal set of housekeeping genes from the list of common HKG for rectal tumor gene expression analysis. Methods The expression of five potential housekeeping genes GAPDH, RPNI, PUM1, B2M, and PMM1 was analyzed through qPCR and Bestkeeper software (http://www.wzw.tum.de/gene-quantification/bestkeeper.html) in 20 stage II-IV rectal cancer samples to check for uniformity in their expression pattern. Cancer stem cell (CSC) marker ALDH1 and epithelial-mesenchymal transition marker (EMT) markers E cadherin, vimentin, Twist, and SNAI2 expression were evaluated in conjunction with the two optimal reference genes in 10 rectal cancers as part of validation. Results The standard deviation of the cycle threshold value of GAPDH was found the lowest at 0.65 followed by RPN1 at 0.88, PUM1 at 0.94, PMM1 at 0.94, and B2M at 1.21 when analyzed with BestKeeper software. Using GAPDH and PUM1 as the reference gene for the validation phase, rectal cancer patients with stage III/IV showed a 4.79-fold change (P=0.006) in ALDH1 expression, and an 11.76-fold change in Twist expression (P=0.003) with respect to stage II rectal tumor when normalized with GAPDH and PUM1. Conclusion GAPDH and PUM1 can be used as an optimal set of housekeeping genes for gene expression-related experiments in rectal tumors. ALDH1 and Twist were found significantly overexpressed in stage III/IV rectal tumors in comparison to stage II rectal cancer. Genes associated with cancer stem cells and EMT markers could be optimally analyzed by normalizing them with GAPDH and PUM1 as housekeeping genes.
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Affiliation(s)
| | - Rajeev Kumar
- Research, Cachar Cancer Hospital and Research Centre, Silchar, IND
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Domdom MA, Brest P, Grosjean I, Roméo B, Landi MT, Gal J, Klionsky DJ, Hofman P, Mograbi B. A multifactorial score including autophagy for prognosis and care of COVID-19 patients. Autophagy 2020; 16:2276-2281. [PMID: 33249989 PMCID: PMC7751655 DOI: 10.1080/15548627.2020.1844433] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023] Open
Abstract
In less than eleven months, the world was brought to a halt by the COVID-19 outbreak. With hospitals becoming overwhelmed, one of the highest priorities concerned critical care triage to ration the scarce resources of intensive care units. Which patient should be treated first? Based on what clinical and biological criteria? A global joint effort rapidly led to sequencing the genomes of tens of thousands of COVID-19 patients to determine the patients' genetic signature that causes them to be at risk of suddenly developing severe disease. In this commentary, we would like to consider some points concerning the use of a multifactorial risk score for COVID-19 severity. This score includes macroautophagy (hereafter referred to as autophagy), a critical host process that controls all steps harnessed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Abbreviation list: ATG5: autophagy related 5; BECN1: beclin 1; COVID-19: coronavirus infectious disease-2019; EGR1: early growth response 1; ER: endoplasmic reticulum; DMVs: double-membrane vesicles; IBV: infectious bronchitis virus; MAP1LC3: microtubule associated protein 1 light chain 3; LC3-I: proteolytically processed, non-lipidated MAP1LC3; LC3-II: lipidated MAP1LC3; MEFs: mouse embryonic fibroblasts; MERS-CoV: Middle East respiratory syndrome-coronavirus; MHV: mouse hepatitis virus; NSP: non-structural protein; PEDV: porcine epidemic diarrhea virus; PLP2-TM: membrane-associated papain-like protease 2; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TGEV: transmissible gastroenteritis virus.
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Affiliation(s)
- Marie-Angela Domdom
- Université Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, Nice, France
| | - Patrick Brest
- Université Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, Nice, France
| | - Iris Grosjean
- Université Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, Nice, France
| | - Barnabé Roméo
- Université Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, Nice, France
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics,National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jocelyn Gal
- University Côte d’Azur, Centre Antoine Lacassagne, Epidemiology and Biostatistics Department, Nice, France
| | - Daniel J. Klionsky
- University of Michigan, Department of Molecular, Cellular, and Developmental Biology, and Life Sciences Institute, Ann Arbor, MI, USA
| | - Paul Hofman
- Université Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, Nice, France
- Université Côte d’Azur, Centre Hospitallier Universitaire De Nice, Pasteur Hospital, Laboratory of Clinical and Experimental Pathology, and Biobank (BB003300025), Nice, France
| | - Baharia Mograbi
- Université Côte d’Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne, Nice, France
- TRANSAUTOPHAGY: European Network for Multidisciplinary Research and Translation of Autophagy Knowledge, COST Action CA15138
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Simabuco FM, Tamura RE, Pavan ICB, Morale MG, Ventura AM. Molecular mechanisms and pharmacological interventions in the replication cycle of human coronaviruses. Genet Mol Biol 2020; 44:e20200212. [PMID: 33237152 PMCID: PMC7731901 DOI: 10.1590/1678-4685-gmb-2020-0212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), as well as SARS-CoV from 2003 along with MERS-CoV from 2012, is a member of the Betacoronavirus genus of the Nidovirales order and is currently the cause of the pandemic called COVID-19 (or Coronavirus disease 2019). COVID-19, which is characterized by cough, fever, fatigue, and severe cases of pneumonia, has affected more than 23 million people worldwide until August 25th, 2020. Here, we present a review of the cellular mechanisms associated with human coronavirus replication, including the unique molecular events related to the replication transcription complex (RTC) of coronaviruses. We also present information regarding the interactions between each viral protein and cellular proteins associated to known host-pathogen implications for the coronavirus biology. Finally, a specific topic addresses the current attempts for pharmacological interventions against COVID-19, highlighting the possible effects of each drug on the molecular events of viral replication. This review intends to aid future studies for a better understanding of the SARS-CoV-2 replication cycle and the development of pharmacological approaches targeting COVID-19.
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Affiliation(s)
- Fernando Moreira Simabuco
- Universidade Estadual de Campinas, Faculdade de Ciências Aplicadas (FCA), Laboratório Multidisciplinar em Alimentos e Saúde (LABMAS), Limeira, SP, Brazil
| | - Rodrigo Esaki Tamura
- Universidade Federal de São Paulo (UNIFESP), Departmento de Ciências Biológicas, Diadema, SP, Brazil
| | - Isadora Carolina Betim Pavan
- Universidade Estadual de Campinas, Faculdade de Ciências Aplicadas (FCA), Laboratório Multidisciplinar em Alimentos e Saúde (LABMAS), Limeira, SP, Brazil.,Universidade Estadual de Campinas, Faculdade de Ciências Farmacêuticas (FCF), Campinas, SP, Brazil
| | - Mirian Galliote Morale
- Universidade de São Paulo (USP), Departamento de Radiologia e Oncologia, Faculdade de Medicina, Centro de Oncologia Translacional, Instituto do Câncer do Estado de São Paulo (ICESP), São Paulo, SP, Brazil
| | - Armando Morais Ventura
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas (ICB), Departamento de Microbiologia, São Paulo, SP, Brazil
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Khurana P, Gupta A, Sugadev R, Sharma YK, Varshney R, Ganju L, Kumar B. nSARS-Cov-2, pulmonary edema and thrombosis: possible molecular insights using miRNA-gene circuits in regulatory networks. ACTA ACUST UNITED AC 2020; 2:16. [PMID: 33209992 PMCID: PMC7596315 DOI: 10.1186/s41544-020-00057-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/18/2020] [Indexed: 12/11/2022]
Abstract
Background Given the worldwide spread of the novel Severe Acute Respiratory Syndrome Coronavirus 2 (nSARS-CoV-2) infection pandemic situation, research to repurpose drugs, identify novel drug targets, vaccine candidates have created a new race to curb the disease. While the molecular signature of nSARS-CoV-2 is still under investigation, growing literature shows similarity among nSARS-CoV-2, pulmonary edema, and thromboembolic disorders due to common symptomatic features. A network medicine approach is used to to explore the molecular complexity of the disease and to uncover common molecular trajectories of edema and thrombosis with nSARS-CoV-2. Results and conclusion A comprehensive nSARS-CoV-2 responsive miRNA: Transcription Factor (TF): gene co-regulatory network was built using host-responsive miRNAs and it’s associated tripartite, Feed-Forward Loops (FFLs) regulatory circuits were identified. These regulatory circuits regulate signaling pathways like virus endocytosis, viral replication, inflammatory response, pulmonary vascularization, cell cycle control, virus spike protein stabilization, antigen presentation, etc. A unique miRNA-gene regulatory circuit containing a consortium of four hub FFL motifs is proposed to regulate the virus-endocytosis and antigen-presentation signaling pathways. These regulatory circuits also suggest potential correlations/similarity in the molecular mechanisms during nSARS-CoV-2 infection, pulmonary diseases and thromboembolic disorders and thus could pave way for repurposing of drugs. Some important miRNAs and genes have also been proposed as potential candidate markers. A detailed molecular snapshot of TGF signaling as the common pathway, that could play an important role in controlling common pathophysiologies among diseases, is also put forth. Supplementary information Supplementary information accompanies this paper at 10.1186/s41544-020-00057-y.
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Affiliation(s)
- P Khurana
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - A Gupta
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - R Sugadev
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - Y K Sharma
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - R Varshney
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - L Ganju
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - B Kumar
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
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Patteson AE, Vahabikashi A, Goldman RD, Janmey PA. Mechanical and Non-Mechanical Functions of Filamentous and Non-Filamentous Vimentin. Bioessays 2020; 42:e2000078. [PMID: 32893352 PMCID: PMC8349470 DOI: 10.1002/bies.202000078] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/04/2020] [Indexed: 12/20/2022]
Abstract
Intermediate filaments (IFs) formed by vimentin are less understood than their cytoskeletal partners, microtubules and F-actin, but the unique physical properties of IFs, especially their resistance to large deformations, initially suggest a mechanical function. Indeed, vimentin IFs help regulate cell mechanics and contractility, and in crowded 3D environments they protect the nucleus during cell migration. Recently, a multitude of studies, often using genetic or proteomic screenings show that vimentin has many non-mechanical functions within and outside of cells. These include signaling roles in wound healing, lipogenesis, sterol processing, and various functions related to extracellular and cell surface vimentin. Extracellular vimentin is implicated in marking circulating tumor cells, promoting neural repair, and mediating the invasion of host cells by viruses, including SARS-CoV, or bacteria such as Listeria and Streptococcus. These findings underscore the fundamental role of vimentin in not only cell mechanics but also a range of physiological functions. Also see the video abstract here https://youtu.be/YPfoddqvz-g.
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Affiliation(s)
- Alison E Patteson
- Physics Department, Syracuse University, Syracuse, NY 13244
- BioInspired Institute, Syracuse University, Syracuse, NY 13244
| | - Amir Vahabikashi
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL 60611
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL 60611
| | - Paul A. Janmey
- Institute for Medicine and Engineering, Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104
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