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Edalat F, Khakpour N, Heli H, Letafati A, Ramezani A, Hosseini SY, Moattari A. Immunological mechanisms of the nucleocapsid protein in COVID-19. Sci Rep 2024; 14:3711. [PMID: 38355695 PMCID: PMC10867304 DOI: 10.1038/s41598-024-53906-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
The emergence of corona virus disease 2019 (COVID-19), resulting from Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has left an indelible mark on a global scale, causing countless infections and fatalities. This investigation delves into the role of the SARS-CoV-2 nucleocapsid (N) protein within the HEK293 cells, shedding light on its influence over apoptosis, interferon signaling, and cytokines production. The N gene was amplified, inserted into the pAdTrack-CMV vector, and then transfected to the HEK293 cells. Changes in the expression of IRF3, IRF7, IFN-β, BAK, BAX, and BCL-2 genes were evaluated. The levels of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α were also determined. The N protein exhibited an anti-apoptotic effect by modulating critical genes associated with apoptosis, including BAK, BAX, and BCL-2. This effect potentially prolonged the survival of infected cells. The N protein also played a role in immune evasion by suppressing the interferon pathway, evidenced by the downregulation of essential interferon regulatory factors of IRF3 and IRF7, and IFN-β expression. The N protein expression led to a substantial increase in the production of proinflammatory cytokines of IL-6, IL-12, IL-1β, and TNF-α. The N protein emerged as a versatile factor and was exerted over apoptosis, interferon signaling, and cytokine production. These findings carry potential implications for the development of targeted therapies to combat COVID-19 and mitigate its global health impact.
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Affiliation(s)
- Fahime Edalat
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Heli
- Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Younes Hosseini
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran.
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2
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Wójcik P, Jastrzębski MK, Zięba A, Matosiuk D, Kaczor AA. Caspases in Alzheimer's Disease: Mechanism of Activation, Role, and Potential Treatment. Mol Neurobiol 2023:10.1007/s12035-023-03847-1. [PMID: 38135855 DOI: 10.1007/s12035-023-03847-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023]
Abstract
With the aging of the population, treatment of conditions emerging in old age, such as neurodegenerative disorders, has become a major medical challenge. Of these, Alzheimer's disease, leading to cognitive dysfunction, is of particular interest. Neuronal loss plays an important role in the pathophysiology of this condition, and over the years, a great effort has been made to determine the role of various factors in this process. Unfortunately, until now, the exact pathomechanism of this condition remains unknown. However, the most popular theories associate AD with abnormalities in the Tau and β-amyloid (Aβ) proteins, which lead to their deposition and result in neuronal death. Neurons, like all cells, die in a variety of ways, among which pyroptosis, apoptosis, and necroptosis are associated with the activation of various caspases. It is worth mentioning that Tau and Aβ proteins are considered to be one of the caspase activators, leading to cell death. Moreover, the protease activity of caspases influences both of the previously mentioned proteins, Tau and Aβ, converting them into more toxic derivatives. Due to the variety of ways caspases impact the development of AD, drugs targeting caspases could potentially be useful in the treatment of this condition. Therefore, there is a constant need to search for novel caspase inhibitors and evaluate them in preclinical and clinical trials.
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Affiliation(s)
- Piotr Wójcik
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20093, Lublin, Poland.
| | - Michał K Jastrzębski
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20093, Lublin, Poland
| | - Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20093, Lublin, Poland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20093, Lublin, Poland
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., 20093, Lublin, Poland.
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, 70211, Kuopio, Finland.
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Hao S, Ning K, Kuz CA, Xiong M, Zou W, Park SY, McFarlin S, Yan Z, Qiu J. SARS-CoV-2 infection of polarized human airway epithelium induces necroptosis that causes airway epithelial barrier dysfunction. J Med Virol 2023; 95:e29076. [PMID: 37671751 PMCID: PMC10754389 DOI: 10.1002/jmv.29076] [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: 07/14/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause the ongoing pandemic of coronavirus disease 2019 (COVID19). One key feature associated with COVID-19 is excessive pro-inflammatory cytokine production that leads to severe acute respiratory distress syndrome. Although the cytokine storm induces inflammatory cell death in the host, which type of programmed cell death mechanism that occurs in various organs and cells remains elusive. Using an in vitro culture model of polarized human airway epithelium (HAE), we observed that necroptosis, but not apoptosis or pyroptosis, plays an essential role in the damage of the epithelial barrier of polarized HAE infected with SARS-CoV-2. Pharmacological inhibitors of necroptosis, necrostatin-2 and necrosulfonamide, efficiently prevented cell death and epithelial barrier dysfunction caused by SARS-CoV-2 infection. Moreover, the silencing of genes that are involved in necroptosis, RIPK1, RIPK3, and MLKL, ameliorated airway epithelial damage of the polarized HAE infected with SARS-CoV-2. This study, for the first time, confirms that SARS-CoV-2 infection triggers necroptosis that disrupts the barrier function of human airway epithelia in vitro.
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Affiliation(s)
- Siyuan Hao
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Kang Ning
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cagla A Kuz
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Min Xiong
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Wei Zou
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Soo Y Park
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA
| | - Shane McFarlin
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Ziying Yan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
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Antropova EA, Khlebodarova TM, Demenkov PS, Volianskaia AR, Venzel AS, Ivanisenko NV, Gavrilenko AD, Ivanisenko TV, Adamovskaya AV, Revva PM, Kolchanov NA, Lavrik IN, Ivanisenko VA. Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection. J Integr Bioinform 2023; 20:jib-2023-0013. [PMID: 37978846 PMCID: PMC10757076 DOI: 10.1515/jib-2023-0013] [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: 04/30/2023] [Accepted: 07/31/2023] [Indexed: 11/19/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has been associated with hepatitis C viral (HCV) infection as a potential risk factor. Nonetheless, the precise genetic regulatory mechanisms triggered by the virus, leading to virus-induced hepatocarcinogenesis, remain unclear. We hypothesized that HCV proteins might modulate the activity of aberrantly methylated HCC genes through regulatory pathways. Virus-host regulatory pathways, interactions between proteins, gene expression, transport, and stability regulation, were reconstructed using the ANDSystem. Gene expression regulation was statistically significant. Gene network analysis identified four out of 70 HCC marker genes whose expression regulation by viral proteins may be associated with HCC: DNA-binding protein inhibitor ID - 1 (ID1), flap endonuclease 1 (FEN1), cyclin-dependent kinase inhibitor 2A (CDKN2A), and telomerase reverse transcriptase (TERT). It suggested the following viral protein effects in HCV/human protein heterocomplexes: HCV NS3(p70) protein activates human STAT3 and NOTC1; NS2-3(p23), NS5B(p68), NS1(E2), and core(p21) activate SETD2; NS5A inhibits SMYD3; and NS3 inhibits CCN2. Interestingly, NS3 and E1(gp32) activate c-Jun when it positively regulates CDKN2A and inhibit it when it represses TERT. The discovered regulatory mechanisms might be key areas of focus for creating medications and preventative therapies to decrease the likelihood of HCC development during HCV infection.
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Affiliation(s)
| | - Tamara M. Khlebodarova
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel S. Demenkov
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Artur S. Venzel
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikita V. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexandr D. Gavrilenko
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Timofey V. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anna V. Adamovskaya
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Polina M. Revva
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Inna N. Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106Magdeburg, Germany
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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Mehta P, Chattopadhyay P, Ravi V, Tarai B, Budhiraja S, Pandey R. SARS-CoV-2 infection severity and mortality is modulated by repeat-mediated regulation of alternative splicing. Microbiol Spectr 2023; 11:e0135123. [PMID: 37604131 PMCID: PMC10580830 DOI: 10.1128/spectrum.01351-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/16/2023] [Indexed: 08/23/2023] Open
Abstract
Like single-stranded RNA viruses, SARS-CoV-2 hijacks the host transcriptional machinery for its own replication. Numerous traditional differential gene expression-based investigations have examined the diverse clinical symptoms caused by SARS-CoV-2 infection. The virus, on the other hand, also affects the host splicing machinery, causing host transcriptional dysregulation, which can lead to diverse clinical outcomes. Hence, in this study, we performed host transcriptome sequencing of 125 hospital-admitted COVID-19 patients to understand the transcriptomic differences between the severity sub-phenotypes of mild, moderate, severe, and mortality. We performed transcript-level differential expression analysis, investigated differential isoform usage, looked at the splicing patterns within the differentially expressed transcripts (DET), and elucidated the possible genome regulatory features. Our DTE analysis showed evidence of diminished transcript length and diversity as well as altered promoter site usage in the differentially expressed protein-coding transcripts in the COVID-19 mortality patients. We also investigated the potential mechanisms driving the alternate splicing and discovered a compelling differential enrichment of repeats in the promoter region and a specific enrichment of SINE (Alu) near the splicing sites of differentially expressed transcripts. These findings suggested a repeat-mediated plausible regulation of alternative splicing as a potential modulator of COVID-19 disease severity. In this work, we emphasize the role of scarcely elucidated functional role of alternative splicing in influencing COVID-19 disease severity sub-phenotypes, clinical outcomes, and its putative mechanism. IMPORTANCE The wide range of clinical symptoms reported during the COVID-19 pandemic inherently highlights the numerous factors that influence the progression and prognosis of SARS-CoV-2 infection. While several studies have investigated the host response and discovered immunological dysregulation during severe infection, most of them have the common theme of focusing only up to the gene level. Viruses, especially RNA viruses, are renowned for hijacking the host splicing machinery for their own proliferation, which inadvertently puts pressure on the host transcriptome, exposing another side of the host response to the pathogen challenge. Therefore, in this study, we examine host response at the transcript-level to discover a transcriptional difference that culminates in differential gene-level expression. Importantly, this study highlights diminished transcript diversity and possible regulation of transcription by differentially abundant repeat elements near the promoter region and splicing sites in COVID-19 mortality patients, which together with differentially expressed isoforms hold the potential to elaborate disease severity and outcome.
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Affiliation(s)
- Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Varsha Ravi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Kwak MS, Choi S, Kim J, Lee H, Park IH, Oh J, Mai DN, Cho NH, Nam KT, Shin JS. SARS-CoV-2 Infection Induces HMGB1 Secretion Through Post-Translational Modification and PANoptosis. Immune Netw 2023; 23:e26. [PMID: 37416931 PMCID: PMC10320423 DOI: 10.4110/in.2023.23.e26] [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: 12/23/2022] [Revised: 03/30/2023] [Accepted: 04/09/2023] [Indexed: 07/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection induces excessive pro-inflammatory cytokine release and cell death, leading to organ damage and mortality. High-mobility group box 1 (HMGB1) is one of the damage-associated molecular patterns that can be secreted by pro-inflammatory stimuli, including viral infections, and its excessive secretion levels are related to a variety of inflammatory diseases. Here, the aim of the study was to show that SARS-CoV-2 infection induced HMGB1 secretion via active and passive release. Active HMGB1 secretion was mediated by post-translational modifications, such as acetylation, phosphorylation, and oxidation in HEK293E/ACE2-C-GFP and Calu-3 cells during SARS-CoV-2 infection. Passive release of HMGB1 has been linked to various types of cell death; however, we demonstrated for the first time that PANoptosis, which integrates other cell death pathways, including pyroptosis, apoptosis, and necroptosis, is related to passive HMGB1 release during SARS-CoV-2 infection. In addition, cytoplasmic translocation and extracellular secretion or release of HMGB1 were confirmed via immunohistochemistry and immunofluorescence in the lung tissues of humans and angiotensin-converting enzyme 2-overexpressing mice infected with SARS-CoV-2.
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Affiliation(s)
- Man Sup Kwak
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Seoyeon Choi
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jiseon Kim
- Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hoojung Lee
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - In Ho Park
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jooyeon Oh
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Duong Ngoc Mai
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, Korea
- Department of Pediatrics, University of Medicine and Pharmacy, Ho Chi Minh 700000, Vietnam
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Ki Taek Nam
- Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeon-Soo Shin
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 FOUR Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
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Khlebodarova TM, Demenkov PS, Ivanisenko TV, Antropova EA, Lavrik IN, Ivanisenko VA. Primary and Secondary micro-RNA Modulation the Extrinsic Pathway of Apoptosis in Hepatocellular Carcinoma. Mol Biol 2023; 57:165-175. [PMID: 37128213 PMCID: PMC10131518 DOI: 10.1134/s0026893323020103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 05/03/2023]
Abstract
Abstract-One of the most common malignant liver diseases is hepatocellular carcinoma, which has a high recurrence rate and a low five-year survival rate. It is very heterogeneous both in structure and between patients, which complicates the diagnosis, prognosis and response to treatment. In this regard, an individualized, patient-centered approach becomes important, in which the use of mimetics and hsa-miRNA inhibitors involved in the pathogenesis of the disease may be determinative. From this point of view hsa-miRNAs are of interest, their aberrant expression is associated with poor prognosis for patients and is associated with tumor progression due to dysregulation of programmed cell death (apoptosis). However, the effect of hsa-miRNA on tumor development depends not only on its direct effect on expression of genes, the primary targets, but also on secondary targets mediated by regulatory pathways. While the former are actively studied, the role of secondary targets of these hsa-miRNAs in modulating apoptosis is still unclear. The present work summarizes data on hsa-miRNAs whose primary targets are key genes of the extrinsic pathway of apoptosis. Their aberrant expression is associated with early disease relapse and poor patient outcome. For these hsa-miRNAs, using the software package ANDSystem, we reconstructed the regulation of the expression of secondary targets and analyzed their impact on the activity of the extrinsic pathway of apoptosis. The potential effect of hsa-miRNAs mediated by action on secondary targets is shown to negatively correlate with the number of primary targets. It is also shown that hsa-miR-373, hsa-miR-106b and hsa-miR-96 have the highest priority as markers of hepatocellular carcinoma, whose action on secondary targets enhances their anti-apoptotic effect.
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Affiliation(s)
- T. M. Khlebodarova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - P. S. Demenkov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - T. V. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - E. A. Antropova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - I. N. Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - V. A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
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8
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Lundstrom K, Hromić-Jahjefendić A, Bilajac E, Aljabali AAA, Baralić K, Sabri NA, Shehata EM, Raslan M, Ferreira ACBH, Orlandi L, Serrano-Aroca Á, Tambuwala MM, Uversky VN, Azevedo V, Alzahrani KJ, Alsharif KF, Halawani IF, Alzahrani FM, Redwan EM, Barh D. COVID-19 signalome: Pathways for SARS-CoV-2 infection and impact on COVID-19 associated comorbidity. Cell Signal 2023; 101:110495. [PMID: 36252792 PMCID: PMC9568271 DOI: 10.1016/j.cellsig.2022.110495] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic has been the focus of research the past two years. The major breakthrough was made by discovering pathways related to SARS-CoV-2 infection through cellular interaction by angiotensin-converting enzyme (ACE2) and cytokine storm. The presence of ACE2 in lungs, intestines, cardiovascular tissues, brain, kidneys, liver, and eyes shows that SARS-CoV-2 may have targeted these organs to further activate intracellular signalling pathways that lead to cytokine release syndrome. It has also been reported that SARS-CoV-2 can hijack coatomer protein-I (COPI) for S protein retrograde trafficking to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), which, in turn, acts as the assembly site for viral progeny. In infected cells, the newly synthesized S protein in endoplasmic reticulum (ER) is transported first to the Golgi body, and then from the Golgi body to the ERGIC compartment resulting in the formation of specific a motif at the C-terminal end. This review summarizes major events of SARS-CoV-2 infection route, immune response following host-cell infection as an important factor for disease outcome, as well as comorbidity issues of various tissues and organs arising due to COVID-19. Investigations on alterations of host-cell machinery and viral interactions with multiple intracellular signaling pathways could represent a major factor in more effective disease management.
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Affiliation(s)
| | - Altijana Hromić-Jahjefendić
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka Cesta 15, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Esma Bilajac
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka Cesta 15, 71000 Sarajevo, Bosnia and Herzegovina
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, P.O. Box 566, Irbid 21163, Jordan.
| | - Katarina Baralić
- Department of Toxicology "Akademik Danilo Soldatović", University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11221 Belgrade, Serbia.
| | - Nagwa A Sabri
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo 11865, Egypt.
| | - Eslam M Shehata
- Drug Research Center, Clinical Research and Bioanalysis Department, Cairo 11865, Egypt.
| | - Mohamed Raslan
- Drug Research Center, Clinical Research and Bioanalysis Department, Cairo 11865, Egypt.
| | - Ana Cláudia B H Ferreira
- Campinas State University, Campinas, São Paulo, Brazil; University Center of Lavras (UNILAVRAS), Lavras, Minas Gerais, Brazil.
| | - Lidiane Orlandi
- University Center of Lavras (UNILAVRAS), Lavras, Minas Gerais, Brazil.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Laboratory, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain.
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Khalaf F Alsharif
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Ibrahim F Halawani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Fuad M Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia.
| | - Debmalya Barh
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, India.
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9
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Tojo K, Yamamoto N, Tamada N, Mihara T, Abe M, Nishii M, Takeuchi I, Goto T. Early alveolar epithelial cell necrosis is a potential driver of COVID-19-induced acute respiratory distress syndrome. iScience 2022; 26:105748. [PMID: 36507222 PMCID: PMC9722615 DOI: 10.1016/j.isci.2022.105748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) with COVID-19 is aggravated by hyperinflammatory responses even after the peak of the viral load has passed; however, its underlying mechanisms remain unclear. In the present study, analysis of the alveolar tissue injury markers and epithelial cell death markers in patients with COVID-19 revealed that COVID-19-induced ARDS was characterized by alveolar epithelial necrosis at an early disease stage. Serum levels of HMGB-1, one of the DAMPs released from necrotic cells, were also significantly elevated in these patients. Further analysis using a mouse model mimicking COVID-19-induced ARDS showed that the alveolar epithelial cell necrosis involved two forms of programmed necrosis, namely necroptosis, and pyroptosis. Finally, the neutralization of HMGB-1 attenuated alveolar tissue injury in the mouse model. Collectively, necrosis, including necroptosis and pyroptosis, is the predominant form of alveolar epithelial cell death at an early disease stage and subsequent release of DAMPs is a potential driver of COVID-19-induced ARDS.
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Affiliation(s)
- Kentaro Tojo
- Department of Anesthesiology and Critical Care Medicine, Yokohama City University School of Medicine, Yokohama, Kanagawa, Japan,Corresponding author
| | - Natsuhiro Yamamoto
- Department of Anesthesiology and Critical Care Medicine, Yokohama City University School of Medicine, Yokohama, Kanagawa, Japan
| | - Nao Tamada
- Department of Anesthesiology and Critical Care Medicine, Yokohama City University School of Medicine, Yokohama, Kanagawa, Japan,Department of Paramedic, Kyorin University Faculty of Health Sciences, Mitaka, Tokyo, Japan
| | - Takahiro Mihara
- Department of Health Data Science, Yokohama City University Graduate School of Data Science, Yokohama, Kanagawa, Japan
| | - Miyo Abe
- Department of Anesthesiology and Critical Care Medicine, Yokohama City University School of Medicine, Yokohama, Kanagawa, Japan
| | - Mototsugu Nishii
- Department of Emergency Medicine, Yokohama City University School of Medicine, Yokohama, Kanagawa, Japan
| | - Ichiro Takeuchi
- Department of Emergency Medicine, Yokohama City University School of Medicine, Yokohama, Kanagawa, Japan
| | - Takahisa Goto
- Department of Anesthesiology and Critical Care Medicine, Yokohama City University School of Medicine, Yokohama, Kanagawa, Japan
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10
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Antropova E, Khlebodarova T, Demenkov P, Venzel A, Ivanisenko N, Gavrilenko A, Ivanisenko T, Adamovskaya A, Revva P, Lavrik I, Ivanisenko V. Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins. Vavilovskii Zhurnal Genet Selektsii 2022; 26:733-742. [PMID: 36714033 PMCID: PMC9840909 DOI: 10.18699/vjgb-22-89] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023] Open
Abstract
Hepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aberrant DNA methylation is a mediator of epigenetic changes that are closely associated with the HCC pathogenesis and considered a biomarker for its early diagnosis. The ANDSystem software package was used to reconstruct and evaluate the statistical significance of the pathways HCV could potentially use to regulate 32 hypermethylated genes in HCC, including both oncosuppressor and protumorigenic ones identified by genome-wide analysis of DNA methylation. The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, protein activity, stability, and transport regulations, the expression regulation pathways being statistically significant. It has been shown that 8 out of 10 HCV proteins were involved in these pathways, the HCV NS3 protein being implicated in the largest number of regulatory pathways. NS3 was associated with the regulation of 5 tumor-suppressor genes, which may be the evidence of its central role in HCC pathogenesis. Analysis of the reconstructed pathways has demonstrated that following the transcription factor inhibition caused by binding to viral proteins, the expression of a number of oncosuppressors (WT1, MGMT, SOCS1, P53) was suppressed, while the expression of others (RASF1, RUNX3, WIF1, DAPK1) was activated. Thus, the performed gene-network reconstruction has shown that HCV proteins can influence not only the methylation status of oncosuppressor genes, but also their transcriptional regulation. The results obtained can be used in the search for pharmacological targets to develop new drugs against HCV-induced HCC.
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Affiliation(s)
- E.A. Antropova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, Russia
| | - T.M. Khlebodarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - P.S. Demenkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.S. Venzel
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - N.V. Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.D. Gavrilenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - T.V. Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.V. Adamovskaya
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - P.M. Revva
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - I.N. Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - V.A. Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
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11
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Plasma metabolomics and gene regulatory networks analysis reveal the role of nonstructural SARS-CoV-2 viral proteins in metabolic dysregulation in COVID-19 patients. Sci Rep 2022; 12:19977. [PMID: 36404352 PMCID: PMC9676188 DOI: 10.1038/s41598-022-24170-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022] Open
Abstract
Metabolomic analysis of blood plasma samples from COVID-19 patients is a promising approach allowing for the evaluation of disease progression. We performed the metabolomic analysis of plasma samples of 30 COVID-19 patients and the 19 controls using the high-performance liquid chromatography (HPLC) coupled with tandem mass spectrometric detection (LC-MS/MS). In our analysis, we identified 103 metabolites enriched in KEGG metabolic pathways such as amino acid metabolism and the biosynthesis of aminoacyl-tRNAs, which differed significantly between the COVID-19 patients and the controls. Using ANDSystem software, we performed the reconstruction of gene networks describing the potential genetic regulation of metabolic pathways perturbed in COVID-19 patients by SARS-CoV-2 proteins. The nonstructural proteins of SARS-CoV-2 (orf8 and nsp5) and structural protein E were involved in the greater number of regulatory pathways. The reconstructed gene networks suggest the hypotheses on the molecular mechanisms of virus-host interactions in COVID-19 pathology and provide a basis for the further experimental and computer studies of the regulation of metabolic pathways by SARS-CoV-2 proteins. Our metabolomic analysis suggests the need for nonstructural protein-based vaccines and the control strategy to reduce the disease progression of COVID-19.
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12
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Suzuki S, Imamura M, Mouri M, Tsuchida T, Tomita H, Matsuoka S, Takita M, Kakinuma K, Kawasaki T, Sakurai K, Yamazaki K, Kurokawa MS, Kunishima H, Matsuda T, Mineshita M, Takemura H, Fujitani S, Ooka S, Sugihara T, Kato T, Kawahata K. Serum gasdermin D levels are associated with the chest computed tomography findings and severity of COVID-19. Respir Investig 2022; 60:750-761. [PMID: 35934631 PMCID: PMC9273659 DOI: 10.1016/j.resinv.2022.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/27/2022] [Accepted: 06/12/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND The role of programmed cell death, especially pyroptosis and apoptosis, in unfavorable immune responses in COVID-19 remains to be elucidated. METHODS We conducted a cross-sectional analysis to investigate the association between the serum gasdermin D (GSDMD) levels, a pyroptotic marker, and caspase-cleaved cytokeratin 18 fragment (M30), an apoptotic marker, and the clinical status and abnormal chest computed tomography (CT) findings in patients with COVID-19. RESULTS In this study, 46 patients diagnosed with COVID-19 were divided into the following three groups according to the disease severity: mild to moderate group (n = 10), severe group (n = 14), and critical group (n = 22). The serum GSDMD levels were higher in the critical group than in the mild to moderate group (P = 0.016). In contrast, serum M30 levels were lower in the critical group than in the severe group (P = 0.048). Patients who required mechanical ventilation or died had higher serum GSDMD levels than those who did not (P = 0.007). Area of consolidation only and of ground glass opacity plus consolidation positively correlated with serum GSDMD levels (r = 0.56, P < 0.001 and r = 0.53, P < 0.001, respectively). CONCLUSION Higher serum GSDMD levels are associated with critical respiratory status and the consolidation area on chest CT in patients with COVID-19, suggesting that excessive activation of pyroptosis may affect the clinical manifestations in patients with COVID-19.
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Affiliation(s)
- Shotaro Suzuki
- Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Mitsuru Imamura
- Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan,Corresponding author. Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University, School of Medicine, 2-16-1, Sugao, Miyamae-ku, Kawasaki, Kanagawa, Japan. Fax: +81-44-977-8593
| | - Mariko Mouri
- Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Tomoya Tsuchida
- Division of General Internal Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Hayato Tomita
- Department of Radiology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Shin Matsuoka
- Department of Radiology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Mumon Takita
- Department of Emergency and Critical Care Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Kazutaka Kakinuma
- Division of Respiratory and Infectious Diseases, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Tatsuya Kawasaki
- Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Keiichi Sakurai
- Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Kazuko Yamazaki
- Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Manae S. Kurokawa
- Disease Biomarker Analysis and Molecular Regulation, St. Marianna University Graduate School of Medicine, Kawasaki, Kanagawa, Japan
| | - Hiroyuki Kunishima
- Department of Infectious Diseases, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Takahide Matsuda
- Division of General Internal Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Masamichi Mineshita
- Division of Respiratory and Infectious Diseases, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Hiromu Takemura
- Department of Microbiology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Shigeki Fujitani
- Department of Emergency and Critical Care Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Seido Ooka
- Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Takahiko Sugihara
- Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Tomohiro Kato
- Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine, Kawasaki, Kanagawa, Japan
| | - Kimito Kawahata
- Division of Rheumatology and Allergology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
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13
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Sun C, Han Y, Zhang R, Liu S, Wang J, Zhang Y, Chen X, Jiang C, Wang J, Fan X, Wang J. Regulated necrosis in COVID-19: A double-edged sword. Front Immunol 2022; 13:917141. [PMID: 36090995 PMCID: PMC9452688 DOI: 10.3389/fimmu.2022.917141] [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: 04/10/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
COVID-19 caused by SARS-CoV-2 can cause various systemic diseases such as acute pneumonia with cytokine storm. Constituted of necroptosis, pyroptosis, and ferroptosis, regulated necrosis constitutes the cell death patterns under the low apoptosis condition commonly observed in COVID-19. Regulated necrosis is involved in the release of cytokines like TNF-α, IL-1 β, and IL-6 and cell contents such as alarmins, PAMPs, and DAMPs, leading to more severe inflammation. Uncontrolled regulated necrosis may explain the poor prognosis and cytokine storm observed in COVID-19. In this review, the pathophysiology and mechanism of regulated necrosis with the double-edged sword effect in COVID-19 are thoroughly discussed in detail. Furthermore, this review also focuses on the biomarkers and potential therapeutic targets of the regulated necrosis pathway in COVID-19, providing practical guidance to judge the severity, prognosis, and clinical treatment of COVID-19 and guiding the development of clinical anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Chen Sun
- Department of Pain Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yunze Han
- Department of Pain Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruoyu Zhang
- Department of Pain Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Simon Liu
- Medical Genomics Unit, National Human Genome Research Institute, Bethesda, MD, United States
| | - Jing Wang
- Department of Pain Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuqing Zhang
- Department of Pain Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuemei Chen
- Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chao Jiang
- Department of Neurology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junmin Wang
- Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- *Correspondence: Jian Wang, ; Junmin Wang, ; Xiaochong Fan,
| | - Xiaochong Fan
- Department of Pain Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Jian Wang, ; Junmin Wang, ; Xiaochong Fan,
| | - Jian Wang
- Department of Pain Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Human Anatomy, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- *Correspondence: Jian Wang, ; Junmin Wang, ; Xiaochong Fan,
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14
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Yang Y, Li W, You B, Zhou C. Advances in cell death mechanisms involved in viral myocarditis. Front Cardiovasc Med 2022; 9:968752. [PMID: 36017100 PMCID: PMC9395613 DOI: 10.3389/fcvm.2022.968752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022] Open
Abstract
Viral myocarditis is an acute inflammatory disease of the myocardium. Although many etiopathogenic factors exist, coxsackievirus B3 is a the leading cause of viral myocarditis. Abnormal cardiomyocyte death is the underlying problem for most cardiovascular diseases and fatalities. Various types of cell death occur and are regulated to varying degrees. In this review, we discuss the different cell death mechanisms in viral myocarditis and the potential interactions between them. We also explore the role and mechanism of cardiomyocyte death with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Exploring the mechanisms may help in the early identification and the development of effective treatments, thus improving the quality of life of patients with viral myocarditis. We believe that the inhibition of cardiomyocyte death has immense therapeutic potential in increasing the longevity and health of the heart.
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Affiliation(s)
- Yang Yang
- Taizhou People’s Hospital Affiliated to Nanjing Medical University, Taizhou, China
- Clinical Laboratory Center, Jiangsu Taizhou People’s Hospital, Taizhou, China
- *Correspondence: Yang Yang,
| | - Wang Li
- Taizhou People’s Hospital Affiliated to Nanjing Medical University, Taizhou, China
- Clinical Laboratory Center, Jiangsu Taizhou People’s Hospital, Taizhou, China
| | - Benshuai You
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Chenglin Zhou
- Taizhou People’s Hospital Affiliated to Nanjing Medical University, Taizhou, China
- Clinical Laboratory Center, Jiangsu Taizhou People’s Hospital, Taizhou, China
- Chenglin Zhou,
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15
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Smith CD, Maines LW, Keller SN, Katz Ben-Yair V, Fathi R, Plasse TF, Levitt ML. Recent Progress in the Development of Opaganib for the Treatment of Covid-19. Drug Des Devel Ther 2022; 16:2199-2211. [PMID: 35855741 PMCID: PMC9288228 DOI: 10.2147/dddt.s367612] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/02/2022] [Indexed: 12/15/2022] Open
Abstract
The Covid-19 pandemic driven by the SARS-CoV-2 virus continues to exert extensive humanitarian and economic stress across the world. Although antivirals active against mild disease have been identified recently, new drugs to treat moderate and severe Covid-19 patients are needed. Sphingolipids regulate key pathologic processes, including viral proliferation and pathologic host inflammation. Opaganib (aka ABC294640) is a first-in-class clinical drug targeting sphingolipid metabolism for the treatment of cancer and inflammatory diseases. Recent work demonstrates that opaganib also has antiviral activity against several viruses including SARS-CoV-2. A recently completed multinational Phase 2/3 clinical trial of opaganib in patients hospitalized with Covid-19 demonstrated that opaganib can be safely administered to these patients, and more importantly, resulted in a 62% decrease in mortality in a large subpopulation of patients with moderately severe Covid-19. Furthermore, acceleration of the clearance of the virus was observed in opaganib-treated patients. Understanding the biochemical mechanism for the anti-SARS-CoV-2 activity of opaganib is essential for optimizing Covid-19 treatment protocols. Opaganib inhibits three key enzymes in sphingolipid metabolism: sphingosine kinase-2 (SK2); dihydroceramide desaturase (DES1); and glucosylceramide synthase (GCS). Herein, we describe a tripartite model by which opaganib suppresses infection and replication of SARS-CoV-2 by inhibiting SK2, DES1 and GCS. The potential impact of modulation of sphingolipid signaling on multi-organ dysfunction in Covid-19 patients is also discussed.
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Affiliation(s)
- Charles D Smith
- Apogee Biotechnology Corporation, Hummelstown, PA, USA
- Correspondence: Charles D Smith, Apogee Biotechnology Corporation, 1214 Research Blvd, Suite 2015, Hummelstown, PA, 17036, USA, Tel +1 843 814 9257, Email
| | - Lynn W Maines
- Apogee Biotechnology Corporation, Hummelstown, PA, USA
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16
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Panda M, Kalita E, Singh S, Kumar K, Rao A, Prajapati VK. MiRNA-SARS-CoV-2 dialogue and prospective anti-COVID-19 therapies. Life Sci 2022; 305:120761. [PMID: 35787998 PMCID: PMC9249409 DOI: 10.1016/j.lfs.2022.120761] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 02/08/2023]
Abstract
COVID-19 is a highly transmissible disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), affects 226 countries and continents, and has resulted in >6.2 million deaths worldwide. Despite the efforts of all scientific institutions worldwide to identify potential therapeutics, no specific drug has been approved by the FDA to treat the COVID-19 patient. SARS-CoV-2 variants of concerns make the potential of publicly known therapeutics to respond to and detect disease onset highly improbable. The quest for universal therapeutics pointed to the ability of RNA-based molecules to shield and detect the adverse effects of the COVID-19 illness. One such candidate, miRNA (microRNA), works on regulating the differential expression of the target gene post-transcriptionally. The prime focus of this review is to report the critical miRNA molecule and their regular expression in patients with COVID-19 infection and associated comorbidities. Viral and host miRNAs control the etiology of COVID-19 infection throughout the life cycle and host inflammatory response, where host miRNAs are identified as a double-edged showing as a proviral and antiviral response. The review also covered the role of viral miRNAs in mediating host cell signaling expression during disease pathology. Studying molecular interactions between the host and the SARS-CoV-2 virus during COVID-19 pathogenesis offers the chance to use miRNA-based therapeutics to reduce the severity of the illness. By utilizing an appropriate delivery vehicle, these small non-coding RNA could be envisioned as a promising biomarker in designing a practical RNAi-based treatment approach of clinical significance.
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Affiliation(s)
- Mamta Panda
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Elora Kalita
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Ketan Kumar
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Abhishek Rao
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India.
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17
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Rex DAB, Keshava Prasad TS, Kandasamy RK. Revisiting Regulated Cell Death Responses in Viral Infections. Int J Mol Sci 2022; 23:ijms23137023. [PMID: 35806033 PMCID: PMC9266763 DOI: 10.3390/ijms23137023] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/07/2023] Open
Abstract
The fate of a viral infection in the host begins with various types of cellular responses, such as abortive, productive, latent, and destructive infections. Apoptosis, necroptosis, and pyroptosis are the three major types of regulated cell death mechanisms that play critical roles in viral infection response. Cell shrinkage, nuclear condensation, bleb formation, and retained membrane integrity are all signs of osmotic imbalance-driven cytoplasmic swelling and early membrane damage in necroptosis and pyroptosis. Caspase-driven apoptotic cell demise is considered in many circumstances as an anti-inflammatory, and some pathogens hijack the cell death signaling routes to initiate a targeted attack against the host. In this review, the selected mechanisms by which viruses interfere with cell death were discussed in-depth and were illustrated by compiling the general principles and cellular signaling mechanisms of virus–host-specific molecule interactions.
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Affiliation(s)
| | - Thottethodi Subrahmanya Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
- Correspondence: (T.S.K.P.); (R.K.K.)
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O Box 505055, United Arab Emirates
- Correspondence: (T.S.K.P.); (R.K.K.)
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18
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Soares-Schanoski A, Sauerwald N, Goforth CW, Periasamy S, Weir DL, Lizewski S, Lizewski R, Ge Y, Kuzmina NA, Nair VD, Vangeti S, Marjanovic N, Cappuccio A, Cheng WS, Mofsowitz S, Miller CM, Yu XB, George MC, Zaslavsky E, Bukreyev A, Troyanskaya OG, Sealfon SC, Letizia AG, Ramos I. Asymptomatic SARS-CoV-2 Infection Is Associated With Higher Levels of Serum IL-17C, Matrix Metalloproteinase 10 and Fibroblast Growth Factors Than Mild Symptomatic COVID-19. Front Immunol 2022; 13:821730. [PMID: 35479098 PMCID: PMC9037090 DOI: 10.3389/fimmu.2022.821730] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Young adults infected with SARS-CoV-2 are frequently asymptomatic or develop only mild disease. Because capturing representative mild and asymptomatic cases require active surveillance, they are less characterized than moderate or severe cases of COVID-19. However, a better understanding of SARS-CoV-2 asymptomatic infections might shed light into the immune mechanisms associated with the control of symptoms and protection. To this aim, we have determined the temporal dynamics of the humoral immune response, as well as the serum inflammatory profile, of mild and asymptomatic SARS-CoV-2 infections in a cohort of 172 initially seronegative prospectively studied United States Marine recruits, 149 of whom were subsequently found to be SARS-CoV-2 infected. The participants had blood samples taken, symptoms surveyed and PCR tests for SARS-CoV-2 performed periodically for up to 105 days. We found similar dynamics in the profiles of viral load and in the generation of specific antibody responses in asymptomatic and mild symptomatic participants. A proteomic analysis using an inflammatory panel including 92 analytes revealed a pattern of three temporal waves of inflammatory and immunoregulatory mediators, and a return to baseline for most of the inflammatory markers by 35 days post-infection. We found that 23 analytes were significantly higher in those participants that reported symptoms at the time of the first positive SARS-CoV-2 PCR compared with asymptomatic participants, including mostly chemokines and cytokines associated with inflammatory response or immune activation (i.e., TNF-α, TNF-β, CXCL10, IL-8). Notably, we detected 7 analytes (IL-17C, MMP-10, FGF-19, FGF-21, FGF-23, CXCL5 and CCL23) that were higher in asymptomatic participants than in participants with symptoms; these are known to be involved in tissue repair and may be related to the control of symptoms. Overall, we found a serum proteomic signature that differentiates asymptomatic and mild symptomatic infections in young adults, including potential targets for developing new therapies and prognostic tests.
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Affiliation(s)
| | - Natalie Sauerwald
- Center for Computational Biology, Flatiron Institute, New York, NY, United States
| | - Carl W Goforth
- Naval Medical Research Center, Silver Spring, MD, United States
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Galveston National Laboratory, Galveston, TX, United States
| | - Dawn L Weir
- Naval Medical Research Center, Silver Spring, MD, United States
| | | | | | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Natalia A Kuzmina
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Galveston National Laboratory, Galveston, TX, United States
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nada Marjanovic
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wan Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sagie Mofsowitz
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Clare M Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Xuechen B Yu
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mary-Catherine George
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Galveston National Laboratory, Galveston, TX, United States.,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States.,Department of Computer Science, Princeton University, Princeton, NJ, United States
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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19
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Zhou H, Zhang Y, Wang J, Yan Y, Liu Y, Shi X, Zhang Q, Xu X. The CREB and AP-1-Dependent Cell Communication Network Factor 1 Regulates Porcine Epidemic Diarrhea Virus-Induced Cell Apoptosis Inhibiting Virus Replication Through the p53 Pathway. Front Microbiol 2022; 13:831852. [PMID: 35418961 PMCID: PMC8996185 DOI: 10.3389/fmicb.2022.831852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) infection causes severe diarrhea, dehydration, and high mortality in sick pigs, causing huge economic losses to the pig industry. However, the relationship between cell communication network factor 1 (CCN1) and PEDV infection has not been reported. In this study, we showed that the expression of CCN1 was enhanced by PEDV infection, and we observed that PEDV promotes the CREB and AP-1 activation to promote CCN1 expression. The PKA and p38 inhibitors significantly suppress CCN1 expression, indicating that PEDV-induced CCN1 expression may be through PKA and p38 pathway. Further tests confirmed that CREB and AP-1 are regulated by PKA and p38, respectively. Overexpression of CCN1 decreased the replication of PEDV, whereas knockdown of CCN1 increased the replication of PEDV. We proved that the overexpression of CCN1 increased the phosphorylation level of p53, promoted the expresion of Bax and the cleavage of caspase 9 and caspase 3, and inhibited the production of Bcl-2. CCN1 knockdown decreased the phosphorylation level of p53, inhibited the production of Bax and the cleavage of caspase 9 and caspase 3, and promoted the expression of Bcl-2. The treatment of PFT-α (p53 inhibitor) significantly suppressed the expression of cleaved caspase 9 and caspase 3, leading to the decrease of apoptosis. Together, these studies showed that PEDV promotes the activation of CREB and AP-1 to increase the expression of CCN1. Overexpression of CCN1 promotes apoptosis by elevating p53 protein phosphorylation and inhibits PEDV replication, and knockdown of CCN1 inhibits apoptosis by decreasing p53 protein phosphorylation and promotes PEDV replication. Our study could provide some reference for the molecular mechanisms of PEDV-induced CCN1 induction and supply a new therapeutic target for PEDV.
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Affiliation(s)
- Hongchao Zhou
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yuting Zhang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Jingjing Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yuchao Yan
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yi Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Xiaojie Shi
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Qi Zhang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Xingang Xu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
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20
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Ahmed FF, Reza MS, Sarker MS, Islam MS, Mosharaf MP, Hasan S, Mollah MNH. Identification of host transcriptome-guided repurposable drugs for SARS-CoV-1 infections and their validation with SARS-CoV-2 infections by using the integrated bioinformatics approaches. PLoS One 2022; 17:e0266124. [PMID: 35390032 PMCID: PMC8989220 DOI: 10.1371/journal.pone.0266124] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 03/15/2022] [Indexed: 12/18/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is one of the most severe global pandemic due to its high pathogenicity and death rate starting from the end of 2019. Though there are some vaccines available against SAER-CoV-2 infections, we are worried about their effectiveness, due to its unstable sequence patterns. Therefore, beside vaccines, globally effective supporting drugs are also required for the treatment against SARS-CoV-2 infection. To explore commonly effective repurposable drugs for the treatment against different variants of coronavirus infections, in this article, an attempt was made to explore host genomic biomarkers guided repurposable drugs for SARS-CoV-1 infections and their validation with SARS-CoV-2 infections by using the integrated bioinformatics approaches. At first, we identified 138 differentially expressed genes (DEGs) between SARS-CoV-1 infected and control samples by analyzing high throughput gene-expression profiles to select drug target key receptors. Then we identified top-ranked 11 key DEGs (SMAD4, GSK3B, SIRT1, ATM, RIPK1, PRKACB, MED17, CCT2, BIRC3, ETS1 and TXN) as hub genes (HubGs) by protein-protein interaction (PPI) network analysis of DEGs highlighting their functions, pathways, regulators and linkage with other disease risks that may influence SARS-CoV-1 infections. The DEGs-set enrichment analysis significantly detected some crucial biological processes (immune response, regulation of angiogenesis, apoptotic process, cytokine production and programmed cell death, response to hypoxia and oxidative stress), molecular functions (transcription factor binding and oxidoreductase activity) and pathways (transcriptional mis-regulation in cancer, pathways in cancer, chemokine signaling pathway) that are associated with SARS-CoV-1 infections as well as SARS-CoV-2 infections by involving HubGs. The gene regulatory network (GRN) analysis detected some transcription factors (FOXC1, GATA2, YY1, FOXL1, TP53 and SRF) and micro-RNAs (hsa-mir-92a-3p, hsa-mir-155-5p, hsa-mir-106b-5p, hsa-mir-34a-5p and hsa-mir-19b-3p) as the key transcriptional and post- transcriptional regulators of HubGs, respectively. We also detected some chemicals (Valproic Acid, Cyclosporine, Copper Sulfate and arsenic trioxide) that may regulates HubGs. The disease-HubGs interaction analysis showed that our predicted HubGs are also associated with several other diseases including different types of lung diseases. Then we considered 11 HubGs mediated proteins and their regulatory 6 key TFs proteins as the drug target proteins (receptors) and performed their docking analysis with the SARS-CoV-2 3CL protease-guided top listed 90 anti-viral drugs out of 3410. We found Rapamycin, Tacrolimus, Torin-2, Radotinib, Danoprevir, Ivermectin and Daclatasvir as the top-ranked 7 candidate-drugs with respect to our proposed target proteins for the treatment against SARS-CoV-1 infections. Then, we validated these 7 candidate-drugs against the already published top-ranked 11 target proteins associated with SARS-CoV-2 infections by molecular docking simulation and found their significant binding affinity scores with our proposed candidate-drugs. Finally, we validated all of our findings by the literature review. Therefore, the proposed candidate-drugs might play a vital role for the treatment against different variants of SARS-CoV-2 infections with comorbidities, since the proposed HubGs are also associated with several comorbidities.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
- Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi, Bangladesh
| | - Md. Selim Reza
- Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi, Bangladesh
| | - Md. Shahin Sarker
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Samiul Islam
- Department of Plant Pathology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Md. Parvez Mosharaf
- Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi, Bangladesh
| | - Sohel Hasan
- Department of Biochemistry and Molecular Biology, Rajshahi University, Rajshhi, Bangladesh
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab., Department of Statistics, Rajshahi University, Rajshahi, Bangladesh
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21
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Abstract
The process of adaptation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to humans probably had started decades ago, when its ancestor diverged from the bat coronavirus. The adaptive process comprises strategies the virus uses to overcome the respiratory tract defense barriers and replicate and shed in the host cells. These strategies include the impairment of interferon production, hiding immunogenic motifs, avoiding viral RNA detection, manipulating cell autophagy, triggering host cell death, inducing lymphocyte exhaustion and depletion, and finally, mutation and escape from immunity. In addition, SARS-CoV-2 employs strategies to take advantage of host cell resources for its benefits, such as inhibiting the ubiquitin-proteasome system, hijacking mitochondria functions, and usage of enhancing antibodies. It may be anticipated that as the tradeoffs of adaptation progress, the virus destructive burden will gradually subside. Some evidence suggests that SARS-CoV-2 will become part of the human respiratory virome, as had occurred with other coronaviruses, and coevolve with its host.
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Affiliation(s)
- Eduardo Tosta
- Universidade de Brasília, Faculdade de Medicina, Brasília, DF, Brasil
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22
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Kumar R, Chauhan D, Saini G, Kumar R, Kumar S, Sharma D, Sharma M, Kumar Bharti V, Kumar A, Ghosh A. Down-regulation of RdRp complex and activated immune response due to increased arsenic level leads to decreased corona virus replication. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100162. [PMID: 36090585 PMCID: PMC9444337 DOI: 10.1016/j.crmicr.2022.100162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Corona virus is pandemic and responsible for more than 5.6 million deaths. It was observed that its severity was reported in varied ways in different countries and even in different states of India. This variation was critically evaluated in the area with high contamination of Arsenic (As) to understand the arsenic toxicity and Covid epidemiology and associated health effects in the human population. It was reported that the area with low arsenic contamination has a very high incidence rate of Corona infection in the world. Even in the Indian scenario, high As-contaminated states like West Bengal, Jharkhand and Bihar, the incidence rate is 1.994%, 1.114% and 0.661%, respectively. In contrast, states with the least arsenic contamination have a very high corona incidence rate like 6.308, 17.289 and 4.351, respectively. It was evident that Arsenic inhibits the RdRp complex, which leads to the inhibition of viral genome replication. The PAMP associated pathway was activated by Arsenic and effectively bound with viral spike proteins leading to effective clearance of virus through activation of TNF alpha and IL-1. It finally leads to increased production of IgE, IgG and IGA. Arsenic also enhances inflammatory response against the virus through increased production of cytokine. The high arsenic level also induces apoptosis in viral infected cells through Bax/Bak pathway. It activates cytochrome-c and caspase-3 activity, inducing apoptosis in viral infected cells through PARP activation in the nucleus. These combined findings suggest that high arsenic contamination causes replication inhibition, activates an inflammatory response, increases antibody production, and finally leads to apoptosis through the mitochondrial pathway. People residing in arsenic hit areas are at a very low threat of corona infection.
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Affiliation(s)
- Ranjit Kumar
- Department of Animal Science, Central University of Himachal Pradesh, Dharamshala, India
- Corresponding author.
| | - Disha Chauhan
- Department of Animal Science, Central University of Himachal Pradesh, Dharamshala, India
| | - Geetika Saini
- Department of Animal Science, Central University of Himachal Pradesh, Dharamshala, India
| | - Rakesh Kumar
- Department of Animal Science, Central University of Himachal Pradesh, Dharamshala, India
| | - Sunil Kumar
- Department of Animal Science, Central University of Himachal Pradesh, Dharamshala, India
| | - Dixit Sharma
- Department of Animal Science, Central University of Himachal Pradesh, Dharamshala, India
| | - Munish Sharma
- Department of Plant Science, Central University of Himachal Pradesh, Dharamshala, India
| | - Vijay Kumar Bharti
- DRDO-Defence Institute of High Altitude Research (DIHAR), UT Ladakh, India
| | - Arun Kumar
- Mahavir Cancer Institute and Research Centre, Patna, India
| | - Ashok Ghosh
- Mahavir Cancer Institute and Research Centre, Patna, India
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23
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Yapasert R, Khaw-on P, Banjerdpongchai R. Coronavirus Infection-Associated Cell Death Signaling and Potential Therapeutic Targets. Molecules 2021; 26:7459. [PMID: 34946543 PMCID: PMC8706825 DOI: 10.3390/molecules26247459] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19 is the name of the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that occurred in 2019. The virus-host-specific interactions, molecular targets on host cell deaths, and the involved signaling are crucial issues, which become potential targets for treatment. Spike protein, angiotensin-converting enzyme 2 (ACE2), cathepsin L-cysteine peptidase, transmembrane protease serine 2 (TMPRSS2), nonstructural protein 1 (Nsp1), open reading frame 7a (ORF7a), viral main protease (3C-like protease (3CLpro) or Mpro), RNA dependent RNA polymerase (RdRp) (Nsp12), non-structural protein 13 (Nsp13) helicase, and papain-like proteinase (PLpro) are molecules associated with SARS-CoV infection and propagation. SARS-CoV-2 can induce host cell death via five kinds of regulated cell death, i.e., apoptosis, necroptosis, pyroptosis, autophagy, and PANoptosis. The mechanisms of these cell deaths are well established and can be disrupted by synthetic small molecules or natural products. There are a variety of compounds proven to play roles in the cell death inhibition, such as pan-caspase inhibitor (z-VAD-fmk) for apoptosis, necrostatin-1 for necroptosis, MCC950, a potent and specific inhibitor of the NLRP3 inflammasome in pyroptosis, and chloroquine/hydroxychloroquine, which can mitigate the corresponding cell death pathways. However, NF-κB signaling is another critical anti-apoptotic or survival route mediated by SARS-CoV-2. Such signaling promotes viral survival, proliferation, and inflammation by inducing the expression of apoptosis inhibitors such as Bcl-2 and XIAP, as well as cytokines, e.g., TNF. As a result, tiny natural compounds functioning as proteasome inhibitors such as celastrol and curcumin can be used to modify NF-κB signaling, providing a responsible method for treating SARS-CoV-2-infected patients. The natural constituents that aid in inhibiting viral infection, progression, and amplification of coronaviruses are also emphasized, which are in the groups of alkaloids, flavonoids, terpenoids, diarylheptanoids, and anthraquinones. Natural constituents derived from medicinal herbs have anti-inflammatory and antiviral properties, as well as inhibitory effects, on the viral life cycle, including viral entry, replication, assembly, and release of COVID-19 virions. The phytochemicals contain a high potential for COVID-19 treatment. As a result, SARS-CoV-2-infected cell death processes and signaling might be of high efficacy for therapeutic targeting effects and yielding encouraging outcomes.
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Affiliation(s)
- Rittibet Yapasert
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Patompong Khaw-on
- Faculty of Nursing, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Ratana Banjerdpongchai
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
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24
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Over Fifty Years of Life, Death, and Cannibalism: A Historical Recollection of Apoptosis and Autophagy. Int J Mol Sci 2021; 22:ijms222212466. [PMID: 34830349 PMCID: PMC8618802 DOI: 10.3390/ijms222212466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/18/2023] Open
Abstract
Research in biomedical sciences has changed dramatically over the past fifty years. There is no doubt that the discovery of apoptosis and autophagy as two highly synchronized and regulated mechanisms in cellular homeostasis are among the most important discoveries in these decades. Along with the advancement in molecular biology, identifying the genetic players in apoptosis and autophagy has shed light on our understanding of their function in physiological and pathological conditions. In this review, we first describe the history of key discoveries in apoptosis with a molecular insight and continue with apoptosis pathways and their regulation. We touch upon the role of apoptosis in human health and its malfunction in several diseases. We discuss the path to the morphological and molecular discovery of autophagy. Moreover, we dive deep into the precise regulation of autophagy and recent findings from basic research to clinical applications of autophagy modulation in human health and illnesses and the available therapies for many diseases caused by impaired autophagy. We conclude with the exciting crosstalk between apoptosis and autophagy, from the early discoveries to recent findings.
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25
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Kleinehr J, Wilden JJ, Boergeling Y, Ludwig S, Hrincius ER. Metabolic Modifications by Common Respiratory Viruses and Their Potential as New Antiviral Targets. Viruses 2021; 13:2068. [PMID: 34696497 PMCID: PMC8540840 DOI: 10.3390/v13102068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/22/2021] [Accepted: 10/09/2021] [Indexed: 12/11/2022] Open
Abstract
Respiratory viruses are known to be the most frequent causative mediators of lung infections in humans, bearing significant impact on the host cell signaling machinery due to their host-dependency for efficient replication. Certain cellular functions are actively induced by respiratory viruses for their own benefit. This includes metabolic pathways such as glycolysis, fatty acid synthesis (FAS) and the tricarboxylic acid (TCA) cycle, among others, which are modified during viral infections. Here, we summarize the current knowledge of metabolic pathway modifications mediated by the acute respiratory viruses respiratory syncytial virus (RSV), rhinovirus (RV), influenza virus (IV), parainfluenza virus (PIV), coronavirus (CoV) and adenovirus (AdV), and highlight potential targets and compounds for therapeutic approaches.
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Affiliation(s)
- Jens Kleinehr
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (J.K.); (J.J.W.); (Y.B.); (S.L.)
| | - Janine J. Wilden
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (J.K.); (J.J.W.); (Y.B.); (S.L.)
| | - Yvonne Boergeling
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (J.K.); (J.J.W.); (Y.B.); (S.L.)
| | - Stephan Ludwig
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (J.K.); (J.J.W.); (Y.B.); (S.L.)
- Cells in Motion Interfaculty Centre (CiMIC), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany
| | - Eike R. Hrincius
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (J.K.); (J.J.W.); (Y.B.); (S.L.)
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26
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Myocardial Damage by SARS-CoV-2: Emerging Mechanisms and Therapies. Viruses 2021; 13:v13091880. [PMID: 34578462 PMCID: PMC8473126 DOI: 10.3390/v13091880] [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: 08/03/2021] [Revised: 09/06/2021] [Accepted: 09/18/2021] [Indexed: 01/01/2023] Open
Abstract
Evidence is emerging that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect various organs of the body, including cardiomyocytes and cardiac endothelial cells in the heart. This review focuses on the effects of SARS-CoV-2 in the heart after direct infection that can lead to myocarditis and an outline of potential treatment options. The main points are: (1) Viral entry: SARS-CoV-2 uses specific receptors and proteases for docking and priming in cardiac cells. Thus, different receptors or protease inhibitors might be effective in SARS-CoV-2-infected cardiac cells. (2) Viral replication: SARS-CoV-2 uses RNA-dependent RNA polymerase for replication. Drugs acting against ssRNA(+) viral replication for cardiac cells can be effective. (3) Autophagy and double-membrane vesicles: SARS-CoV-2 manipulates autophagy to inhibit viral clearance and promote SARS-CoV-2 replication by creating double-membrane vesicles as replication sites. (4) Immune response: Host immune response is manipulated to evade host cell attacks against SARS-CoV-2 and increased inflammation by dysregulating immune cells. Efficiency of immunosuppressive therapy must be elucidated. (5) Programmed cell death: SARS-CoV-2 inhibits programmed cell death in early stages and induces apoptosis, necroptosis, and pyroptosis in later stages. (6) Energy metabolism: SARS-CoV-2 infection leads to disturbed energy metabolism that in turn leads to a decrease in ATP production and ROS production. (7) Viroporins: SARS-CoV-2 creates viroporins that lead to an imbalance of ion homeostasis. This causes apoptosis, altered action potential, and arrhythmia.
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27
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Ku C, Chen I, Lai M. Infection-induced inflammation from specific inborn errors of immunity to COVID-19. FEBS J 2021; 288:5021-5041. [PMID: 33971084 PMCID: PMC8236961 DOI: 10.1111/febs.15961] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/10/2021] [Accepted: 05/07/2021] [Indexed: 01/07/2023]
Abstract
Inborn errors of immunity (IEIs) are a group of genetically defined disorders leading to defective immunity. Some IEIs have been linked to mutations of immune receptors or signaling molecules, resulting in defective signaling of respective cascades essential for combating specific pathogens. However, it remains incompletely understood why in selected IEIs, such as X-linked lymphoproliferative syndrome type 2 (XLP-2), hypo-immune response to specific pathogens results in persistent inflammation. Moreover, mechanisms underlying the generation of anticytokine autoantibodies are mostly unknown. Recently, IEIs have been associated with coronavirus disease 2019 (COVID-19), with a small proportion of patients that contract severe COVID-19 displaying loss-of-function mutations in genes associated with type I interferons (IFNs). Moreover, approximately 10% of patients with severe COVID-19 possess anti-type I IFN-neutralizing autoantibodies. Apart from IEIs that impair immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV-2 encodes several proteins that suppress early type I IFN production. One primary consequence of the lack of type I IFNs during early SARS-CoV-2 infection is the increased inflammation associated with COVID-19. In XLP-2, resolution of inflammation rescued experimental subjects from infection-induced mortality. Recent studies also indicate that targeting inflammation could alleviate COVID-19. In this review, we discuss infection-induced inflammation in IEIs, using XLP-2 and COVID-19 as examples. We suggest that resolving inflammation may represent an effective therapeutic approach to these diseases.
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Affiliation(s)
- Cheng‐Lung Ku
- Laboratory of Human Immunology and Infectious DiseasesGraduate Institute of Clinical Medical SciencesChang Gung UniversityTaoyuanTaiwan,Department of NephrologyLinkou Chang Gung Memorial HospitalTaoyuanTaiwan
| | - I‐Ting Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Ming‐Zong Lai
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
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Anisul M, Shilts J, Schwartzentruber J, Hayhurst J, Buniello A, Shaikho Elhaj Mohammed E, Zheng J, Holmes M, Ochoa D, Carmona M, Maranville J, Gaunt TR, Emilsson V, Gudnason V, McDonagh EM, Wright GJ, Ghoussaini M, Dunham I. A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance. eLife 2021; 10:e69719. [PMID: 34402426 PMCID: PMC8457835 DOI: 10.7554/elife.69719] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/07/2021] [Indexed: 12/16/2022] Open
Abstract
Background The virus SARS-CoV-2 can exploit biological vulnerabilities (e.g. host proteins) in susceptible hosts that predispose to the development of severe COVID-19. Methods To identify host proteins that may contribute to the risk of severe COVID-19, we undertook proteome-wide genetic colocalisation tests, and polygenic (pan) and cis-Mendelian randomisation analyses leveraging publicly available protein and COVID-19 datasets. Results Our analytic approach identified several known targets (e.g. ABO, OAS1), but also nominated new proteins such as soluble Fas (colocalisation probability >0.9, p=1 × 10-4), implicating Fas-mediated apoptosis as a potential target for COVID-19 risk. The polygenic (pan) and cis-Mendelian randomisation analyses showed consistent associations of genetically predicted ABO protein with several COVID-19 phenotypes. The ABO signal is highly pleiotropic, and a look-up of proteins associated with the ABO signal revealed that the strongest association was with soluble CD209. We demonstrated experimentally that CD209 directly interacts with the spike protein of SARS-CoV-2, suggesting a mechanism that could explain the ABO association with COVID-19. Conclusions Our work provides a prioritised list of host targets potentially exploited by SARS-CoV-2 and is a precursor for further research on CD209 and FAS as therapeutically tractable targets for COVID-19. Funding MAK, JSc, JH, AB, DO, MC, EMM, MG, ID were funded by Open Targets. J.Z. and T.R.G were funded by the UK Medical Research Council Integrative Epidemiology Unit (MC_UU_00011/4). JSh and GJW were funded by the Wellcome Trust Grant 206194. This research was funded in part by the Wellcome Trust [Grant 206194]. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.
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Affiliation(s)
- Mohd Anisul
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Jarrod Shilts
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - Jeremy Schwartzentruber
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
| | - James Hayhurst
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | - Annalisa Buniello
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | | | - Jie Zheng
- Medical Research Council (MRC) Integrative Epidemiology Unit, Department of Population Health Sciences, University of BristolBristolUnited Kingdom
| | - Michael Holmes
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
- Medical Research Council Population Health Research Unit (MRC PHRU), Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
| | - David Ochoa
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | - Miguel Carmona
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | | | - Tom R Gaunt
- Medical Research Council (MRC) Integrative Epidemiology Unit, Department of Population Health Sciences, University of BristolBristolUnited Kingdom
| | - Valur Emilsson
- Icelandic Heart AssociationKopavogurIceland
- Faculty of Medicine, University of IcelandReykjavikIceland
| | - Vilmundur Gudnason
- Icelandic Heart AssociationKopavogurIceland
- Faculty of Medicine, University of IcelandReykjavikIceland
| | - Ellen M McDonagh
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
| | - Gavin J Wright
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Department of Biology, York Biomedical Research Institute, Hull York Medical School, University of YorkYorkUnited Kingdom
| | - Maya Ghoussaini
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Open Targets, Wellcome Genome CampusHinxtonUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
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Low level of plasminogen increases risk for mortality in COVID-19 patients. Cell Death Dis 2021; 12:773. [PMID: 34354045 PMCID: PMC8340078 DOI: 10.1038/s41419-021-04070-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022]
Abstract
The pathophysiology of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and especially of its complications is still not fully understood. In fact, a very high number of patients with COVID-19 die because of thromboembolic causes. A role of plasminogen, as precursor of fibrinolysis, has been hypothesized. In this study, we aimed to investigate the association between plasminogen levels and COVID-19-related outcomes in a population of 55 infected Caucasian patients (mean age: 69.8 ± 14.3, 41.8% female). Low levels of plasminogen were significantly associated with inflammatory markers (CRP, PCT, and IL-6), markers of coagulation (D-dimer, INR, and APTT), and markers of organ dysfunctions (high fasting blood glucose and decrease in the glomerular filtration rate). A multidimensional analysis model, including the correlation of the expression of coagulation with inflammatory parameters, indicated that plasminogen tended to cluster together with IL-6, hence suggesting a common pathway of activation during disease's complication. Moreover, low levels of plasminogen strongly correlated with mortality in COVID-19 patients even after multiple adjustments for presence of confounding. These data suggest that plasminogen may play a pivotal role in controlling the complex mechanisms beyond the COVID-19 complications, and may be useful both as biomarker for prognosis and for therapeutic target against this extremely aggressive infection.
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30
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Cell Death in Coronavirus Infections: Uncovering Its Role during COVID-19. Cells 2021; 10:cells10071585. [PMID: 34201847 PMCID: PMC8306954 DOI: 10.3390/cells10071585] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Cell death mechanisms are crucial to maintain an appropriate environment for the functionality of healthy cells. However, during viral infections, dysregulation of these processes can be present and can participate in the pathogenetic mechanisms of the disease. In this review, we describe some features of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and some immunopathogenic mechanisms characterizing the present coronavirus disease (COVID-19). Lymphopenia and monocytopenia are important contributors to COVID-19 immunopathogenesis. The fine mechanisms underlying these phenomena are still unknown, and several hypotheses have been raised, some of which assign a role to cell death as far as the reduction of specific types of immune cells is concerned. Thus, we discuss three major pathways such as apoptosis, necroptosis, and pyroptosis, and suggest that all of them likely occur simultaneously in COVID-19 patients. We describe that SARS-CoV-2 can have both a direct and an indirect role in inducing cell death. Indeed, on the one hand, cell death can be caused by the virus entry into cells, on the other, the excessive concentration of cytokines and chemokines, a process that is known as a COVID-19-related cytokine storm, exerts deleterious effects on circulating immune cells. However, the overall knowledge of these mechanisms is still scarce and further studies are needed to delineate new therapeutic strategies.
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31
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Yong SJ. Diseased lungs may hinder COVID-19 development: A possible reason for the low prevalence of COPD in COVID-19 patients. Med Hypotheses 2021; 153:110628. [PMID: 34139599 PMCID: PMC8188770 DOI: 10.1016/j.mehy.2021.110628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022]
Abstract
Presently, it remains unclear why the prevalence of lung diseases, namely chronic obstructive pulmonary disease (COPD), is much lower than other medical comorbidities and the general population among patients with coronavirus disease 2019 (COVID-19). If COVID-19 is a respiratory disease, why is COPD not the leading risk factor for contracting COVID-19? The same odd phenomenon was also observed with other pathogenic human coronaviruses causing severe acute respiratory distress syndrome (SARS) and Middle East respiratory syndrome (MERS), but not other respiratory viral infections such as influenza and respiratory syncytial viruses. One commonly proposed reason for the low COPD rates among COVID-19 patients is the usage of inhaled corticosteroids or bronchodilators that may protect against COVID-19. However, another possible reason not discussed elsewhere is that lungs in a diseased state may not be conducive for the severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) to establish COVID-19. For one, COPD causes mucous plugging in large and small airways, which may hinder SARS-CoV-2 from reaching deeper parts of the lungs (i.e., alveoli). Thus, SARS-CoV-2 may only localize to the upper respiratory tract of persons with COPD, causing mild or asymptomatic infections requiring no hospital attention. Even if SARS-CoV-2 reaches the alveoli, cells therein are probably under a heavy burden of endoplasmic reticulum (ER) stress and extensively damaged where it may not support efficient viral replication. As a result, limited SARS-CoV-2 virions would be produced in diseased lungs, preventing the development of COVID-19.
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Affiliation(s)
- Shin Jie Yong
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor, Malaysia.
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32
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Wu Y, Ma L, Cai S, Zhuang Z, Zhao Z, Jin S, Xie W, Zhou L, Zhang L, Zhao J, Cui J. RNA-induced liquid phase separation of SARS-CoV-2 nucleocapsid protein facilitates NF-κB hyper-activation and inflammation. Signal Transduct Target Ther 2021; 6:167. [PMID: 33895773 PMCID: PMC8065320 DOI: 10.1038/s41392-021-00575-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/06/2021] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
The ongoing 2019 novel coronavirus disease (COVID-19) caused by SARS-CoV-2 has posed a worldwide pandemic and a major global public health threat. The severity and mortality of COVID-19 are associated with virus-induced dysfunctional inflammatory responses and cytokine storms. However, the interplay between host inflammatory responses and SARS-CoV-2 infection remains largely unknown. Here, we demonstrate that SARS-CoV-2 nucleocapsid (N) protein, the major structural protein of the virion, promotes the virus-triggered activation of NF-κB signaling. After binding to viral RNA, N protein robustly undergoes liquid-liquid phase separation (LLPS), which recruits TAK1 and IKK complex, the key kinases of NF-κB signaling, to enhance NF-κB activation. Moreover, 1,6-hexanediol, the inhibitor of LLPS, can attenuate the phase separation of N protein and restrict its regulatory functions in NF-κB activation. These results suggest that LLPS of N protein provides a platform to induce NF-κB hyper-activation, which could be a potential therapeutic target against COVID-19 severe pneumonia.
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Affiliation(s)
- Yaoxing Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ling Ma
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Sihui Cai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhiyao Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shouheng Jin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weihong Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lingli Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Jun Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
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Liu Y, Garron TM, Chang Q, Su Z, Zhou C, Qiu Y, Gong EC, Zheng J, Yin YW, Ksiazek T, Brasel T, Jin Y, Boor P, Comer JE, Gong B. Cell-Type Apoptosis in Lung during SARS-CoV-2 Infection. Pathogens 2021; 10:pathogens10050509. [PMID: 33922476 PMCID: PMC8145065 DOI: 10.3390/pathogens10050509] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 pandemic has inspired renewed interest in understanding the fundamental pathology of acute respiratory distress syndrome (ARDS) following infection. However, the pathogenesis of ARDS following SRAS-CoV-2 infection remains largely unknown. In the present study, we examined apoptosis in postmortem lung sections from COVID-19 patients and in lung tissues from a non-human primate model of SARS-CoV-2 infection, in a cell-type manner, including type 1 and 2 alveolar cells and vascular endothelial cells (ECs), macrophages, and T cells. Multiple-target immunofluorescence assays and Western blotting suggest both intrinsic and extrinsic apoptotic pathways are activated during SARS-CoV-2 infection. Furthermore, we observed that SARS-CoV-2 fails to induce apoptosis in human bronchial epithelial cells (i.e., BEAS2B cells) and primary human umbilical vein endothelial cells (HUVECs), which are refractory to SARS-CoV-2 infection. However, infection of co-cultured Vero cells and HUVECs or Vero cells and BEAS2B cells with SARS-CoV-2 induced apoptosis in both Vero cells and HUVECs/BEAS2B cells but did not alter the permissiveness of HUVECs or BEAS2B cells to the virus. Post-exposure treatment of the co-culture of Vero cells and HUVECs with a novel non-cyclic nucleotide small molecule EPAC1-specific activator reduced apoptosis in HUVECs. These findings may help to delineate a novel insight into the pathogenesis of ARDS following SARS-CoV-2 infection.
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Affiliation(s)
- Yakun Liu
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (Y.L.); (Q.C.); (Z.S.); (C.Z.); (Y.Q.); (E.C.G.); (T.K.)
| | - Tania M. Garron
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (T.M.G.); (T.B.)
| | - Qing Chang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (Y.L.); (Q.C.); (Z.S.); (C.Z.); (Y.Q.); (E.C.G.); (T.K.)
| | - Zhengchen Su
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (Y.L.); (Q.C.); (Z.S.); (C.Z.); (Y.Q.); (E.C.G.); (T.K.)
| | - Changcheng Zhou
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (Y.L.); (Q.C.); (Z.S.); (C.Z.); (Y.Q.); (E.C.G.); (T.K.)
| | - Yuan Qiu
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (Y.L.); (Q.C.); (Z.S.); (C.Z.); (Y.Q.); (E.C.G.); (T.K.)
| | - Eric C. Gong
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (Y.L.); (Q.C.); (Z.S.); (C.Z.); (Y.Q.); (E.C.G.); (T.K.)
| | - Junying Zheng
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Thomas Ksiazek
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (Y.L.); (Q.C.); (Z.S.); (C.Z.); (Y.Q.); (E.C.G.); (T.K.)
| | - Trevor Brasel
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (T.M.G.); (T.B.)
| | - Yang Jin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University Medical Campus, Boston, MA 02118, USA;
| | - Paul Boor
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (Y.L.); (Q.C.); (Z.S.); (C.Z.); (Y.Q.); (E.C.G.); (T.K.)
- Correspondence: (P.B.); (J.E.C.); (B.G.); Tel.: +1-409-772-2813 (P.B.); +1-409-266-6915 (J.E.C.); +1-409-266-6682 (B.G.)
| | - Jason E. Comer
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (T.M.G.); (T.B.)
- Correspondence: (P.B.); (J.E.C.); (B.G.); Tel.: +1-409-772-2813 (P.B.); +1-409-266-6915 (J.E.C.); +1-409-266-6682 (B.G.)
| | - Bin Gong
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; (Y.L.); (Q.C.); (Z.S.); (C.Z.); (Y.Q.); (E.C.G.); (T.K.)
- Correspondence: (P.B.); (J.E.C.); (B.G.); Tel.: +1-409-772-2813 (P.B.); +1-409-266-6915 (J.E.C.); +1-409-266-6682 (B.G.)
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Abedi F, Rezaee R, Hayes AW, Nasiripour S, Karimi G. MicroRNAs and SARS-CoV-2 life cycle, pathogenesis, and mutations: biomarkers or therapeutic agents? Cell Cycle 2021; 20:143-153. [PMID: 33382348 PMCID: PMC7889196 DOI: 10.1080/15384101.2020.1867792] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
To date, proposed therapies and antiviral drugs have been failed to cure coronavirus disease 2019 (COVID-19) patients. However, at least two drug companies have applied for emergency use authorization with the United States Food and Drug Administration for their coronavirus vaccine candidates and several other vaccines are in various stages of development to determine safety and efficacy. Recently, some studies have shown the role of different human and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) microRNAs (miRNAs) in the pathophysiology of COVID-19. miRNAs are non-coding single-stranded RNAs, which are involved in several physiological and pathological conditions, such as cell proliferation, differentiation, and metabolism. They act as negative regulators of protein synthesis through binding to the 3' untranslated region (3' UTR) of the complementary target mRNA, leading to mRNA degradation or inhibition. The databases of Google Scholar, Scopus, PubMed, and Web of Science were searched for literature regarding the importance of miRNAs in the SARS-CoV-2 life cycle, pathogenesis, and genomic mutations. Furthermore, promising miRNAs as a biomarker or antiviral agent in COVID-19 therapy are reviewed.
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Affiliation(s)
- Farshad Abedi
- Pharmaceutical Research Center, Institute of Pharmaceutical Technology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ramin Rezaee
- Clinical Research Unit, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - A. Wallace Hayes
- University of South Florida, Tampa, FL, USA
- Michigan State University, East Lansing, MI, USA
| | - Somayyeh Nasiripour
- Department of Clinical Pharmacy, School of Pharmacy, Iran University of Medical Sciences, Iran
| | - Gholamreza Karimi
- Pharmaceutical Research Center, Institute of Pharmaceutical Technology, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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35
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Celardo I, Pace L, Cifaldi L, Gaudio C, Barnaba V. The immune system view of the coronavirus SARS-CoV-2. Biol Direct 2020; 15:30. [PMID: 33371901 PMCID: PMC7769684 DOI: 10.1186/s13062-020-00283-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022] Open
Abstract
Knowing the "point of view" of the immune system is essential to understand the characteristic of a pandemic, such as that generated by the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2, responsible for the Coronavirus Disease (COVID)-19. In this review, we will discuss the general host/pathogen interactions dictating protective immune response or immunopathology, addressing the role of immunity or immunopathology in influencing the clinical infection outcome, and debate the potential immunoprophylactic and immunotherapy strategies required to fight the virus infection.
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Affiliation(s)
- Ivana Celardo
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari, Sapienza Università di Roma, Rome, Italy
| | - Luigia Pace
- Armenise-Harvard Immune Regulation Unit, Italian Institute for Genomic Medicine, FPO IRCCS Candiolo, Turin, Italy
| | - Loredana Cifaldi
- Academic Department of Pediatrics (DPUO),, Ospedale Pediatrico Bambino Gesù,, IRCCS, Rome,, 00165, Italy.,Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, Rome, 00133, Italy
| | - Carlo Gaudio
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari, Sapienza Università di Roma, Rome, Italy
| | - Vincenzo Barnaba
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari, Sapienza Università di Roma, Rome, Italy.
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36
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Liu Y, Garron TM, Chang Q, Su Z, Zhou C, Gong EC, Zheng J, Yin Y, Ksiazek T, Brasel T, Jin Y, Boor P, Comer JE, Gong B. Cell-type apoptosis in lung during SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33398280 DOI: 10.1101/2020.12.23.424254] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The SARS-CoV-2 pandemic has inspired renewed interest in understanding the fundamental pathology of acute respiratory distress syndrome (ARDS) following infection because fatal COVID-19 cases are commonly linked to respiratory failure due to ARDS. The pathologic alteration known as diffuse alveolar damage in endothelial and epithelial cells is a critical feature of acute lung injury in ARDS. However, the pathogenesis of ARDS following SRAS-CoV-2 infection remains largely unknown. In the present study, we examined apoptosis in post-mortem lung sections from COVID-19 patients and lung tissues from a non-human primate model of SARS-CoV-2 infection, in a cell-type manner, including type 1 and 2 alveolar cells and vascular endothelial cells (ECs), macrophages, and T cells. Multiple-target immunofluorescence (IF) assays and western blotting suggest both intrinsic and extrinsic apoptotic pathways are activated during SARS-CoV-2 infection. Furthermore, we observed that SARS-CoV-2 fails to induce apoptosis in human bronchial epithelial cells (i.e., BEAS2B cells) and primary human umbilical vein endothelial cells (HUVECs), which are refractory to SARS-CoV-2 infection. However, infection of co-cultured Vero cells and HUVECs or Vero cells and BEAS2B cells with SARS-CoV-2 induced apoptosis in both Vero cells and HUVECs/BEAS2B cells, but did not alter the permissiveness of HUVECs or BEAS2B cells to the virus. Post-exposure treatment of the co-culture of Vero cells and HUVECs with an EPAC1-specific activator ameliorated apoptosis in HUVECs. These findings may help to delineate a novel insight into the pathogenesis of ARDS following SARS-CoV-2 infection.
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