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Veth TS, Nouwen LV, Zwaagstra M, Lyoo H, Wierenga KA, Westendorp B, Altelaar MAFM, Berkers C, van Kuppeveld FJM, Heck AJR. Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection. Mol Cell Proteomics 2024; 23:100757. [PMID: 38556169 PMCID: PMC11067349 DOI: 10.1016/j.mcpro.2024.100757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/16/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Picornaviridae represent a large family of single-stranded positive RNA viruses of which different members can infect both humans and animals. These include the enteroviruses (e.g., poliovirus, coxsackievirus, and rhinoviruses) as well as the cardioviruses (e.g., encephalomyocarditis virus). Picornaviruses have evolved to interact with, use, and/or evade cellular host systems to create the optimal environment for replication and spreading. It is known that viruses modify kinase activity during infection, but a proteome-wide overview of the (de)regulation of cellular kinases during picornavirus infection is lacking. To study the kinase activity landscape during picornavirus infection, we here applied dedicated targeted mass spectrometry-based assays covering ∼40% of the human kinome. Our data show that upon infection, kinases of the MAPK pathways become activated (e.g., ERK1/2, RSK1/2, JNK1/2/3, and p38), while kinases involved in regulating the cell cycle (e.g., CDK1/2, GWL, and DYRK3) become inactivated. Additionally, we observed the activation of CHK2, an important kinase involved in the DNA damage response. Using pharmacological kinase inhibitors, we demonstrate that several of these activated kinases are essential for the replication of encephalomyocarditis virus. Altogether, the data provide a quantitative understanding of the regulation of kinome activity induced by picornavirus infection, providing a resource important for developing novel antiviral therapeutic interventions.
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Affiliation(s)
- Tim S Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Lonneke V Nouwen
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Marleen Zwaagstra
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Heyrhyoung Lyoo
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Kathryn A Wierenga
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Bart Westendorp
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Celia Berkers
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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Thariat J, Little MP, Zablotska LB, Samson P, O’Banion MK, Leuraud K, Bergom C, Girault G, Azimzadeh O, Bouffler S, Hamada N. Radiotherapy for non-cancer diseases: benefits and long-term risks. Int J Radiat Biol 2024; 100:505-526. [PMID: 38180039 PMCID: PMC11039429 DOI: 10.1080/09553002.2023.2295966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
PURPOSE The discovery of X-rays was followed by a variety of attempts to treat infectious diseases and various other non-cancer diseases with ionizing radiation, in addition to cancer. There has been a recent resurgence of interest in the use of such radiotherapy for non-cancer diseases. Non-cancer diseases for which use of radiotherapy has currently been proposed include refractory ventricular tachycardia, neurodegenerative diseases (e.g. Alzheimer's disease and dementia), and Coronavirus Disease 2019 (COVID-19) pneumonia, all with ongoing clinical studies that deliver radiation doses of 0.5-25 Gy in a single fraction or in multiple daily fractions. In addition to such non-cancer effects, historical indications predominantly used in some countries (e.g. Germany) include osteoarthritis and degenerative diseases of the bones and joints. This narrative review gives an overview of the biological rationale and ongoing preclinical and clinical studies for radiotherapy proposed for various non-cancer diseases, discusses the plausibility of the proposed biological rationale, and considers the long-term radiation risks of cancer and non-cancer diseases. CONCLUSIONS A growing body of evidence has suggested that radiation represents a double-edged sword, not only for cancer, but also for non-cancer diseases. At present, clinical evidence has shown some beneficial effects of radiotherapy for ventricular tachycardia, but there is little or no such evidence of radiotherapy for other newly proposed non-cancer diseases (e.g. Alzheimer's disease, COVID-19 pneumonia). Patients with ventricular tachycardia and COVID-19 pneumonia have thus far been treated with radiotherapy when they are an urgent life threat with no efficient alternative treatment, but some survivors may encounter a paradoxical situation where patients were rescued by radiotherapy but then get harmed by radiotherapy. Further studies are needed to justify the clinical use of radiotherapy for non-cancer diseases, and optimize dose to diseased tissue while minimizing dose to healthy tissue.
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Affiliation(s)
- Juliette Thariat
- Department of Radiation Oncology, Comprehensive Cancer Centre François Baclesse, Caen, France
- Laboratoire de Physique Corpusculaire IN2P3, ENSICAEN/CNRS UMR 6534, Normandie Université, Caen, France
| | - Mark P. Little
- Radiation Epidemiology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Lydia B. Zablotska
- Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco (UCSF), San Francisco, California, USA
| | - Pamela Samson
- Department of Radiation Oncology, Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - M. Kerry O’Banion
- Department of Neuroscience, Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Klervi Leuraud
- Research Department on Biological and Health Effects of Ionizing Radiation (SESANE), Institute for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses, France
| | - Carmen Bergom
- Department of Radiation Oncology, Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
- Cardio-Oncology Center of Excellence, Washington University, St. Louis, Missouri, USA
| | - Gilles Girault
- Comprehensive Cancer Centre François Baclesse, Medical Library, Caen, France
| | - Omid Azimzadeh
- Federal Office for Radiation Protection (BfS), Section Radiation Biology, Neuherberg, Germany
| | - Simon Bouffler
- Radiation Protection Sciences Division, UK Health Security Agency (UKHSA), Chilton, Didcot, UK
| | - Nobuyuki Hamada
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), Abiko, Chiba, Japan
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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Kankaya S, Yavuz F, Tari A, Aygun AB, Gunes EG, Bektan Kanat B, Ulugerger Avci G, Yavuzer H, Dincer Y. Glutathione-related antioxidant defence, DNA damage, and DNA repair in patients suffering from post-COVID conditions. Mutagenesis 2023; 38:216-226. [PMID: 37422797 DOI: 10.1093/mutage/gead021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023] Open
Abstract
Post-COVID conditions are defined as the continuation of the symptoms of Coronavirus Disease 2019 (COVID-19) 3 months after the initial Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, with no other explanation. Post-COVID conditions are seen among 30%-60% of patients with asymptomatic or mild forms of COVID-19. The underlying pathophysiological mechanisms of post-COVID conditions are not known. In SARS-CoV-2 infection, activation of the immune system leads to increased production of reactive oxygen molecules, depleted antioxidant reserve, and finally occurrence of oxidative stress. In oxidative stress conditions, DNA damage increases and DNA repair systems impair. In this study, glutathione (GSH) level, glutathione peroxidase (GPx) activity, 8-hydroxydeoxyguanosine (8-OHdG) level, basal, induced, and post-repair DNA damage were investigated in individuals suffering from post-COVID conditions. In the red blood cells, GSH levels and GPx activities were measured with a spectrophotometric assay and a commercial kit. Basal, in vitro H2O2 (hydrogen peroxide)-induced, and post-repair DNA damage (DNA damage after a repair incubation following H2O2-treatment, in vitro) were determined in lymphocytes by the comet assay. The urinary 8-OHdG levels were measured by using a commercial ELISA kit. No significant difference was found between the patient and control groups for GSH level, GPx activity, and basal and H2O2-induced DNA damage. Post-repair DNA damage was found to be higher in the patient group than those in the control group. Urinary 8-OHdG level was lower in the patient group compared to the control group. In the control group, GSH level and post-repair DNA damage were higher in the vaccinated individuals. In conclusion, oxidative stress formed due to the immune response against SARS-COV-2 may impair DNA repair mechanisms. Defective DNA repair may be an underlying pathological mechanism of post-COVID conditions.
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Affiliation(s)
- Selin Kankaya
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Fatih Yavuz
- Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Alper Tari
- Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ahmet Bera Aygun
- Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Esra Gizem Gunes
- Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Bahar Bektan Kanat
- Department of Internal Medicine, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Gulru Ulugerger Avci
- Department of Internal Medicine, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Hakan Yavuzer
- Department of Internal Medicine, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Yildiz Dincer
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
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Jamir E, Sarma H, Priyadarsinee L, Kiewhuo K, Nagamani S, Sastry GN. Polypharmacology guided drug repositioning approach for SARS-CoV2. PLoS One 2023; 18:e0289890. [PMID: 37556478 PMCID: PMC10411734 DOI: 10.1371/journal.pone.0289890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Drug repurposing has emerged as an important strategy and it has a great potential in identifying therapeutic applications for COVID-19. An extensive virtual screening of 4193 FDA approved drugs has been carried out against 24 proteins of SARS-CoV2 (NSP1-10 and NSP12-16, envelope, membrane, nucleoprotein, spike, ORF3a, ORF6, ORF7a, ORF8, and ORF9b). The drugs were classified into top 10 and bottom 10 drugs based on the docking scores followed by the distribution of their therapeutic indications. As a result, the top 10 drugs were found to have therapeutic indications for cancer, pain, neurological disorders, and viral and bacterial diseases. As drug resistance is one of the major challenges in antiviral drug discovery, polypharmacology and network pharmacology approaches were employed in the study to identify drugs interacting with multiple targets and drugs such as dihydroergotamine, ergotamine, bisdequalinium chloride, midostaurin, temoporfin, tirilazad, and venetoclax were identified among the multi-targeting drugs. Further, a pathway analysis of the genes related to the multi-targeting drugs was carried which provides insight into the mechanism of drugs and identifying targetable genes and biological pathways involved in SARS-CoV2.
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Affiliation(s)
- Esther Jamir
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
| | - Lipsa Priyadarsinee
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kikrusenuo Kiewhuo
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G. Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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