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Bärreiter VA, Meister TL. Renal implications of coronavirus disease 2019: insights into viral tropism and clinical outcomes. Curr Opin Microbiol 2024; 79:102475. [PMID: 38615393 DOI: 10.1016/j.mib.2024.102475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024]
Abstract
In recent years, multiple coronaviruses have emerged, with the latest one, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing a global pandemic. Besides respiratory symptoms, some patients experienced extrapulmonary effects, such as cardiac damage or renal injury, indicating the broad tropism of SARS-CoV-2. The ability of the virus to effectively invade the renal cellular environment can eventually cause tissue-specific damage and disease. Indeed, patients with severe coronavirus disease 2019 exhibited a variety of symptoms such as acute proximal tubular injury, ischemic collapse, and severe acute tubular necrosis resulting in irreversible kidney failure. This review summarizes the current knowledge on how it is believed that SARS-CoV-2 influences the renal environment and induces kidney disease, as well as current therapy approaches.
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Affiliation(s)
- Valentin A Bärreiter
- Institute for Infection Research and Vaccine Development (IIRVD), Centre for Internal Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany; Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Toni L Meister
- Institute for Infection Research and Vaccine Development (IIRVD), Centre for Internal Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany; Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany; German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
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2
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Zhang Z. The Initial COVID-19 Reliable Interactive DNA Methylation Markers and Biological Implications. BIOLOGY 2024; 13:245. [PMID: 38666857 PMCID: PMC11048280 DOI: 10.3390/biology13040245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/22/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Earlier research has established the existence of reliable interactive genomic biomarkers. However, reliable DNA methylation biomarkers, not to mention interactivity, have yet to be identified at the epigenetic level. This study, drawing from 865,859 methylation sites, discovered two miniature sets of Infinium MethylationEPIC sites, each having eight CpG sites (genes) to interact with each other and disease subtypes. They led to the nearly perfect (96.87-100% accuracy) prediction of COVID-19 patients from patients with other diseases or healthy controls. These CpG sites can jointly explain some post-COVID-19-related conditions. These CpG sites and the optimally performing genomic biomarkers reported in the literature become potential druggable targets. Among these CpG sites, cg16785077 (gene MX1), cg25932713 (gene PARP9), and cg22930808 (gene PARP9) at DNA methylation levels indicate that the initial SARS-CoV-2 virus may be better treated as a transcribed viral DNA into RNA virus, i.e., not as an RNA virus that has concerned scientists in the field. Such a discovery can significantly change the scientific thinking and knowledge of viruses.
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Affiliation(s)
- Zhengjun Zhang
- School of Computer, Data and Information Sciences, University of Wisconsin, Madison, WI 53706, USA
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Koch B, Filzmayer M, Patyna S, Wetzstein N, Lampe S, Schmid T, Geiger H, Baer PC, Dolnik O. Transcriptomics of Marburg virus-infected primary proximal tubular cells reveals negative correlation of immune response and energy metabolism. Virus Res 2024; 342:199337. [PMID: 38346476 PMCID: PMC10875301 DOI: 10.1016/j.virusres.2024.199337] [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: 12/11/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
Marburg virus, a member of the Filoviridae, is the causative agent of Marburg virus disease (MVD), a hemorrhagic fever with a case fatality rate of up to 90 %. Acute kidney injury is common in MVD and is associated with increased mortality, but its pathogenesis in MVD remains poorly understood. Interestingly, autopsies show the presence of viral proteins in different parts of the nephron, particularly in proximal tubular cells (PTC). These findings suggest a potential role for the virus in the development of MVD-related kidney injury. To shed light on this effect, we infected primary human PTC with Lake Victoria Marburg virus and conducted transcriptomic analysis at multiple time points. Unexpectedly, infection did not induce marked cytopathic effects in primary tubular cells at 20 and 40 h post infection. However, gene expression analysis revealed robust renal viral replication and dysregulation of genes essential for different cellular functions. The gene sets mainly downregulated in PTC were associated with the targets of the transcription factors MYC and E2F, DNA repair, the G2M checkpoint, as well as oxidative phosphorylation. Importantly, the downregulated factors comprise PGC-1α, a well-known factor in acute and chronic kidney injury. By contrast, the most highly upregulated gene sets were those related to the inflammatory response and cholesterol homeostasis. In conclusion, Marburg virus infects and replicates in human primary PTC and induces downregulation of processes known to be relevant for acute kidney injury as well as a strong inflammatory response.
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Affiliation(s)
- Benjamin Koch
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine 4, Nephrology, Theodor-Stern-Kai 7, Frankfurt am Main 60596, Germany.
| | - Maximilian Filzmayer
- Goethe University Frankfurt, University Hospital, Department of Urology, Frankfurt am Main 60596, Germany
| | - Sammy Patyna
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine 4, Nephrology, Theodor-Stern-Kai 7, Frankfurt am Main 60596, Germany
| | - Nils Wetzstein
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Infectious Diseases, Frankfurt am Main 60596, Germany
| | - Sebastian Lampe
- Goethe University Frankfurt, University Hospital, Faculty of Medicine, Institute for Biochemistry I, Frankfurt am Main 60596, Germany
| | - Tobias Schmid
- Goethe University Frankfurt, University Hospital, Faculty of Medicine, Institute for Biochemistry I, Frankfurt am Main 60596, Germany
| | - Helmut Geiger
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine 4, Nephrology, Theodor-Stern-Kai 7, Frankfurt am Main 60596, Germany
| | - Patrick C Baer
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine 4, Nephrology, Theodor-Stern-Kai 7, Frankfurt am Main 60596, Germany
| | - Olga Dolnik
- Philipps University Marburg, Institute of Virology, Hans-Meerwein-Str. 2, Marburg 35043, Germany.
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Metzler M, Tharyan RG, Klann K, Grikscheit K, Bojkova D, Cinatl J, Tascher G, Ciesek S, Münch C. SARS-CoV-2 variants show different host cell proteome profiles with delayed immune response activation in Omicron-infected cells. Mol Cell Proteomics 2023; 22:100537. [PMID: 37001587 PMCID: PMC10060015 DOI: 10.1016/j.mcpro.2023.100537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 02/21/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
The ancestral SARS-CoV-2 strain that initiated the Covid-19 pandemic at the end of 2019 has rapidly mutated into multiple variants of concern with variable pathogenicity and increasing immune escape strategies. However, differences in host cellular antiviral responses upon infection with SARS-CoV-2 variants remains elusive. Leveraging whole cell proteomics, we determined host signalling pathways that are differentially modulated upon infection with the clinical isolates of the ancestral SARS-CoV-2 B.1 and the variants of concern Delta and Omicron BA.1. Our findings illustrate alterations in the global host proteome landscape upon infection with SARS-CoV-2 variants and the resulting host immune responses. Additionally, viral proteome kinetics reveal declining levels of viral protein expression during Omicron BA.1 infection when compared to ancestral B.1 and Delta variants, consistent with its reduced replication rates. Moreover, molecular assays reveal deferral activation of specific host antiviral signalling upon Omicron BA.1 and BA.2 infections. Our study provides an overview of host proteome profile of multiple SARS-CoV-2 variants and brings forth a better understanding of the instigation of key immune signalling pathways causative for the differential pathogenicity of SARS-CoV-2 variants.
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Affiliation(s)
- Melinda Metzler
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Rebecca George Tharyan
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Kevin Klann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Katharina Grikscheit
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Denisa Bojkova
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Jindrich Cinatl
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Sandra Ciesek
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Frankfurt, Germany; German Center for Infection Research, DZIF, External Partner Site, Frankfurt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany; Frankfurt Cancer Institute, Goethe University, Frankfurt, Germany; Cardio-Pulmonary Institute, Goethe University, Frankfurt, Germany.
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Pires De Souza GA, Le Bideau M, Boschi C, Wurtz N, Colson P, Aherfi S, Devaux C, La Scola B. Choosing a cellular model to study SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:1003608. [PMID: 36339347 PMCID: PMC9634005 DOI: 10.3389/fcimb.2022.1003608] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/03/2022] [Indexed: 08/04/2023] Open
Abstract
As new pathogens emerge, new challenges must be faced. This is no different in infectious disease research, where identifying the best tools available in laboratories to conduct an investigation can, at least initially, be particularly complicated. However, in the context of an emerging virus, such as SARS-CoV-2, which was recently detected in China and has become a global threat to healthcare systems, developing models of infection and pathogenesis is urgently required. Cell-based approaches are crucial to understanding coronavirus infection biology, growth kinetics, and tropism. Usually, laboratory cell lines are the first line in experimental models to study viral pathogenicity and perform assays aimed at screening antiviral compounds which are efficient at blocking the replication of emerging viruses, saving time and resources, reducing the use of experimental animals. However, determining the ideal cell type can be challenging, especially when several researchers have to adapt their studies to specific requirements. This review strives to guide scientists who are venturing into studying SARS-CoV-2 and help them choose the right cellular models. It revisits basic concepts of virology and presents the currently available in vitro models, their advantages and disadvantages, and the known consequences of each choice.
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Affiliation(s)
- Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Marion Le Bideau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Céline Boschi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Christian Devaux
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Department of Biological Sciences (INSB), Centre National de la Recherche Scientifique, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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Gene Networks of Hyperglycemia, Diabetic Complications, and Human Proteins Targeted by SARS-CoV-2: What Is the Molecular Basis for Comorbidity? Int J Mol Sci 2022; 23:ijms23137247. [PMID: 35806251 PMCID: PMC9266766 DOI: 10.3390/ijms23137247] [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: 06/04/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 12/10/2022] Open
Abstract
People with diabetes are more likely to have severe COVID-19 compared to the general population. Moreover, diabetes and COVID-19 demonstrate a certain parallelism in the mechanisms and organ damage. In this work, we applied bioinformatics analysis of associative molecular networks to identify key molecules and pathophysiological processes that determine SARS-CoV-2-induced disorders in patients with diabetes. Using text-mining-based approaches and ANDSystem as a bioinformatics tool, we reconstructed and matched networks related to hyperglycemia, diabetic complications, insulin resistance, and beta cell dysfunction with networks of SARS-CoV-2-targeted proteins. The latter included SARS-CoV-2 entry receptors (ACE2 and DPP4), SARS-CoV-2 entry associated proteases (TMPRSS2, CTSB, and CTSL), and 332 human intracellular proteins interacting with SARS-CoV-2. A number of genes/proteins targeted by SARS-CoV-2 (ACE2, BRD2, COMT, CTSB, CTSL, DNMT1, DPP4, ERP44, F2RL1, GDF15, GPX1, HDAC2, HMOX1, HYOU1, IDE, LOX, NUTF2, PCNT, PLAT, RAB10, RHOA, SCARB1, and SELENOS) were found in the networks of vascular diabetic complications and insulin resistance. According to the Gene Ontology enrichment analysis, the defined molecules are involved in the response to hypoxia, reactive oxygen species metabolism, immune and inflammatory response, regulation of angiogenesis, platelet degranulation, and other processes. The results expand the understanding of the molecular basis of diabetes and COVID-19 comorbidity.
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