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Lezcano OM, Fuhrmann L, Ramakrishnan G, Beerenwinkel N, Huynen MA, van Rij RP. Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster. Virus Evol 2023; 9:vead074. [PMID: 38162315 PMCID: PMC10757409 DOI: 10.1093/ve/vead074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
Virus evolution is strongly affected by antagonistic co-evolution of virus and host. Host immunity positively selects for viruses that evade the immune response, which in turn may drive counter-adaptations in host immune genes. We investigated how host immune pressure shapes virus populations, using the fruit fly Drosophila melanogaster and its natural pathogen Drosophila C virus (DCV), as a model. We performed an experimental evolution study in which DCV was serially passaged for ten generations in three fly genotypes differing in their antiviral RNAi response: wild-type flies and flies in which the endonuclease gene Dicer-2 was either overexpressed or inactivated. All evolved virus populations replicated more efficiently in vivo and were more virulent than the parental stock. The number of polymorphisms increased in all three host genotypes with passage number, which was most pronounced in Dicer-2 knockout flies. Mutational analysis showed strong parallel evolution, as mutations accumulated in a specific region of the VP3 capsid protein in every lineage in a host genotype-independent manner. The parental tyrosine at position ninety-five of VP3 was substituted with either one of five different amino acids in fourteen out of fifteen lineages. However, no consistent amino acid changes were observed in the viral RNAi suppressor gene 1A, nor elsewhere in the genome in any of the host backgrounds. Our study indicates that the RNAi response restricts the sequence space that can be explored by viral populations. Moreover, our study illustrates how evolution towards higher virulence can be a highly reproducible, yet unpredictable process.
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Affiliation(s)
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel 4056, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
| | - Gayatri Ramakrishnan
- Department of Medical BioSciences, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel 4056, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
- Department of Medical Microbiology, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| | | | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
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Föhse K, Geckin B, Zoodsma M, Kilic G, Liu Z, Röring RJ, Overheul GJ, van de Maat J, Bulut O, Hoogerwerf JJ, Ten Oever J, Simonetti E, Schaal H, Adams O, Müller L, Ostermann PN, van de Veerdonk FL, Joosten LAB, Haagmans BL, van Crevel R, van Rij RP, GeurtsvanKessel C, de Jonge MI, Li Y, Domínguez-Andrés J, Netea MG. The impact of BNT162b2 mRNA vaccine on adaptive and innate immune responses. Clin Immunol 2023; 255:109762. [PMID: 37673225 DOI: 10.1016/j.clim.2023.109762] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/04/2023] [Accepted: 09/02/2023] [Indexed: 09/08/2023]
Abstract
The mRNA-based BNT162b2 protects against severe disease and mortality caused by SARS-CoV-2 via induction of specific antibody and T-cell responses. Much less is known about its broad effects on immune responses against other pathogens. Here, we investigated the adaptive immune responses induced by BNT162b2 vaccination against various SARS-CoV-2 variants and its effects on the responsiveness of immune cells upon stimulation with heterologous stimuli. BNT162b2 vaccination induced effective humoral and cellular immunity against SARS-CoV-2 that started to wane after six months. We also observed long-term transcriptional changes in immune cells after vaccination. Additionally, vaccination with BNT162b2 modulated innate immune responses as measured by inflammatory cytokine production after stimulation - higher IL-1/IL-6 release and decreased IFN-α production. Altogether, these data expand our knowledge regarding the overall immunological effects of this new class of vaccines and underline the need for additional studies to elucidate their effects on both innate and adaptive immune responses.
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Affiliation(s)
- Konstantin Föhse
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Büsra Geckin
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Martijn Zoodsma
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Gizem Kilic
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Zhaoli Liu
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Rutger J Röring
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Josephine van de Maat
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ozlem Bulut
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jacobien J Hoogerwerf
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jaap Ten Oever
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elles Simonetti
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Ortwin Adams
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Philipp Niklas Ostermann
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Marien I de Jonge
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
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3
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Qu J, Betting V, van Iterson R, Kwaschik FM, van Rij RP. Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA biogenesis in mosquitoes. Cell Rep 2023; 42:112257. [PMID: 36930642 DOI: 10.1016/j.celrep.2023.112257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
The piRNA pathway in mosquitoes differs substantially from other model organisms, with an expanded PIWI gene family and functions in antiviral defense. Here, we define core piRNA clusters as genomic loci that show ubiquitous piRNA expression in both somatic and germline tissues. These core piRNA clusters are enriched for non-retroviral endogenous viral elements (nrEVEs) in antisense orientation and depend on key biogenesis factors, Veneno, Tejas, Yb, and Shutdown. Combined transcriptome and chromatin state analyses identify transcriptional readthrough as a conserved mechanism for cluster-derived piRNA biogenesis in the vector mosquitoes Aedes aegypti, Aedes albopictus, Culex quinquefasciatus, and Anopheles gambiae. Comparative analyses between the two Aedes species suggest that piRNA clusters function as traps for nrEVEs, allowing adaptation to environmental challenges such as virus infection. Our systematic transcriptome and chromatin state analyses lay the foundation for studies of gene regulation, genome evolution, and piRNA function in these important vector species.
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Affiliation(s)
- Jieqiong Qu
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Valerie Betting
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Ruben van Iterson
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Florence M Kwaschik
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands.
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Moonen JP, Schinkel M, van der Most T, Miesen P, van Rij RP. Composition and global distribution of the mosquito virome - A comprehensive database of insect-specific viruses. One Health 2023; 16:100490. [PMID: 36817977 PMCID: PMC9929601 DOI: 10.1016/j.onehlt.2023.100490] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Mosquitoes are vectors for emerging and re-emerging infectious viral diseases of humans, livestock and other animals. In addition to these arthropod-borne (arbo)viruses, mosquitoes are host to an array of insect-specific viruses, collectively referred to as the mosquito virome. Mapping the mosquito virome and understanding if and how its composition modulates arbovirus transmission is critical to understand arboviral disease emergence and outbreak dynamics. In recent years, next-generation sequencing as well as PCR and culture-based methods have been extensively used to identify mosquito-associated viruses, providing insights into virus ecology and evolution. Until now, the large amount of mosquito virome data, specifically those acquired by metagenomic sequencing, has not been comprehensively integrated. We have constructed a searchable database of insect-specific viruses associated with vector mosquitoes from 175 studies, published between October 2000 and February 2022. We identify the most frequently detected and widespread viruses of the Culex, Aedes and Anopheles mosquito genera and report their global distribution. In addition, we highlight the challenges of extracting and integrating published virome data and we propose that a standardized reporting format will facilitate data interpretation and re-use by other scientists. We expect our comprehensive database, summarizing mosquito virome data collected over 20 years, to be a useful resource for future studies.
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Garishah FM, Boahen CK, Vadaq N, Pramudo SG, Tunjungputri RN, Riswari SF, van Rij RP, Alisjahbana B, Gasem MH, van der Ven AJAM, de Mast Q. Longitudinal proteomic profiling of the inflammatory response in dengue patients. PLoS Negl Trop Dis 2023; 17:e0011041. [PMID: 36595532 PMCID: PMC9838874 DOI: 10.1371/journal.pntd.0011041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 01/13/2023] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The immunopathogenesis of dengue virus (DENV) infection remains incompletely understood. To increase our understanding of inflammatory response in non-severe dengue, we assessed longitudinal changes in the inflammatory proteome in patients with an acute DENV infection. METHODS Using a multiplex proximity extension assay (PEA), we measured relative levels of 368 inflammatory markers in plasma samples from hospitalized patients with non-severe DENV infection in the acute (n = 43) and convalescence (n = 35) phase of the infection and samples of healthy controls (n = 10). RESULTS We identified 203 upregulated and 39 downregulated proteins in acute versus convalescent plasma samples. The upregulated proteins had a strong representation of interferon (IFN) and IFN-inducible effector proteins, cytokines (e.g. IL-10, IL-33) and cytokine receptors, chemokines, pro-apoptotic proteins (e.g. granzymes) and endothelial markers. A number of differentially expressed proteins (DEPs) have not been reported in previous studies. Functional network analysis highlighted a central role for IFNγ, IL-10, IL-33 and chemokines. We identified different novel associations between inflammatory proteins and circulating concentrations of the endothelial glycocalyx disruption surrogate marker syndecan-1. Conclusion: This unbiased proteome analysis provides a comprehensive insight in the inflammatory response in DENV infection and its association with glycocalyx disruption.
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Affiliation(s)
- Fadel Muhammad Garishah
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Collins K. Boahen
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nadira Vadaq
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Setyo G. Pramudo
- Department of Internal Medicine, Diponegoro National University Hospital, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
- Department of Internal Medicine, William Booth Hospital, Semarang, Indonesia
| | - Rahajeng N. Tunjungputri
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Silvita Fitri Riswari
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ronald P. van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bachti Alisjahbana
- Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhammad Hussein Gasem
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
- Department of Internal Medicine, Diponegoro National University Hospital, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - André J. A. M. van der Ven
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail:
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Reimer KC, Jansen J, Overheul GJ, Miesen P, van Rij RP, Triana SH, Smeets B, Schneider RK, Kramann R. Using human iPSC-derived kidney organoids to decipher SARS-CoV-2 pathology on single cell level. STAR Protoc 2022; 3:101612. [PMID: 35983169 PMCID: PMC9293950 DOI: 10.1016/j.xpro.2022.101612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We describe a protocol for single-cell RNA sequencing of SARS-CoV-2-infected human induced pluripotent stem cell (iPSC)-derived kidney organoids. After inoculation of kidney organoids with virus, we use mechanical and enzymatic disruption to obtain single cell suspensions. Next, we process the organoid-derived cells into sequencing-ready SARS-CoV-2-targeted libraries. Subsequent sequencing analysis reveals changes in kidney cells after virus infection. The protocol was designed for kidney organoids cultured in a 6-well transwell format but can be adapted to organoids with different organ backgrounds. For complete details on the use and execution of this protocol, please refer to Jansen et al. (2022). Inoculation of human kidney organoids with SARS-CoV-2 models COVID-19 in kidney Mechanic and enzymatic tissue digestion yield single cells in safety level 3 laboratory Generation of a targeted single-cell RNA sequencing library identifies infected cells
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Kurver L, van den Kieboom CH, Lanke K, Diavatopoulos DA, Overheul GJ, Netea MG, ten Oever J, van Crevel R, Mulders-Manders K, van de Veerdonk FL, Wertheim H, Schouten J, Rahamat-Langendoen J, van Rij RP, Bousema T, van Laarhoven A, de Jonge MI. SARS-CoV-2 RNA in exhaled air of hospitalized COVID-19 patients. Sci Rep 2022; 12:8991. [PMID: 35637284 PMCID: PMC9151771 DOI: 10.1038/s41598-022-13008-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/26/2022] [Indexed: 02/08/2023] Open
Abstract
Knowledge about contagiousness is key to accurate management of hospitalized COVID-19 patients. Epidemiological studies suggest that in addition to transmission through droplets, aerogenic SARS-CoV-2 transmission contributes to the spread of infection. However, the presence of virus in exhaled air has not yet been sufficiently demonstrated. In pandemic situations low tech disposable and user-friendly bedside devices are required, while commercially available samplers are unsuitable for application in patients with respiratory distress. We included 49 hospitalized COVID-19 patients and used a disposable modular breath sampler to measure SARS-CoV-2 RNA load in exhaled air samples and compared these to SARS-CoV-2 RNA load of combined nasopharyngeal throat swabs and saliva. Exhaled air sampling using the modular breath sampler has proven feasible in a clinical COVID-19 setting and demonstrated viral detection in 25% of the patients.
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8
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Bezemer B, van Cleef KW, Overheul GJ, Miesen P, van Rij RP. The calcium channel inhibitor lacidipine inhibits Zika virus replication in neural progenitor cells. Antiviral Res 2022; 202:105313. [DOI: 10.1016/j.antiviral.2022.105313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/21/2022] [Accepted: 03/27/2022] [Indexed: 01/04/2023]
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Bousema T, Burtscher L, van Rij RP, Barret D, Whitfield K. The critical role of funders in shrinking the carbon footprint of research. Lancet Planet Health 2022; 6:e4-e6. [PMID: 34998458 DOI: 10.1016/s2542-5196(21)00276-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Teun Bousema
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Didier Barret
- Institut de Recherche en Astrophysique et Planétologie, CNRS, CNES and Université de Toulouse, France
| | - Kate Whitfield
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, 08036, Spain.
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Buijsers B, Garishah FM, Riswari SF, van Ast RM, Pramudo SG, Tunjungputri RN, Overheul GJ, van Rij RP, van der Ven A, Alisjahbana B, Gasem MH, de Mast Q, van der Vlag J. Increased Plasma Heparanase Activity and Endothelial Glycocalyx Degradation in Dengue Patients Is Associated With Plasma Leakage. Front Immunol 2021; 12:759570. [PMID: 34987504 PMCID: PMC8722520 DOI: 10.3389/fimmu.2021.759570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background Endothelial hyper-permeability with plasma leakage and thrombocytopenia are predominant features of severe dengue virus infection. It is well established that heparanase, the endothelial glycocalyx degrading enzyme, plays a major role in various diseases with vascular leakage. It is yet to be elucidated whether heparanase activity plays a major role in dengue-associated plasma leakage. Moreover, the major source of heparanase secretion and activation in dengue remains elusive. Since a relatively high amount of heparanase is stored in platelets, we postulate that heparanase released by activated platelets contributes to the increased plasma heparanase activity during dengue virus infection. Methods Heparanase activity (plasma and urine), and heparan sulfate and syndecan-1 (plasma levels) were measured in dengue patients with thrombocytopenia in acute phase (n=30), during course of disease (n=10) and in convalescent phase (n=25). Associations with clinical parameters and plasma leakage markers were explored. Platelets from healthy donors were stimulated with dengue non-structural protein-1, DENV2 virus and thrombin to evaluate heparanase release and activity ex vivo. Results Heparanase activity was elevated in acute dengue and normalized during convalescence. Similarly, glycocalyx components, such as heparan sulfate and syndecan-1, were increased in acute dengue and restored during convalescence. Increased heparanase activity correlated with the endothelial dysfunction markers heparan sulfate and syndecan-1, as well as clinical markers of plasma leakage such as ascites, hematocrit concentration and gall-bladder wall thickening. Notably, platelet number inversely correlated with heparanase activity. Ex vivo incubation of platelets with thrombin and live DENV2 virus, but not dengue virus-2-derived non-structural protein 1 induced heparanase release from platelets. Conclusion Taken together, our findings suggest that the increase of heparanase activity in dengue patients is associated with endothelial glycocalyx degradation and plasma leakage. Furthermore, thrombin or DENV2 activated platelets may be considered as a potential source of heparanase.
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Affiliation(s)
- Baranca Buijsers
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Fadel Muhammad Garishah
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Silvita Fitri Riswari
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Rosalie M. van Ast
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Setyo Gundi Pramudo
- Department of Internal Medicine, Diponegoro National University Hospital, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
- Department of Internal Medicine, William Booth Hospital, Semarang, Indonesia
| | - Rahajeng N. Tunjungputri
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Gijs J. Overheul
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ronald P. van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - André van der Ven
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bachti Alisjahbana
- Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhammad Hussein Gasem
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
- Department of Internal Medicine, Diponegoro National University Hospital, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Quirijn de Mast
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johan van der Vlag
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- *Correspondence: Johan van der Vlag,
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11
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Jansen J, Reimer KC, Nagai JS, Varghese FS, Overheul GJ, de Beer M, Roverts R, Daviran D, Fermin LA, Willemsen B, Beukenboom M, Djudjaj S, von Stillfried S, van Eijk LE, Mastik M, Bulthuis M, Dunnen WD, van Goor H, Hillebrands JL, Triana SH, Alexandrov T, Timm MC, van den Berge BT, van den Broek M, Nlandu Q, Heijnert J, Bindels EM, Hoogenboezem RM, Mooren F, Kuppe C, Miesen P, Grünberg K, Ijzermans T, Steenbergen EJ, Czogalla J, Schreuder MF, Sommerdijk N, Akiva A, Boor P, Puelles VG, Floege J, Huber TB, van Rij RP, Costa IG, Schneider RK, Smeets B, Kramann R, Achdout H, Aimon A, Bar-David E, Barr H, Ben-Shmuel A, Bennett J, Boby ML, Borden B, Bowman GR, Brun J, BVNBS S, Calmiano M, Carbery A, Cattermole E, Chernychenko E, Choder JD, Clyde A, Coffland JE, Cohen G, Cole J, Contini A, Cox L, Cvitkovic M, Dias A, Donckers K, Dotson DL, Douangamath A, Duberstein S, Dudgeon T, Dunnett L, Eastman PK, Erez N, Eyermann CJ, Fairhead M, Fate G, Fearon D, Federov O, Ferla M, Fernandes RS, Ferrins L, Foster R, Foster H, Gabizon R, Garcia-Sastre A, Gawriljuk VO, Gehrtz P, Gileadi C, Giroud C, Glass WG, Glen R, Itai glinert, Godoy AS, Gorichko M, Gorrie-Stone T, Griffen EJ, Hart SH, Heer J, Henry M, Hill M, Horrell S, Hurley MF, Israely T, Jajack A, Jnoff E, Jochmans D, John T, De Jonghe S, Kantsadi AL, Kenny PW, Kiappes J, Koekemoer L, Kovar B, Krojer T, Lee AA, Lefker BA, Levy H, London N, Lukacik P, Macdonald HB, Maclean B, Malla TR, Matviiuk T, McCorkindale W, McGovern BL, Melamed S, Michurin O, Mikolajek H, Milne BF, Morris A, Morris GM, Morwitzer MJ, Moustakas D, Nakamura AM, Neto JB, Neyts J, Nguyen L, Noske GD, Oleinikovas V, Oliva G, Overheul GJ, Owen D, Psenak V, Pai R, Pan J, Paran N, Perry B, Pingle M, Pinjari J, Politi B, Powell A, Puni R, Rangel VL, Reddi RN, Reid SP, Resnick E, Ripka EG, Robinson MC, Robinson RP, Rodriguez-Guerra J, Rosales R, Rufa D, Schofield C, Shafeev M, Shaikh A, Shi J, Shurrush K, Sing S, Sittner A, Skyner R, Smalley A, Smilova MD, Solmesky LJ, Spencer J, Strain-Damarell C, Swamy V, Tamir H, Tennant R, Thompson W, Thompson A, Thompson W, Tomasia S, Tumber A, Vakonakis I, van Rij RP, van Geel L, Varghese FS, Vaschetto M, Vitner EB, Voelz V, Volkamer A, von Delft F, von Delft A, Walsh M, Ward W, Weatherall C, Weiss S, White KM, Wild CF, Wittmann M, Wright N, Yahalom-Ronen Y, Zaidmann D, Zidane H, Zitzmann N. SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids. Cell Stem Cell 2021; 29:217-231.e8. [PMID: 35032430 PMCID: PMC8709832 DOI: 10.1016/j.stem.2021.12.010] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022]
Abstract
Kidney failure is frequently observed during and after COVID-19, but it remains elusive whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects kidney cells and is associated with increased tubule-interstitial kidney fibrosis in patient autopsy samples. To study direct effects of the virus on the kidney independent of systemic effects of COVID-19, we infected human-induced pluripotent stem-cell-derived kidney organoids with SARS-CoV-2. Single-cell RNA sequencing indicated injury and dedifferentiation of infected cells with activation of profibrotic signaling pathways. Importantly, SARS-CoV-2 infection also led to increased collagen 1 protein expression in organoids. A SARS-CoV-2 protease inhibitor was able to ameliorate the infection of kidney cells by SARS-CoV-2. Our results suggest that SARS-CoV-2 can directly infect kidney cells and induce cell injury with subsequent fibrosis. These data could explain both acute kidney injury in COVID-19 patients and the development of chronic kidney disease in long COVID. COVID-19 patients present tubulo-interstitial kidney fibrosis compared with controls SARS-CoV-2 infection stimulates profibrotic signaling in human kidney organoids SARS-CoV-2 infection can be inhibited by a protease blocker in human kidney organoids
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12
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Varghese FS, Meutiawati F, Teppor M, Jacobs S, de Keyzer C, Taşköprü E, van Woudenbergh E, Overheul GJ, Bouma E, Smit JM, Delang L, Merits A, van Rij RP. Posaconazole inhibits multiple steps of the alphavirus replication cycle. Antiviral Res 2021; 197:105223. [PMID: 34856248 DOI: 10.1016/j.antiviral.2021.105223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 11/28/2022]
Abstract
Repurposing drugs is a promising strategy to identify therapeutic interventions against novel and re-emerging viruses. Posaconazole is an antifungal drug used to treat invasive aspergillosis and candidiasis. Recently, posaconazole and its structural analog, itraconazole were shown to inhibit replication of multiple viruses by modifying intracellular cholesterol homeostasis. Here, we show that posaconazole inhibits replication of the alphaviruses Semliki Forest virus (SFV), Sindbis virus and chikungunya virus with EC50 values ranging from 1.4 μM to 9.5 μM. Posaconazole treatment led to a significant reduction of virus entry in an assay using a temperature-sensitive SFV mutant, but time-of-addition and RNA transfection assays indicated that posaconazole also inhibits post-entry stages of the viral replication cycle. Virus replication in the presence of posaconazole was partially rescued by the addition of exogenous cholesterol. A transferrin uptake assay revealed that posaconazole considerably slowed down cellular endocytosis. A single point mutation in the SFV E2 glycoprotein, H255R, provided partial resistance to posaconazole as well as to methyl-β-cyclodextrin, corroborating the effect of posaconazole on cholesterol and viral entry. Our results indicate that posaconazole inhibits multiple steps of the alphavirus replication cycle and broaden the spectrum of viruses that can be targeted in vitro by posaconazole, which could be further explored as a therapeutic agent against emerging viruses.
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Affiliation(s)
- Finny S Varghese
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Febrina Meutiawati
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mona Teppor
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Sofie Jacobs
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Carolien de Keyzer
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Ezgi Taşköprü
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Esther van Woudenbergh
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ellen Bouma
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jolanda M Smit
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Leen Delang
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
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13
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van Laarhoven A, Kurver L, Overheul GJ, Kooistra EJ, Abdo WF, van Crevel R, Duivenvoorden R, Kox M, Ten Oever J, Schouten J, van de Veerdonk FL, van der Hoeven H, Rahamat-Langendoen J, van Rij RP, Pickkers P, Netea MG. Interferon gamma immunotherapy in five critically ill COVID-19 patients with impaired cellular immunity: A case series. Med (N Y) 2021; 2:1163-1170.e2. [PMID: 34568856 PMCID: PMC8452508 DOI: 10.1016/j.medj.2021.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/06/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022]
Abstract
Background Prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding has been described in immunocompromised coronavirus disease 2019 (COVID-19) patients, resulting in protracted disease and poor outcome. Specific therapy to improve viral clearance and outcome for this group of patients is currently unavailable. Methods Five critically ill COVID-19 patients with severe defects in cellular immune responses, high SARS-CoV-2 viral RNA loads, and no respiratory improvement were treated with interferon gamma, 100 μg subcutaneously, thrice weekly. Bronchial secretion was collected every 48 h for routine diagnostic SARS-CoV-2 RT-PCR and viral culture. Findings Interferon gamma administration was followed by a rapid decline in SARS-CoV-2 load and a positive-to-negative viral culture conversion. Four patients recovered, and no signs of hyperinflammation were observed. Conclusions Interferon gamma may be considered as adjuvant immunotherapy in a subset of immunocompromised COVID-19 patients. Funding A.v.L. and R.v.C. are supported by National Institutes of Health (R01AI145781). G.J.O. and R.P.v.R. are supported by a VICI grant (016.VICI.170.090) from the Dutch Research Council (NWO). W.F.A. is supported by a clinical fellowship grant (9071561) of Netherlands Organization for Health Research and Development. M.G.N. is supported by an ERC advanced grant (833247) and a Spinoza grant of the Netherlands Organization for Scientific Research.
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Affiliation(s)
- Arjan van Laarhoven
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Lisa Kurver
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Emma J Kooistra
- Department of Intensive Care Medicine, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Wilson F Abdo
- Department of Intensive Care Medicine, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Raphaël Duivenvoorden
- Department of Nephrology, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Matthijs Kox
- Department of Intensive Care Medicine, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Jaap Ten Oever
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Jeroen Schouten
- Department of Intensive Care Medicine, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Hans van der Hoeven
- Department of Intensive Care Medicine, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Janette Rahamat-Langendoen
- Department of Medical Microbiology, Radboud Centre for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Peter Pickkers
- Department of Intensive Care Medicine, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Center, 6525 GA, Nijmegen, the Netherlands.,Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
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14
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Halbach R, Miesen P, van Rij RP. Zooming in on targets of mosquito small RNAs. Trends Parasitol 2021; 37:687-689. [PMID: 34147336 DOI: 10.1016/j.pt.2021.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 11/19/2022]
Abstract
Small RNAs are crucial for the regulation of basic cellular processes and protection against viruses and transposons in mosquitoes. Rozen-Gagnon et al. established CLIP (cross-linking and immunoprecipitation) for Argonaute proteins in Aedes aegypti. Their study sheds light on small RNA-target interactions in mosquitoes and provides an important resource for further study.
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Affiliation(s)
- Rebecca Halbach
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
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15
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Garishah FM, Rother N, Riswari SF, Alisjahbana B, Overheul GJ, van Rij RP, van der Ven A, van der Vlag J, de Mast Q. Neutrophil Extracellular Traps in Dengue Are Mainly Generated NOX-Independently. Front Immunol 2021; 12:629167. [PMID: 34122402 PMCID: PMC8187769 DOI: 10.3389/fimmu.2021.629167] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/05/2021] [Indexed: 01/12/2023] Open
Abstract
Neutrophil extracellular traps (NETs) are increasingly recognized to play a role in the pathogenesis of viral infections, including dengue. NETs can be formed NADPH oxidase (NOX)-dependently or NOX-independently. NOX-independent NETs can be induced by activated platelets and are very potent in activating the endothelium. Platelet activation with thrombocytopenia and endothelial dysfunction are prominent features of dengue virus infection. We postulated that dengue infection is associated with NOX-independent NET formation, which is related to platelet activation, endothelial perturbation and increased vascular permeability. Using our specific NET assays, we investigated the time course of NET formation in a cohort of Indonesian dengue patients. We found that plasma levels of NETs were profoundly elevated and that these NETs were predominantly NOX-independent NETs. During early recovery phase (7-13 days from fever onset), total NETs correlated negatively with platelet number and positively with platelet P-selectin expression, the binding of von Willebrand factor to platelets and levels of Syndecan-1. Patients with gall bladder wall thickening, an early marker of plasma leakage, had a higher median level of total NETs. Ex vivo, platelets induced NOX-independent NET formation in a dengue virus non-structural protein 1 (NS1)-dependent manner. We conclude that NOX-independent NET formation is enhanced in dengue, which is most likely mediated by NS1 and activated platelets.
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Affiliation(s)
- Fadel Muhammad Garishah
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Nils Rother
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Silvita Fitri Riswari
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia.,Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Bachti Alisjahbana
- Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia.,Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - André van der Ven
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johan van der Vlag
- Department of Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
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16
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Crava CM, Varghese FS, Pischedda E, Halbach R, Palatini U, Marconcini M, Gasmi L, Redmond S, Afrane Y, Ayala D, Paupy C, Carballar‐Lejarazu R, Miesen P, van Rij RP, Bonizzoni M. Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements. Mol Ecol 2021; 30:1594-1611. [PMID: 33432714 PMCID: PMC8048955 DOI: 10.1111/mec.15798] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
Horizontal gene transfer from viruses to eukaryotic cells is a pervasive phenomenon. Somatic viral integrations are linked to persistent viral infection whereas integrations into germline cells are maintained in host genomes by vertical transmission and may be co-opted for host functions. In the arboviral vector Aedes aegypti, an endogenous viral element from a nonretroviral RNA virus (nrEVE) was shown to produce PIWI-interacting RNAs (piRNAs) to limit infection with a cognate virus. Thus, nrEVEs may constitute a heritable, sequence-specific mechanism for antiviral immunity, analogous to piRNA-mediated silencing of transposable elements. Here, we combine population genomics and evolutionary approaches to analyse the genomic architecture of nrEVEs in A. aegypti. We conducted a genome-wide screen for adaptive nrEVEs and searched for novel population-specific nrEVEs in the genomes of 80 individual wild-caught mosquitoes from five geographical populations. We show a dynamic landscape of nrEVEs in mosquito genomes and identified five novel nrEVEs derived from two currently circulating viruses, providing evidence of the environmental-dependent modification of a piRNA cluster. Overall, our results show that virus endogenization events are complex with only a few nrEVEs contributing to adaptive evolution in A. aegypti.
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Affiliation(s)
- Cristina M. Crava
- Department of Biology and BiotechnologyUniversity of PaviaPaviaItaly
- Present address:
Institute of Biotechnology and BiomedicineUniversitat de ValènciaBurjassotSpain
| | - Finny S. Varghese
- Department of Medical MicrobiologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands
| | - Elisa Pischedda
- Department of Biology and BiotechnologyUniversity of PaviaPaviaItaly
| | - Rebecca Halbach
- Department of Medical MicrobiologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands
| | - Umberto Palatini
- Department of Biology and BiotechnologyUniversity of PaviaPaviaItaly
| | | | - Leila Gasmi
- Department of Biology and BiotechnologyUniversity of PaviaPaviaItaly
| | - Seth Redmond
- Institute of Vector Borne DiseaseMonash UniversityAustralia
| | - Yaw Afrane
- Department of Medical MicrobiologyUniversity of GhanaAccraGhana
| | - Diego Ayala
- MIVEGECUniv. MontpellierIRDCNRSMontpellierFrance
| | | | - Rebeca Carballar‐Lejarazu
- Department of Biology and BiotechnologyUniversity of PaviaPaviaItaly
- Present address:
Department of Molecular Biology and BiochemistryUniversity of California at IrvineIrvineCAUSA
| | - Pascal Miesen
- Department of Medical MicrobiologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands
| | - Ronald P. van Rij
- Department of Medical MicrobiologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands
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17
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Varghese FS, van Woudenbergh E, Overheul GJ, Eleveld MJ, Kurver L, van Heerbeek N, van Laarhoven A, Miesen P, den Hartog G, de Jonge MI, van Rij RP. Berberine and Obatoclax Inhibit SARS-Cov-2 Replication in Primary Human Nasal Epithelial Cells In Vitro. Viruses 2021; 13:282. [PMID: 33670363 PMCID: PMC7918080 DOI: 10.3390/v13020282] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a new human pathogen in late 2019 and it has infected over 100 million people in less than a year. There is a clear need for effective antiviral drugs to complement current preventive measures, including vaccines. In this study, we demonstrate that berberine and obatoclax, two broad-spectrum antiviral compounds, are effective against multiple isolates of SARS-CoV-2. Berberine, a plant-derived alkaloid, inhibited SARS-CoV-2 at low micromolar concentrations and obatoclax, which was originally developed as an anti-apoptotic protein antagonist, was effective at sub-micromolar concentrations. Time-of-addition studies indicated that berberine acts on the late stage of the viral life cycle. In agreement, berberine mildly affected viral RNA synthesis, but it strongly reduced infectious viral titers, leading to an increase in the particle-to-pfu ratio. In contrast, obatoclax acted at the early stage of the infection, which is in line with its activity to neutralize the acidic environment in endosomes. We assessed infection of primary human nasal epithelial cells that were cultured on an air-liquid interface and found that SARS-CoV-2 infection induced and repressed expression of specific sets of cytokines and chemokines. Moreover, both obatoclax and berberine inhibited SARS-CoV-2 replication in these primary target cells. We propose berberine and obatoclax as potential antiviral drugs against SARS-CoV-2 that could be considered for further efficacy testing.
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Affiliation(s)
- Finny S. Varghese
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (F.S.V.); (G.J.O.); (P.M.)
| | - Esther van Woudenbergh
- Section Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (E.v.W.); (M.J.E.); (M.I.d.J.)
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands;
| | - Gijs J. Overheul
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (F.S.V.); (G.J.O.); (P.M.)
| | - Marc J. Eleveld
- Section Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (E.v.W.); (M.J.E.); (M.I.d.J.)
| | - Lisa Kurver
- Department of Internal Medicine, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (L.K.); (A.v.L.)
| | - Niels van Heerbeek
- Department of Otolaryngology, Head and Neck Surgery, Radboudumc, 6500 HB Nijmegen, The Netherlands;
| | - Arjan van Laarhoven
- Department of Internal Medicine, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (L.K.); (A.v.L.)
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (F.S.V.); (G.J.O.); (P.M.)
| | - Gerco den Hartog
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands;
| | - Marien I. de Jonge
- Section Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (E.v.W.); (M.J.E.); (M.I.d.J.)
| | - Ronald P. van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (F.S.V.); (G.J.O.); (P.M.)
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18
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Genzel L, Adan R, Berns A, van den Beucken JJJP, Blokland A, Boddeke EHWGM, Bogers WM, Bontrop R, Bulthuis R, Bousema T, Clevers H, Coenen TCJJ, van Dam AM, Deen PMT, van Dijk KW, Eggen BJL, Elgersma Y, Erdogan I, Englitz B, Fentener van Vlissingen JM, la Fleur S, Fouchier R, Fitzsimons CP, Frieling W, Haagmans B, Heesters BA, Henckens MJAG, Herfst S, Hol E, van den Hove D, de Jonge MI, Jonkers J, Joosten LAB, Kalsbeek A, Kamermans M, Kampinga HH, Kas MJ, Keijer J, Kersten S, Kiliaan AJ, Kooij TWA, Kooijman S, Koopman WJH, Korosi A, Krugers HJ, Kuiken T, Kushner SA, Langermans JAM, Lesscher HMB, Lucassen PJ, Lutgens E, Netea MG, Noldus LPJJ, van der Meer JWM, Meye FJ, Mul JD, van Oers K, Olivier JDA, Pasterkamp RJ, Philippens IHCHM, Prickaerts J, Pollux BJA, Rensen PCN, van Rheenen J, van Rij RP, Ritsma L, Rockx BHG, Roozendaal B, van Schothorst EM, Stittelaar K, Stockhofe N, Swaab DF, de Swart RL, Vanderschuren LJMJ, de Vries TJ, de Vrij F, van Wezel R, Wierenga CJ, Wiesmann M, Willuhn I, de Zeeuw CI, Homberg JR. How the COVID-19 pandemic highlights the necessity of animal research. Curr Biol 2020; 30:4328. [PMID: 33142090 PMCID: PMC7605800 DOI: 10.1016/j.cub.2020.10.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Genzel L, Adan R, Berns A, van den Beucken JJJP, Blokland A, Boddeke EHWGM, Bogers WM, Bontrop R, Bulthuis R, Bousema T, Clevers H, Coenen TCJJ, van Dam AM, Deen PMT, van Dijk KW, Eggen BJL, Elgersma Y, Erdogan I, Englitz B, Fentener van Vlissingen JM, la Fleur S, Fouchier R, Fitzsimons CP, Frieling W, Haagmans B, Heesters BA, Henckens MJAG, Herfst S, Hol E, van den Hove D, de Jonge MI, Jonkers J, Joosten LAB, Kalsbeek A, Kamermans M, Kampinga HH, Kas MJ, Keijer JA, Kersten S, Kiliaan AJ, Kooij TWA, Kooijman S, Koopman WJH, Korosi A, Krugers HJ, Kuiken T, Kushner SA, Langermans JAM, Lesscher HMB, Lucassen PJ, Lutgens E, Netea MG, Noldus LPJJ, van der Meer JWM, Meye FJ, Mul JD, van Oers K, Olivier JDA, Pasterkamp RJ, Philippens IHCHM, Prickaerts J, Pollux BJA, Rensen PCN, van Rheenen J, van Rij RP, Ritsma L, Rockx BHG, Roozendaal B, van Schothorst EM, Stittelaar K, Stockhofe N, Swaab DF, de Swart RL, Vanderschuren LJMJ, de Vries TJ, de Vrij F, van Wezel R, Wierenga CJ, Wiesmann M, Willuhn I, de Zeeuw CI, Homberg JR. How the COVID-19 pandemic highlights the necessity of animal research. Curr Biol 2020; 30:R1014-R1018. [PMID: 32961149 PMCID: PMC7416712 DOI: 10.1016/j.cub.2020.08.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recently, a petition was offered to the European Commission calling for an immediate ban on animal testing. Although a Europe-wide moratorium on the use of animals in science is not yet possible, there has been a push by the non-scientific community and politicians for a rapid transition to animal-free innovations. Although there are benefits for both animal welfare and researchers, advances on alternative methods have not progressed enough to be able to replace animal research in the foreseeable future. This trend has led first and foremost to a substantial increase in the administrative burden and hurdles required to make timely advances in research and treatments for human and animal diseases. The current COVID-19 pandemic clearly highlights how much we actually rely on animal research. COVID-19 affects several organs and systems, and the various animal-free alternatives currently available do not come close to this complexity. In this Essay, we therefore argue that the use of animals is essential for the advancement of human and veterinary health.
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Affiliation(s)
- Lisa Genzel
- Radboud University, 6525 XZ Nijmegen, The Netherlands.
| | - Roger Adan
- University Medical Center, Utrecht Brain Center, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Anton Berns
- Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | | | - Arjan Blokland
- Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Erik H W G M Boddeke
- University of Groningen, 9712 CP Groningen, The Netherlands; University of Groningen, University Medical Center, 9713 GZ Groningen, The Netherlands
| | - Willy M Bogers
- Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands
| | - R Bulthuis
- Metris BV, 2132 NG Hoofddorp, The Netherlands
| | - Teun Bousema
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Hans Clevers
- University Medical Center, 3584 CX Utrecht, The Netherlands
| | | | - Anne-Marie van Dam
- Amsterdam UMC, location VU University Medical Center, De Boelelaan 1105, 1081 HZ Amsterdam, The Netherlands
| | | | - K W van Dijk
- Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Bart J L Eggen
- University of Groningen, 9712 CP Groningen, The Netherlands; University of Groningen, University Medical Center, 9713 GZ Groningen, The Netherlands
| | - Ype Elgersma
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Izel Erdogan
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | | | - Susanne la Fleur
- Amsterdam UMC, location VU University Medical Center, De Boelelaan 1105, 1081 HZ Amsterdam, The Netherlands; Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA Amsterdam, The Netherlands
| | - Ron Fouchier
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Carlos P Fitzsimons
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | | | - Bart Haagmans
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Balthasar A Heesters
- Amsterdam UMC, location VU University Medical Center, De Boelelaan 1105, 1081 HZ Amsterdam, The Netherlands
| | | | - Sander Herfst
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Elly Hol
- University Medical Center, Utrecht Brain Center, Utrecht University, 3584 CG Utrecht, The Netherlands
| | | | - Marien I de Jonge
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Jos Jonkers
- Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Leo A B Joosten
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Andries Kalsbeek
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA Amsterdam, The Netherlands
| | - Maarten Kamermans
- Amsterdam UMC, location VU University Medical Center, De Boelelaan 1105, 1081 HZ Amsterdam, The Netherlands; Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA Amsterdam, The Netherlands
| | - Harm H Kampinga
- University of Groningen, University Medical Center, 9713 GZ Groningen, The Netherlands
| | - Martien J Kas
- University of Groningen, 9712 CP Groningen, The Netherlands
| | - J Aap Keijer
- Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Sander Kersten
- Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Amanda J Kiliaan
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Taco W A Kooij
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sander Kooijman
- Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | | | - Aniko Korosi
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Harm J Krugers
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Thijs Kuiken
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Steven A Kushner
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Jan A M Langermans
- Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands; Utrecht University, 3584 CS Utrecht, The Netherlands
| | | | - Paul J Lucassen
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Esther Lutgens
- Amsterdam UMC, location VU University Medical Center, De Boelelaan 1105, 1081 HZ Amsterdam, The Netherlands
| | - Mihai G Netea
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; Life and Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | | | | | - Frank J Meye
- University Medical Center, Utrecht Brain Center, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Joram D Mul
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Kees van Oers
- Wageningen University, 6700 AH Wageningen, The Netherlands; Netherlands Institute of Ecology(NIOO-KNAW), 6700 AB Wageningen, The Netherlands
| | | | - R Jeroen Pasterkamp
- University Medical Center, Utrecht Brain Center, Utrecht University, 3584 CG Utrecht, The Netherlands
| | | | - Jos Prickaerts
- Maastricht University, 6211 LK Maastricht, The Netherlands
| | - B J A Pollux
- Wageningen University, 6700 AH Wageningen, The Netherlands
| | | | | | - Ronald P van Rij
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Laila Ritsma
- Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Barry H G Rockx
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Benno Roozendaal
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | - K Stittelaar
- Viroclinics Xplore, 5374 RE Schaijk, The Netherlands
| | - Norbert Stockhofe
- Wageningen University, 6700 AH Wageningen, The Netherlands; Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands
| | - Dick F Swaab
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA Amsterdam, The Netherlands
| | - Rik L de Swart
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | | | - Taco J de Vries
- Amsterdam UMC, location VU University Medical Center, De Boelelaan 1105, 1081 HZ Amsterdam, The Netherlands
| | - Femke de Vrij
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | | | | | | | - Ingo Willuhn
- Amsterdam UMC, location VU University Medical Center, De Boelelaan 1105, 1081 HZ Amsterdam, The Netherlands; Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA Amsterdam, The Netherlands
| | - Chris I de Zeeuw
- Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA Amsterdam, The Netherlands
| | - Judith R Homberg
- Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.
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20
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Hermanns K, Marklewitz M, Zirkel F, Overheul GJ, Page RA, Loaiza JR, Drosten C, van Rij RP, Junglen S. Agua Salud alphavirus defines a novel lineage of insect-specific alphaviruses discovered in the New World. J Gen Virol 2020; 101:96-104. [PMID: 31674898 PMCID: PMC7414432 DOI: 10.1099/jgv.0.001344] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The genus Alphavirus harbours mostly insect-transmitted viruses that cause severe disease in humans, livestock and wildlife. Thus far, only three alphaviruses with a host range restricted to insects have been found in mosquitoes from the Old World, namely Eilat virus (EILV), Taï Forest alphavirus (TALV) and Mwinilunga alphavirus (MWAV). In this study, we found a novel alphavirus in one Culex declarator mosquito sampled in Panama. The virus was isolated in C6/36 mosquito cells, and full genome sequencing revealed an 11 468 nt long genome with maximum pairwise nucleotide identity of 62.7 % to Sindbis virus. Phylogenetic analyses placed the virus as a solitary deep rooting lineage in a basal relationship to the Western equine encephalitis antigenic complex and to the clade comprising EILV, TALV and MWAV, indicating the detection of a novel alphavirus, tentatively named Agua Salud alphavirus (ASALV). No growth of ASALV was detected in vertebrate cell lines, including cell lines derived from ectothermic animals, and replication of ASALV was strongly impaired above 31 °C, suggesting that ASALV represents the first insect-restricted alphavirus of the New World.
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Affiliation(s)
- Kyra Hermanns
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marco Marklewitz
- German Center for Infection Research (DZIF), Berlin, Germany.,Smithsonian Tropical Research Institute, Panama City, Republic of Panama.,Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Florian Zirkel
- Present address: Biotest AG, Dreieich, Germany.,Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rachel A Page
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Jose R Loaiza
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama.,Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Panama City, Republic of Panama.,Programa Centroamericano de Maestría en Entomología, Vicerrectoría de Investigación y Postgrado, Universidad de Panamá, Panama, Republic of Panama
| | - Christian Drosten
- German Center for Infection Research (DZIF), Berlin, Germany.,Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Sandra Junglen
- German Center for Infection Research (DZIF), Berlin, Germany.,Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
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21
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Suzuki Y, Baidaliuk A, Miesen P, Frangeul L, Crist AB, Merkling SH, Fontaine A, Lequime S, Moltini-Conclois I, Blanc H, van Rij RP, Lambrechts L, Saleh MC. Non-retroviral Endogenous Viral Element Limits Cognate Virus Replication in Aedes aegypti Ovaries. Curr Biol 2020; 30:3495-3506.e6. [PMID: 32679098 PMCID: PMC7522710 DOI: 10.1016/j.cub.2020.06.057] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/06/2020] [Accepted: 06/16/2020] [Indexed: 12/27/2022]
Abstract
Endogenous viral elements (EVEs) are viral sequences integrated in host genomes. A large number of non-retroviral EVEs was recently detected in Aedes mosquito genomes, leading to the hypothesis that mosquito EVEs may control exogenous infections by closely related viruses. Here, we experimentally investigated the role of an EVE naturally found in Aedes aegypti populations and derived from the widespread insect-specific virus, cell-fusing agent virus (CFAV). Using CRISPR-Cas9 genome editing, we created an Ae. aegypti line lacking the CFAV EVE. Absence of the EVE resulted in increased CFAV replication in ovaries, possibly modulating vertical transmission of the virus. Viral replication was controlled by targeting of viral RNA by EVE-derived P-element-induced wimpy testis-interacting RNAs (piRNAs). Our results provide evidence that antiviral piRNAs are produced in the presence of a naturally occurring EVE and its cognate virus, demonstrating a functional link between non-retroviral EVEs and antiviral immunity in a natural insect-virus interaction. Aedes aegypti harbors EVEs with high sequence identity to a contemporary RNA virus EVE-derived piRNAs target genomic viral RNA in infected mosquitoes Ablation of EVE results in increased viral replication in Aedes aegypti ovaries piRNA pathway fulfills antiviral function in presence of EVE and cognate virus
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Affiliation(s)
- Yasutsugu Suzuki
- Viruses and RNA Interference Unit, Institut Pasteur, UMR3569, CNRS, Paris, France
| | - Artem Baidaliuk
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France; Collège Doctoral, Sorbonne Université, 75005 Paris, France
| | - Pascal Miesen
- Viruses and RNA Interference Unit, Institut Pasteur, UMR3569, CNRS, Paris, France; Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lionel Frangeul
- Viruses and RNA Interference Unit, Institut Pasteur, UMR3569, CNRS, Paris, France
| | - Anna B Crist
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Sarah H Merkling
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Albin Fontaine
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Sebastian Lequime
- Laboratory of Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | - Hervé Blanc
- Viruses and RNA Interference Unit, Institut Pasteur, UMR3569, CNRS, Paris, France
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.
| | - Maria-Carla Saleh
- Viruses and RNA Interference Unit, Institut Pasteur, UMR3569, CNRS, Paris, France.
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22
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Abstract
The phenotypic manifestations of disease induced by viruses and subviral infectious entities are the result of complex molecular interactions between host and viral factors. The viral determinants of the diseased phenotype have traditionally been sought at the level of structural or non-structural proteins. However, the discovery of RNA silencing mechanisms has led to speculations that determinants of the diseased phenotype are caused by viral nucleic acid sequences in addition to proteins. RNA silencing is a gene regulation mechanism conserved within eukaryotic kingdoms (with the exception of some yeast species), and in plants and insects it also functions as an antiviral mechanism. Non-coding RNAs of viral origin, ranging in size from 21 to 24 nucleotides (viral small interfering RNAs, vsiRNAs) accumulate in virus-infected tissues and organs, in some cases to comparable levels as the entire complement of host-encoded small interfering RNAs. Upon incorporation into RNA-induced silencing complexes, vsiRNAs can mediate cleavage or induce translational inhibition of nucleic acid targets in a sequence-specific manner. This review focuses on recent findings that suggest an increased complexity of small RNA-based interactions between virus and host. We mainly address plant viruses, but where applicable discuss insect viruses as well. Prominence is given to studies that have indisputably demonstrated that vsiRNAs determine diseased phenotype by either carrying sequence determinants or, indirectly, by altering host-gene regulatory pathways. Results from these studies suggest biotechnological applications, which are also discussed.
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Affiliation(s)
- Paola Leonetti
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, CNR, Bari, Italy
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Vitantonio Pantaleo
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, CNR, Bari, Italy..
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23
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Affiliation(s)
- Finny S Varghese
- Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen
| | | | - Mona Teppor
- Institute of Technology, University of Tartu, Tartu
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24
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Miesen P, van Rij RP. Crossing the Mucosal Barrier: A Commensal Bacterium Gives Dengue Virus a Leg-Up in the Mosquito Midgut. Cell Host Microbe 2019; 25:1-2. [PMID: 30629911 DOI: 10.1016/j.chom.2018.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Commensal bacteria that colonize the midgut of Aedes aegypti mosquitoes can influence the transmission of arthropod-borne viruses. In this issue of Cell Host & Microbe, Wu et al. (2019) show that Serratia marcescens bacteria secrete enhancin proteins that cleave membrane-bound mucins, thereby facilitating dengue virus infection of midgut epithelial cells.
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Affiliation(s)
- Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands.
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25
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Fareh M, van Lopik J, Katechis I, Bronkhorst AW, Haagsma AC, van Rij RP, Joo C. Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA. Nucleic Acids Res 2019; 46:3187-3197. [PMID: 29325071 PMCID: PMC5888754 DOI: 10.1093/nar/gkx1316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/03/2018] [Indexed: 11/14/2022] Open
Abstract
RNA interference (RNAi) is an indispensable mechanism for antiviral defense in insects, including mosquitoes that transmit human diseases. To escape this antiviral defense system, viruses encode suppressors of RNAi that prevent elimination of viral RNAs, and thus ensure efficient virus accumulation. Although the first animal Viral Suppressor of RNAi (VSR) was identified more than a decade ago, the molecular basis of RNAi suppression by these viral proteins remains unclear. Here, we developed a single-molecule fluorescence assay to investigate how VSRs inhibit the recognition of viral RNAs by Dcr-2, a key endoribonuclease enzyme in the RNAi pathway. Using VSRs from three insect RNA viruses (Culex Y virus, Drosophila X virus and Drosophila C virus), we reveal bimodal physical interactions between RNA molecules and VSRs. During initial interactions, these VSRs rapidly discriminate short RNA substrates from long dsRNA. VSRs engage nearly irreversible binding with long dsRNAs, thereby shielding it from recognition by Dcr-2. We propose that the length-dependent switch from rapid screening to irreversible binding reflects the main mechanism by which VSRs distinguish viral dsRNA from cellular RNA species such as microRNAs.
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Affiliation(s)
- Mohamed Fareh
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Jasper van Lopik
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Iason Katechis
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Alfred W Bronkhorst
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands
| | - Anna C Haagsma
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
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26
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Göertz GP, Miesen P, Overheul GJ, van Rij RP, van Oers MM, Pijlman GP. Mosquito Small RNA Responses to West Nile and Insect-Specific Virus Infections in Aedes and Culex Mosquito Cells. Viruses 2019; 11:v11030271. [PMID: 30889941 PMCID: PMC6466260 DOI: 10.3390/v11030271] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/15/2022] Open
Abstract
Small RNA mediated responses are essential for antiviral defence in mosquitoes, however, they appear to differ per virus-vector combination. To further investigate the diversity of small RNA responses against viruses in mosquitoes, we applied a small RNA deep sequencing approach on five mosquito cell lines: Culex tarsalis CT cells, Aedes albopictus U4.4 and C6/36 cells, Ae. aegypti Aag2 cells (cleared from cell fusing agent virus and Culex Y virus (CYV) by repetitive dsRNA transfections) and Ae. pseudoscutellaris AP-61 cells. De novo assembly of small RNAs revealed the presence of Phasi Charoen-like virus (PCLV), Calbertado virus, Flock House virus and a novel narnavirus in CT cells, CYV in U4.4 cells, and PCLV in Aag2 cells, whereas no insect-specific viruses (ISVs) were detected in C6/36 and AP-61 cells. Next, we investigated the small RNA responses to the identified ISVs and to acute infection with the arthropod-borne West Nile virus (WNV). We demonstrate that AP-61 and C6/36 cells do not produce siRNAs to WNV infection, suggesting that AP-61, like C6/36, are Dicer-2 deficient. CT cells produced a strong siRNA response to the persistent ISVs and acute WNV infection. Interestingly, CT cells also produced viral PIWI-interacting (pi)RNAs to PCLV, but not to WNV or any of the other ISVs. In contrast, in U4.4 and Aag2 cells, WNV siRNAs, and pi-like RNAs without typical ping-pong piRNA signature were observed, while this signature was present in PCLV piRNAs in Aag2 cells. Together, our results demonstrate that mosquito small RNA responses are strongly dependent on both the mosquito cell type and/or the mosquito species and family of the infecting virus.
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Affiliation(s)
- Giel P Göertz
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands.
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands.
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands.
| | - Monique M van Oers
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Riswari SF, Tunjungputri RN, Kullaya V, Garishah FM, Utari GSR, Farhanah N, Overheul GJ, Alisjahbana B, Gasem MH, Urbanus RT, de Groot PG, Lefeber DJ, van Rij RP, van der Ven A, de Mast Q. Desialylation of platelets induced by Von Willebrand Factor is a novel mechanism of platelet clearance in dengue. PLoS Pathog 2019; 15:e1007500. [PMID: 30849118 PMCID: PMC6426266 DOI: 10.1371/journal.ppat.1007500] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 03/20/2019] [Accepted: 12/03/2018] [Indexed: 11/19/2022] Open
Abstract
Thrombocytopenia and platelet dysfunction are commonly observed in patients with dengue virus (DENV) infection and may contribute to complications such as bleeding and plasma leakage. The etiology of dengue-associated thrombocytopenia is multifactorial and includes increased platelet clearance. The binding of the coagulation protein von Willebrand factor (VWF) to the platelet membrane and removal of sialic acid (desialylation) are two well-known mechanisms of platelet clearance, but whether these conditions also contribute to thrombocytopenia in dengue infection is unknown. In two observational cohort studies in Bandung and Jepara, Indonesia, we show that adult patients with dengue not only had higher plasma concentrations of plasma VWF antigen and active VWF, but that circulating platelets had also bound more VWF to their membrane. The amount of platelet-VWF binding correlated well with platelet count. Furthermore, sialic acid levels in dengue patients were significantly reduced as assessed by the binding of Sambucus nigra lectin (SNA) and Maackia amurensis lectin II (MAL-II) to platelets. Sialic acid on the platelet membrane is neuraminidase-labile, but dengue virus has no known neuraminidase activity. Indeed, no detectable activity of neuraminidase was present in plasma of dengue patients and no desialylation was found of plasma transferrin. Platelet sialylation was also not altered by in vitro exposure of platelets to DENV nonstructural protein 1 or cultured DENV. In contrast, induction of binding of VWF to glycoprotein 1b on platelets using the VWF-activating protein ristocetin resulted in the removal of platelet sialic acid by translocation of platelet neuraminidase to the platelet surface. The neuraminidase inhibitor oseltamivir reduced VWF-induced platelet desialylation. Our data demonstrate that excessive binding of VWF to platelets in dengue results in neuraminidase-mediated platelet desialylation and platelet clearance. Oseltamivir might be a novel treatment option for severe thrombocytopenia in dengue infection. Dengue is the most common arbovirus infection in the world. A decrease in the number of blood platelets is an almost universal finding in severe dengue. Binding of the coagulation protein von Willebrand factor (VWF) and loss of sialic acid residues from the platelet membrane are two main mechanisms of clearance of senescent platelets under non-pathological conditions. Here, we show that platelets from patients with acute dengue have bound more VWF and have lost sialic acid from their membrane. Sialic acid can be cleaved by the enzyme neuraminidase. We show that neuraminidase activity in the plasma is not increased and that neither dengue virus itself nor nonstructural protein 1, a protein secreted by dengue virus, cleave sialic acid from the platelet membrane. In contrast, binding of VWF to platelets results in translocation of neuraminidase to the platelet membrane and subsequent cleavage of sialic acid. This process could be inhibited by the neuraminidase inhibitor oseltamivir, a commonly used anti-influenza drug. Altogether, our results indicate that VWF binding to platelets is increased in dengue infection, leading to the removal of sialic acid and platelet clearance. Oseltamivir may prevent this process and thus represent a novel treatment option for low platelet numbers in dengue infection.
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Affiliation(s)
- Silvita Fitri Riswari
- Clinical Infectious Disease Research Center, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rahajeng N. Tunjungputri
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Disease (CENTRID), Faculty of Medicine Diponegoro University, Dr Kariadi Hospital, Semarang, Indonesia
| | - Vesla Kullaya
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Kilimanjaro Christian Medical Center, Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Fadel M. Garishah
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Disease (CENTRID), Faculty of Medicine Diponegoro University, Dr Kariadi Hospital, Semarang, Indonesia
| | - Gloria S. R. Utari
- Center for Tropical and Infectious Disease (CENTRID), Faculty of Medicine Diponegoro University, Dr Kariadi Hospital, Semarang, Indonesia
| | - Nur Farhanah
- Center for Tropical and Infectious Disease (CENTRID), Faculty of Medicine Diponegoro University, Dr Kariadi Hospital, Semarang, Indonesia
| | - Gijs J. Overheul
- Center for Tropical and Infectious Disease (CENTRID), Faculty of Medicine Diponegoro University, Dr Kariadi Hospital, Semarang, Indonesia
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bachti Alisjahbana
- Clinical Infectious Disease Research Center, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - M. Hussein Gasem
- Center for Tropical and Infectious Disease (CENTRID), Faculty of Medicine Diponegoro University, Dr Kariadi Hospital, Semarang, Indonesia
| | - Rolf T. Urbanus
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Philip. G. de Groot
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dirk J. Lefeber
- Department of Neurology, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P. van Rij
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andre van der Ven
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail:
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Merkling SH, Riahi H, Overheul GJ, Schenck A, van Rij RP. Peroxisome-associated Sgroppino links fat metabolism with survival after RNA virus infection in Drosophila. Sci Rep 2019; 9:2065. [PMID: 30765784 PMCID: PMC6375949 DOI: 10.1038/s41598-019-38559-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/31/2018] [Indexed: 12/31/2022] Open
Abstract
The fruit fly Drosophila melanogaster is a valuable model organism for the discovery and characterization of innate immune pathways, but host responses to virus infection remain incompletely understood. Here, we describe a novel player in host defense, Sgroppino (Sgp). Genetic depletion of Sgroppino causes hypersensitivity of adult flies to infections with the RNA viruses Drosophila C virus, cricket paralysis virus, and Flock House virus. Canonical antiviral immune pathways are functional in Sgroppino mutants, suggesting that Sgroppino exerts its activity via an as yet uncharacterized process. We demonstrate that Sgroppino localizes to peroxisomes, organelles involved in lipid metabolism. In accordance, Sgroppino-deficient flies show a defect in lipid metabolism, reflected by higher triglyceride levels, higher body mass, and thicker abdominal fat tissue. In addition, knock-down of Pex3, an essential peroxisome biogenesis factor, increases sensitivity to virus infection. Together, our results establish a genetic link between the peroxisomal protein Sgroppino, fat metabolism, and resistance to virus infection.
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Affiliation(s)
- Sarah H Merkling
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Human Riahi
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Meutiawati F, Bezemer B, Strating JRPM, Overheul GJ, Žusinaite E, van Kuppeveld FJM, van Cleef KWR, van Rij RP. Posaconazole inhibits dengue virus replication by targeting oxysterol-binding protein. Antiviral Res 2018; 157:68-79. [PMID: 29981375 DOI: 10.1016/j.antiviral.2018.06.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/08/2018] [Accepted: 06/30/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) is associated with an estimated 390 million infections per year, occurring across approximately 100 countries in tropical and sub-tropical regions. To date, there are no antiviral drugs or specific therapies to treat DENV infection. Posaconazole and itraconazole are potent antifungal drugs that inhibit ergosterol biosynthesis in fungal cells, but also target a number of human proteins. Here, we show that itraconazole and posaconazole have antiviral activity against DENV. Posaconazole inhibited replication of multiple serotypes of DENV and the related flavivirus Zika virus, and reduced viral RNA replication, but not translation of the viral genome. We used a combination of knockdown and drug sensitization assays to define the molecular target of posaconazole that mediates its antiviral activity. We found that knockdown of oxysterol-binding protein (OSBP) inhibited DENV replication. Moreover, knockdown of OSBP, but not other known targets of posaconazole, enhanced the inhibitory effect of posaconazole. Our findings imply OSBP as a potential target for the development of antiviral compounds against DENV.
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Affiliation(s)
- Febrina Meutiawati
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands; Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bodine Bezemer
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands; Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen R P M Strating
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands; Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eva Žusinaite
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Koen W R van Cleef
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands; Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands; Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.
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30
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Melia CE, van der Schaar HM, Lyoo H, Limpens RWAL, Feng Q, Wahedi M, Overheul GJ, van Rij RP, Snijder EJ, Koster AJ, Bárcena M, van Kuppeveld FJM. Escaping Host Factor PI4KB Inhibition: Enterovirus Genomic RNA Replication in the Absence of Replication Organelles. Cell Rep 2018; 21:587-599. [PMID: 29045829 PMCID: PMC5656745 DOI: 10.1016/j.celrep.2017.09.068] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/25/2017] [Accepted: 09/20/2017] [Indexed: 01/15/2023] Open
Abstract
Enteroviruses reorganize cellular endomembranes into replication organelles (ROs) for genome replication. Although enterovirus replication depends on phosphatidylinositol 4-kinase type IIIβ (PI4KB), its role, and that of its product, phosphatidylinositol 4-phosphate (PI4P), is only partially understood. Exploiting a mutant coxsackievirus resistant to PI4KB inhibition, we show that PI4KB activity has distinct functions both in proteolytic processing of the viral polyprotein and in RO biogenesis. The escape mutation rectifies a proteolytic processing defect imposed by PI4KB inhibition, pointing to a possible escape mechanism. Remarkably, under PI4KB inhibition, the mutant virus could replicate its genome in the absence of ROs, using instead the Golgi apparatus. This impaired RO biogenesis provided an opportunity to investigate the proposed role of ROs in shielding enteroviral RNA from cellular sensors. Neither accelerated sensing of viral RNA nor enhanced innate immune responses was observed. Together, our findings challenge the notion that ROs are indispensable for enterovirus genome replication and immune evasion. PI4KB activity expedites the formation of coxsackievirus replication organelles (ROs) PI4KB inhibition impairs polyprotein processing, which is rescued by a 3A mutation Upon PI4KB inhibition, this mutant replicates at the Golgi in the absence of ROs Innate immune responses are not enhanced when RO biogenesis is delayed
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Affiliation(s)
- Charlotte E Melia
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Hilde M van der Schaar
- Department of Infectious Diseases & Immunology, Utrecht University, Utrecht 3584 CL, the Netherlands
| | - Heyrhyoung Lyoo
- Department of Infectious Diseases & Immunology, Utrecht University, Utrecht 3584 CL, the Netherlands
| | - Ronald W A L Limpens
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Qian Feng
- Department of Infectious Diseases & Immunology, Utrecht University, Utrecht 3584 CL, the Netherlands
| | - Maryam Wahedi
- Department of Infectious Diseases & Immunology, Utrecht University, Utrecht 3584 CL, the Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, the Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, the Netherlands
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Abraham J Koster
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Montserrat Bárcena
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands.
| | - Frank J M van Kuppeveld
- Department of Infectious Diseases & Immunology, Utrecht University, Utrecht 3584 CL, the Netherlands.
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Abstract
The power and ease of Drosophila genetics and the medical relevance of mosquito-transmitted viruses have made dipterans important model organisms in antiviral immunology. Studies of virus-host interactions at the molecular and population levels have illuminated determinants of resistance to virus infection. Here, we review the sources and nature of variation in antiviral immunity and virus susceptibility in model dipteran insects, specifically the fruit fly Drosophila melanogaster and vector mosquitoes of the genera Aedes and Culex. We first discuss antiviral immune mechanisms and describe the virus-specificity of these responses. In the following sections, we review genetic and microbiota-dependent variation in antiviral immunity. In the final sections, we explore less well-studied sources of variation, including abiotic factors, sexual dimorphism, infection history, and endogenous viral elements. We borrow from work on other pathogen types and non-dipteran species when it parallels or complements studies in dipterans. Understanding natural variation in virus-host interactions may lead to the identification of novel restriction factors and immune mechanisms and shed light on the molecular determinants of vector competence.
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Affiliation(s)
- William H Palmer
- Institute of Evolutionary Biology and Centre for Infection, Evolution and Immunity, University of Edinburgh, Edinburgh EH9 3FL UK.
| | - Finny S Varghese
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands.
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands.
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands.
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Abstract
Insects are the most abundant and diverse group of animals on earth, but our knowledge of their viruses is biased toward insect-borne viruses that cause disease in plants, animals, or humans. Recent metagenomic studies and systematic surveys of viruses in wild-caught insects have identified an unanticipated large repertoire of novel viruses and viral sequences. These include new members of existing clades, new clades, and even entirely new virus families. These studies greatly expand the known virosphere in insects, provide opportunities to study virus-host interactions, and generate new insights into virus evolution. In this chapter, we discuss the methods used to identify novel viruses in insects and highlight some notable surprises arising from these studies.
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Affiliation(s)
- Finny S Varghese
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Girardi E, Miesen P, Pennings B, Frangeul L, Saleh MC, van Rij RP. Histone-derived piRNA biogenesis depends on the ping-pong partners Piwi5 and Ago3 in Aedes aegypti. Nucleic Acids Res 2017; 45:4881-4892. [PMID: 28115625 PMCID: PMC5416884 DOI: 10.1093/nar/gkw1368] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 01/04/2017] [Indexed: 12/13/2022] Open
Abstract
The piRNA pathway is of key importance in controlling transposable elements in most animal species. In the vector mosquito Aedes aegypti, the presence of eight PIWI proteins and the accumulation of viral piRNAs upon arbovirus infection suggest additional functions of the piRNA pathway beyond genome defense. To better understand the regulatory potential of this pathway, we analyzed in detail host-derived piRNAs in A. aegypti Aag2 cells. We show that a large repertoire of protein-coding genes and non-retroviral integrated RNA virus elements are processed into genic piRNAs by different combinations of PIWI proteins. Among these, we identify a class of genes that produces piRNAs from coding sequences in an Ago3- and Piwi5-dependent fashion. We demonstrate that the replication-dependent histone gene family is a genic source of ping-pong dependent piRNAs and that histone-derived piRNAs are dynamically expressed throughout the cell cycle, suggesting a role for the piRNA pathway in the regulation of histone gene expression. Moreover, our results establish the Aag2 cell line as an accessible experimental model to study gene-derived piRNAs.
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Affiliation(s)
- Erika Girardi
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Bas Pennings
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Lionel Frangeul
- Institut Pasteur, Viruses and RNA interference, CNRS URM 3569, 75724 Paris Cedex 15, France
| | - Maria-Carla Saleh
- Institut Pasteur, Viruses and RNA interference, CNRS URM 3569, 75724 Paris Cedex 15, France
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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Halbach R, Junglen S, van Rij RP. Mosquito-specific and mosquito-borne viruses: evolution, infection, and host defense. Curr Opin Insect Sci 2017; 22:16-27. [PMID: 28805635 DOI: 10.1016/j.cois.2017.05.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Recent virus discovery programs have identified an extensive reservoir of viruses in arthropods. It is thought that arthropod viruses, including mosquito-specific viruses, are ancestral to vertebrate-pathogenic arboviruses. Mosquito-specific viruses are restricted in vertebrate cells at multiple levels, including entry, RNA replication, assembly, and by the inability to replicate at high temperatures. Moreover, it is likely that the vertebrate immune system suppresses replication of these viruses. The evolution from single to dual-host tropism may also require changes in the course of infection in the mosquito host. In this review we explore the adaptive changes required for a switch from a mosquito-specific to a mosquito-borne transmission cycle.
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Affiliation(s)
- Rebecca Halbach
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Campus Charité Mitte, Charitéplatz 1, 10117 Berlin, Germany; German Centre for Infection Research (DZIF), Berlin, Germany
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
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Palatini U, Miesen P, Carballar-Lejarazu R, Ometto L, Rizzo E, Tu Z, van Rij RP, Bonizzoni M. Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus. BMC Genomics 2017; 18:512. [PMID: 28676109 PMCID: PMC5497376 DOI: 10.1186/s12864-017-3903-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/26/2017] [Indexed: 02/08/2023] Open
Abstract
Background Arthropod-borne viruses (arboviruses) transmitted by mosquito vectors cause many important emerging or resurging infectious diseases in humans including dengue, chikungunya and Zika. Understanding the co-evolutionary processes among viruses and vectors is essential for the development of novel transmission-blocking strategies. Episomal viral DNA fragments are produced from arboviral RNA upon infection of mosquito cells and adults. Additionally, sequences from insect-specific viruses and arboviruses have been found integrated into mosquito genomes. Results We used a bioinformatic approach to analyse the presence, abundance, distribution, and transcriptional activity of integrations from 425 non-retroviral viruses, including 133 arboviruses, across the presently available 22 mosquito genome sequences. Large differences in abundance and types of viral integrations were observed in mosquito species from the same region. Viral integrations are unexpectedly abundant in the arboviral vector species Aedes aegypti and Ae. albopictus, in which they are approximately ~10-fold more abundant than in other mosquito species analysed. Additionally, viral integrations are enriched in piRNA clusters of both the Ae. aegypti and Ae. albopictus genomes and, accordingly, they express piRNAs, but not siRNAs. Conclusions Differences in the number of viral integrations in the genomes of mosquito species from the same geographic area support the conclusion that integrations of viral sequences is not dependent on viral exposure, but that lineage-specific interactions exist. Viral integrations are abundant in Ae. aegypti and Ae. albopictus, and represent a thus far underappreciated component of their genomes. Additionally, the genome locations of viral integrations and their production of piRNAs indicate a functional link between viral integrations and the piRNA pathway. These results greatly expand the breadth and complexity of small RNA-mediated regulation and suggest a role for viral integrations in antiviral defense in these two mosquito species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3903-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Umberto Palatini
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, Nijmegen, The Netherlands
| | | | - Lino Ometto
- Indepenent Researcher, Mezzocorona, Trento, Italy
| | | | - Zhijian Tu
- Department of Biochemistry and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, Nijmegen, The Netherlands
| | - Mariangela Bonizzoni
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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Doublet V, Poeschl Y, Gogol-Döring A, Alaux C, Annoscia D, Aurori C, Barribeau SM, Bedoya-Reina OC, Brown MJF, Bull JC, Flenniken ML, Galbraith DA, Genersch E, Gisder S, Grosse I, Holt HL, Hultmark D, Lattorff HMG, Le Conte Y, Manfredini F, McMahon DP, Moritz RFA, Nazzi F, Niño EL, Nowick K, van Rij RP, Paxton RJ, Grozinger CM. Erratum to: Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens. BMC Genomics 2017; 18:256. [PMID: 28335723 PMCID: PMC5364706 DOI: 10.1186/s12864-017-3624-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 11/16/2022] Open
Affiliation(s)
- Vincent Doublet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany. .,Centre for Ecology and Conservation, University of Exeter, Penryn, UK.
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andreas Gogol-Döring
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.,Technische Hochschule Mittelhessen, Gießen, Germany
| | - Cédric Alaux
- INRA, UR 406 Abeilles et Environnement, Avignon, France
| | - Desiderato Annoscia
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, Udine, Italy
| | - Christian Aurori
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Seth M Barribeau
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Oscar C Bedoya-Reina
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, State College, PA, USA.,Present address: MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK.,Present address: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - James C Bull
- Department of Biosciences, Swansea University, Swansea, UK
| | - Michelle L Flenniken
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - David A Galbraith
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, State College, PA, USA
| | - Elke Genersch
- Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany.,Department of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Gisder
- Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Ivo Grosse
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Holly L Holt
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, State College, PA, USA.,Department of Fisheries, Wildlife, and Conservation Biology, The Monarch Joint Venture, University of Minnesota, St. Paul, MN, USA
| | - Dan Hultmark
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - H Michael G Lattorff
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute for Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.,Present address: International Centre of Insect Physiology and Ecology (icipe), Environmental Health Theme, Nairobi, Kenya
| | - Yves Le Conte
- INRA, UR 406 Abeilles et Environnement, Avignon, France
| | - Fabio Manfredini
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Dino P McMahon
- Institute for Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.,School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Robin F A Moritz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute for Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Francesco Nazzi
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, Udine, Italy
| | - Elina L Niño
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, State College, PA, USA.,Department of Entomology and Nematology, University of California, Davis, CA, USA
| | - Katja Nowick
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Computer Science, TFome Research Group, Bioinformatics Group, Interdisciplinary Center of Bioinformatics, University of Leipzig, Leipzig, Germany.,Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert J Paxton
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute for Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.,School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, State College, PA, USA
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Doublet V, Poeschl Y, Gogol-Döring A, Alaux C, Annoscia D, Aurori C, Barribeau SM, Bedoya-Reina OC, Brown MJF, Bull JC, Flenniken ML, Galbraith DA, Genersch E, Gisder S, Grosse I, Holt HL, Hultmark D, Lattorff HMG, Le Conte Y, Manfredini F, McMahon DP, Moritz RFA, Nazzi F, Niño EL, Nowick K, van Rij RP, Paxton RJ, Grozinger CM. Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens. BMC Genomics 2017; 18:207. [PMID: 28249569 PMCID: PMC5333379 DOI: 10.1186/s12864-017-3597-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/20/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Organisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses to each type of pathogen they encounter. The advent of transcriptomics now makes it possible to test this hypothesis and compare host gene expression responses to multiple pathogens at a genome-wide scale. Here, we performed a meta-analysis of multiple published and new transcriptomes using a newly developed bioinformatics approach that filters genes based on their expression profile across datasets. Thereby, we identified common and unique molecular responses of a model host species, the honey bee (Apis mellifera), to its major pathogens and parasites: the Microsporidia Nosema apis and Nosema ceranae, RNA viruses, and the ectoparasitic mite Varroa destructor, which transmits viruses. RESULTS We identified a common suite of genes and conserved molecular pathways that respond to all investigated pathogens, a result that suggests a commonality in response mechanisms to diverse pathogens. We found that genes differentially expressed after infection exhibit a higher evolutionary rate than non-differentially expressed genes. Using our new bioinformatics approach, we unveiled additional pathogen-specific responses of honey bees; we found that apoptosis appeared to be an important response following microsporidian infection, while genes from the immune signalling pathways, Toll and Imd, were differentially expressed after Varroa/virus infection. Finally, we applied our bioinformatics approach and generated a gene co-expression network to identify highly connected (hub) genes that may represent important mediators and regulators of anti-pathogen responses. CONCLUSIONS Our meta-analysis generated a comprehensive overview of the host metabolic and other biological processes that mediate interactions between insects and their pathogens. We identified key host genes and pathways that respond to phylogenetically diverse pathogens, representing an important source for future functional studies as well as offering new routes to identify or generate pathogen resilient honey bee stocks. The statistical and bioinformatics approaches that were developed for this study are broadly applicable to synthesize information across transcriptomic datasets. These approaches will likely have utility in addressing a variety of biological questions.
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Affiliation(s)
- Vincent Doublet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK.
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andreas Gogol-Döring
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Technische Hochschule Mittelhessen, Gießen, Germany
| | - Cédric Alaux
- INRA, UR 406 Abeilles et Environnement, Avignon, France
| | - Desiderato Annoscia
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, Udine, Italy
| | - Christian Aurori
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Seth M Barribeau
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Oscar C Bedoya-Reina
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, State College, PA, USA
- Present address: MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Present address: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - James C Bull
- Department of Biosciences, Swansea University, Swansea, UK
| | - Michelle L Flenniken
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - David A Galbraith
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, State College, PA, USA
| | - Elke Genersch
- Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
- Department of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Gisder
- Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Ivo Grosse
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Holly L Holt
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, State College, PA, USA
- Department of Fisheries, Wildlife, and Conservation Biology, The Monarch Joint Venture, University of Minnesota, St. Paul, MN, USA
| | - Dan Hultmark
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - H Michael G Lattorff
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute for Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Present address: International Centre of Insect Physiology and Ecology (icipe), Environmental Health Theme, Nairobi, Kenya
| | - Yves Le Conte
- INRA, UR 406 Abeilles et Environnement, Avignon, France
| | - Fabio Manfredini
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Dino P McMahon
- Institute for Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Robin F A Moritz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute for Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Francesco Nazzi
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, Udine, Italy
| | - Elina L Niño
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, State College, PA, USA
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | - Katja Nowick
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Computer Science, TFome Research Group, Bioinformatics Group, Interdisciplinary Center of Bioinformatics, University of Leipzig, Leipzig, Germany
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert J Paxton
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute for Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, State College, PA, USA
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Martina BE, Barzon L, Pijlman GP, de la Fuente J, Rizzoli A, Wammes LJ, Takken W, van Rij RP, Papa A. Human to human transmission of arthropod-borne pathogens. Curr Opin Virol 2016; 22:13-21. [PMID: 27915056 DOI: 10.1016/j.coviro.2016.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/07/2016] [Accepted: 11/11/2016] [Indexed: 12/17/2022]
Abstract
Human-to-human (H2H) transmitted arthropod-borne pathogens are a growing burden worldwide, with malaria and dengue being the most common mosquito-borne H2H transmitted diseases. The ability of vectors to get infected by humans during a blood meal to further propel an epidemic depends on complex interactions between pathogens, vectors and humans, in which human interventions and demographic and environmental conditions play a significant role. Herein, we discuss the distal and proximal drivers affecting H2H vector-borne pathogen transmission and identify knowledge gaps and future perspectives.
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Affiliation(s)
- Byron E Martina
- Viroscience Laboratory, Erasmus Medical Centre, Rotterdam, The Netherlands; Artemis One Health Research Institute, Utrecht, The Netherlands
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain; Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (Trento), Italy
| | - Linda J Wammes
- Department of Microbiology & Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - Willem Takken
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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39
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van Cleef KWR, Overheul GJ, Thomassen MC, Marjakangas JM, van Rij RP. Escape Mutations in NS4B Render Dengue Virus Insensitive to the Antiviral Activity of the Paracetamol Metabolite AM404. Antimicrob Agents Chemother 2016; 60:2554-7. [PMID: 26856827 PMCID: PMC4808173 DOI: 10.1128/aac.02462-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/25/2016] [Indexed: 12/25/2022] Open
Abstract
Despite the enormous disease burden associated with dengue virus infections, a licensed antiviral drug is lacking. Here, we show that the paracetamol (acetaminophen) metabolite AM404 inhibits dengue virus replication. Moreover, we find that mutations in NS4B that were previously found to confer resistance to the antiviral compounds NITD-618 and SDM25N also render dengue virus insensitive to AM404. Our work provides further support for NS4B as a direct or indirect target for antiviral drug development.
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Affiliation(s)
- Koen W R van Cleef
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Michael C Thomassen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Jenni M Marjakangas
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
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40
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Miesen P, Ivens A, Buck AH, van Rij RP. Small RNA Profiling in Dengue Virus 2-Infected Aedes Mosquito Cells Reveals Viral piRNAs and Novel Host miRNAs. PLoS Negl Trop Dis 2016; 10:e0004452. [PMID: 26914027 PMCID: PMC4767436 DOI: 10.1371/journal.pntd.0004452] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/21/2016] [Indexed: 11/18/2022] Open
Abstract
In Aedes mosquitoes, infections with arthropod-borne viruses (arboviruses) trigger or modulate the expression of various classes of viral and host-derived small RNAs, including small interfering RNAs (siRNAs), PIWI interacting RNAs (piRNAs), and microRNAs (miRNAs). Viral siRNAs are at the core of the antiviral RNA interference machinery, one of the key pathways that limit virus replication in invertebrates. Besides siRNAs, Aedes mosquitoes and cells derived from these insects produce arbovirus-derived piRNAs, the best studied examples being viruses from the Togaviridae or Bunyaviridae families. Host miRNAs modulate the expression of a large number of genes and their levels may change in response to viral infections. In addition, some viruses, mostly with a DNA genome, express their own miRNAs to regulate host and viral gene expression. Here, we perform a comprehensive analysis of both viral and host-derived small RNAs in Aedes aegypti Aag2 cells infected with dengue virus 2 (DENV), a member of the Flaviviridae family. Aag2 cells are competent in producing all three types of small RNAs and provide a powerful tool to explore the crosstalk between arboviral infection and the distinct RNA silencing pathways. Interestingly, besides the well-characterized DENV-derived siRNAs, a specific population of viral piRNAs was identified in infected Aag2 cells. Knockdown of Piwi5, Ago3 and, to a lesser extent, Piwi6 results in reduction of vpiRNA levels, providing the first genetic evidence that Aedes PIWI proteins produce DENV-derived small RNAs. In contrast, we do not find convincing evidence for the production of virus-derived miRNAs. Neither do we find that host miRNA expression is strongly changed upon DENV2 infection. Finally, our deep-sequencing analyses detect 30 novel Aedes miRNAs, complementing the repertoire of regulatory small RNAs in this important vector species. Mosquitoes of the Aedes family transmit many important viruses, including dengue virus, between their vertebrate hosts. In the mosquito, the growth of these viruses is limited by the antiviral RNA interference pathway. Key to this pathway is a class of small non-coding RNAs known as small interfering RNAs (siRNAs). In addition, two related but distinct small RNA pathways known as the microRNA (miRNA) and the PIWI-interacting RNA (piRNA) pathway are implicated in regulating virus replication in mosquitoes. Thus, since small RNAs may critically influence the transmission of dengue virus, we set out to analyze the populations of viral and mosquito small RNAs that are produced in infected Aedes mosquito cells. We found that besides the well-known viral siRNAs, dengue virus-derived piRNAs were produced in these cells and we identified the PIWI proteins that these small RNAs rely on. In addition, we found that viral miRNAs were not expressed from the dengue virus genome and that the levels of mosquito miRNAs were barely changed upon infection. Finally, our data allowed for the identification of novel Aedes miRNAs, complementing the repertoire of these important regulatory RNAs in vector mosquitoes.
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Affiliation(s)
- Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Alasdair Ivens
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Amy H. Buck
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Ronald P. van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- * E-mail:
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41
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Fros JJ, Miesen P, Vogels CB, Gaibani P, Sambri V, Martina BE, Koenraadt CJ, van Rij RP, Vlak JM, Takken W, Pijlman GP. Comparative Usutu and West Nile virus transmission potential by local Culex pipiens mosquitoes in north-western Europe. One Health 2015; 1:31-36. [PMID: 28616462 PMCID: PMC5441354 DOI: 10.1016/j.onehlt.2015.08.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 12/17/2022] Open
Abstract
Originating from Africa, Usutu virus (USUV) first emerged in Europe in 2001. This mosquito-borne flavivirus caused high mortality rates in its bird reservoirs, which strongly resembled the introduction of West Nile virus (WNV) in 1999 in the United States. Mosquitoes infected with USUV incidentally transmit the virus to other vertebrates, including humans, which can result in neuroinvasive disease. USUV and WNV co-circulate in parts of southern Europe, but the distribution of USUV extends into central and northwestern Europe. In the field, both viruses have been detected in the northern house mosquito Culex pipiens, of which the potential for USUV transmission is unknown. To understand the transmission dynamics and assess the potential spread of USUV, we determined the vector competence of C. pipiens for USUV and compared it with the well characterized WNV. We show for the first time that northwestern European mosquitoes are highly effective vectors for USUV, with infection rates of 11% at 18 °C and 53% at 23 °C, which are comparable with values obtained for WNV. Interestingly, at a high temperature of 28 °C, mosquitoes became more effectively infected with USUV (90%) than with WNV (58%), which could be attributed to barriers in the mosquito midgut. Small RNA deep sequencing of infected mosquitoes showed for both viruses a strong bias for 21-nucleotide small interfering (si)RNAs, which map across the entire viral genome both on the sense and antisense strand. No evidence for viral PIWI-associated RNA (piRNA) was found, suggesting that the siRNA pathway is the major small RNA pathway that targets USUV and WNV infection in C. pipiens mosquitoes. Northwestern European mosquitoes are highly effective vectors for USUV. Culex pipiens is significantly more competent for USUV than for WNV at 28 °C. The siRNA but not the piRNA pathway targets USUV and WNV infections in C. pipiens. USUV may be a prelude to WNV transmission in northwestern Europe.
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Affiliation(s)
- Jelke J Fros
- Laboratory of Virology Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Chantal B Vogels
- Laboratory of Entomology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Paolo Gaibani
- Regional Reference Centre for Microbiological Emergencies (CRREM), Microbiology Unit, Azienda Ospedaliero-Universitaria di Bologna, Policlinico S. Orsola-Malpighi, Bologna, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Piazza della Liberazione, 60, 47522 Pievesestina, FC, Italy
| | - Byron E Martina
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.,Artemis One Health, Utrecht, The Netherlands
| | - Constantianus J Koenraadt
- Laboratory of Entomology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Just M Vlak
- Laboratory of Virology Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Willem Takken
- Laboratory of Entomology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Gorben P Pijlman
- Laboratory of Virology Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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42
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Abstract
Host defense to virus infection involves both resistance mechanisms that reduce viral burden and tolerance mechanisms that limit detrimental effects of infection. The fruit fly, Drosophila melanogaster, has emerged as a model for identifying and characterizing the genetic basis of resistance and tolerance. This protocol describes how to analyze host responses to virus infection in Drosophila, and it covers the preparation of virus stocks, experimental inoculation of flies and assessment of host survival and virus production, which are indicative of resistance or tolerance. It also provides guidance on how to account for recently identified confounding factors, including natural genetic variation in the pastrel locus and contamination of fly stocks with persistent viruses and the symbiotic bacterium Wolbachia. Our protocol aims to be accessible to newcomers to the field and, although optimized for virus research using Drosophila, some of the techniques could be adapted to other host organisms and/or other microbial pathogens. Preparation of fly stocks requires ∼1 month, virus stock preparation requires 17-20 d, virus injection and survival assays require 10-15 d and virus titration requires 14 d.
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Affiliation(s)
- Sarah H Merkling
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
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43
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Miesen P, Girardi E, van Rij RP. Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Res 2015; 43:6545-56. [PMID: 26068474 PMCID: PMC4513867 DOI: 10.1093/nar/gkv590] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/22/2015] [Indexed: 11/13/2022] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway is essential for transposon silencing in many model organisms. Its remarkable efficiency relies on a sophisticated amplification mechanism known as the ping-pong loop. In Alphavirus-infected Aedes mosquitoes, piRNAs with sequence features that suggest ping-pong-dependent biogenesis are produced from viral RNA. The PIWI family in Aedes mosquitoes is expanded when compared to other model organisms, raising the possibility that individual PIWI proteins have functionally diversified in these insects. Here, we show that Piwi5 and Ago3, but none of the other PIWI family members, are essential for piRNA biogenesis from Sindbis virus RNA in infected Aedes aegypti cells. In contrast, the production of piRNAs from transposons relies on a more versatile set of PIWI proteins, some of which do not contribute to viral piRNA biogenesis. These results indicate that functional specialization allows distinct mosquito PIWI proteins to process RNA from different endogenous and exogenous sources.
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Affiliation(s)
- Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Erika Girardi
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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44
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Bronkhorst AW, van Cleef KWR, Venselaar H, van Rij RP. A dsRNA-binding protein of a complex invertebrate DNA virus suppresses the Drosophila RNAi response. Nucleic Acids Res 2014; 42:12237-48. [PMID: 25274730 PMCID: PMC4231766 DOI: 10.1093/nar/gku910] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invertebrate RNA viruses are targets of the host RNA interference (RNAi) pathway, which limits virus infection by degrading viral RNA substrates. Several insect RNA viruses encode suppressor proteins to counteract this antiviral response. We recently demonstrated that the dsDNA virus Invertebrate iridescent virus 6 (IIV-6) induces an RNAi response in Drosophila. Here, we show that RNAi is suppressed in IIV-6-infected cells and we mapped RNAi suppressor activity to the viral protein 340R. Using biochemical assays, we reveal that 340R binds long dsRNA and prevents Dicer-2-mediated processing of long dsRNA into small interfering RNAs (siRNAs). We demonstrate that 340R additionally binds siRNAs and inhibits siRNA loading into the RNA-induced silencing complex. Finally, we show that 340R is able to rescue a Flock House virus replicon that lacks its viral suppressor of RNAi. Together, our findings indicate that, in analogy to RNA viruses, DNA viruses antagonize the antiviral RNAi response.
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Affiliation(s)
- Alfred W Bronkhorst
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Koen W R van Cleef
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Hanka Venselaar
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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van Mierlo JT, Overheul GJ, Obadia B, van Cleef KWR, Webster CL, Saleh MC, Obbard DJ, van Rij RP. Novel Drosophila viruses encode host-specific suppressors of RNAi. PLoS Pathog 2014; 10:e1004256. [PMID: 25032815 PMCID: PMC4102588 DOI: 10.1371/journal.ppat.1004256] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/03/2014] [Indexed: 12/24/2022] Open
Abstract
The ongoing conflict between viruses and their hosts can drive the co-evolution between host immune genes and viral suppressors of immunity. It has been suggested that an evolutionary ‘arms race’ may occur between rapidly evolving components of the antiviral RNAi pathway of Drosophila and viral genes that antagonize it. We have recently shown that viral protein 1 (VP1) of Drosophila melanogaster Nora virus (DmelNV) suppresses Argonaute-2 (AGO2)-mediated target RNA cleavage (slicer activity) to antagonize antiviral RNAi. Here we show that viral AGO2 antagonists of divergent Nora-like viruses can have host specific activities. We have identified novel Nora-like viruses in wild-caught populations of D. immigrans (DimmNV) and D. subobscura (DsubNV) that are 36% and 26% divergent from DmelNV at the amino acid level. We show that DimmNV and DsubNV VP1 are unable to suppress RNAi in D. melanogaster S2 cells, whereas DmelNV VP1 potently suppresses RNAi in this host species. Moreover, we show that the RNAi suppressor activity of DimmNV VP1 is restricted to its natural host species, D. immigrans. Specifically, we find that DimmNV VP1 interacts with D. immigrans AGO2, but not with D. melanogaster AGO2, and that it suppresses slicer activity in embryo lysates from D. immigrans, but not in lysates from D. melanogaster. This species-specific interaction is reflected in the ability of DimmNV VP1 to enhance RNA production by a recombinant Sindbis virus in a host-specific manner. Our results emphasize the importance of analyzing viral RNAi suppressor activity in the relevant host species. We suggest that rapid co-evolution between RNA viruses and their hosts may result in host species-specific activities of RNAi suppressor proteins, and therefore that viral RNAi suppressors could be host-specificity factors. Viruses and their hosts can engage in an evolutionary arms race. Viruses may select for hosts with more effective immune responses, whereas the immune response of the host may select for viruses that evade the immune system. These viral counter-defenses may in turn drive adaptations in host immune genes. A potential outcome of this perpetual cycle is that the interaction between virus and host becomes more specific. In insects, the host antiviral RNAi machinery exerts strong evolutionary pressure that has led to the evolution of viral proteins that can antagonize the RNAi response. We have identified novel viruses that infect different fruit fly species and we show that the RNAi suppressor proteins of these viruses can be specific to their host. Furthermore, we show that these proteins can enhance virus replication in a host-specific manner. These results are in line with the hypothesis that virus-host co-evolution shapes the genomes of both virus and host. Moreover, our results suggest that RNAi suppressor proteins have the potential to determine host specificity of viruses.
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Affiliation(s)
- Joël T. van Mierlo
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Gijs J. Overheul
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Benjamin Obadia
- Institut Pasteur, Viruses and RNA interference Unit and Centre National de la Recherche Scientifique, UMR 3569, Paris, France
| | - Koen W. R. van Cleef
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Claire L. Webster
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria-Carla Saleh
- Institut Pasteur, Viruses and RNA interference Unit and Centre National de la Recherche Scientifique, UMR 3569, Paris, France
| | - Darren J. Obbard
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (DJO); (RPvR)
| | - Ronald P. van Rij
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- * E-mail: (DJO); (RPvR)
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van Cleef KWR, van Mierlo JT, Miesen P, Overheul GJ, Fros JJ, Schuster S, Marklewitz M, Pijlman GP, Junglen S, van Rij RP. Mosquito and Drosophila entomobirnaviruses suppress dsRNA- and siRNA-induced RNAi. Nucleic Acids Res 2014; 42:8732-44. [PMID: 24939903 PMCID: PMC4117760 DOI: 10.1093/nar/gku528] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RNA interference (RNAi) is a crucial antiviral defense mechanism in insects, including the major mosquito species that transmit important human viruses. To counteract the potent antiviral RNAi pathway, insect viruses encode RNAi suppressors. However, whether mosquito-specific viruses suppress RNAi remains unclear. We therefore set out to study RNAi suppression by Culex Y virus (CYV), a mosquito-specific virus of the Birnaviridae family that was recently isolated from Culex pipiens mosquitoes. We found that the Culex RNAi machinery processes CYV double-stranded RNA (dsRNA) into viral small interfering RNAs (vsiRNAs). Furthermore, we show that RNAi is suppressed in CYV-infected cells and that the viral VP3 protein is responsible for RNAi antagonism. We demonstrate that VP3 can functionally replace B2, the well-characterized RNAi suppressor of Flock House virus. VP3 was found to bind long dsRNA as well as siRNAs and interfered with Dicer-2-mediated cleavage of long dsRNA into siRNAs. Slicing of target RNAs by pre-assembled RNA-induced silencing complexes was not affected by VP3. Finally, we show that the RNAi-suppressive activity of VP3 is conserved in Drosophila X virus, a birnavirus that persistently infects Drosophila cell cultures. Together, our data indicate that mosquito-specific viruses may encode RNAi antagonists to suppress antiviral RNAi.
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Affiliation(s)
- Koen W R van Cleef
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Joël T van Mierlo
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Jelke J Fros
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Susan Schuster
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Marco Marklewitz
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud Str. 25, 53127 Bonn, Germany
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sandra Junglen
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud Str. 25, 53127 Bonn, Germany
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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Bronkhorst AW, van Rij RP. The long and short of antiviral defense: small RNA-based immunity in insects. Curr Opin Virol 2014; 7:19-28. [PMID: 24732439 DOI: 10.1016/j.coviro.2014.03.010] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 03/18/2014] [Accepted: 03/19/2014] [Indexed: 02/03/2023]
Abstract
The host RNA interference (RNAi) pathway of insects senses virus infection and induces an antiviral response to restrict virus replication. Dicer-2 detects viral double-stranded RNA, produced by RNA and DNA viruses, and generates viral small interfering RNAs (vsiRNAs). Recent small RNA profiling studies provided new insights into the viral RNA substrates that trigger vsiRNA biogenesis. The importance of the antiviral RNAi pathway is underscored by the observation that viruses have evolved sophisticated mechanisms to counteract this small RNA-based immune response. More recently, it was proposed that another small RNA silencing mechanism, the piRNA pathway, also processes viral RNAs in Drosophila and mosquitoes. Here, we review recent insights into the mechanism of antiviral RNAi, viral small RNA profiles, and viral counter-defense mechanisms in insects.
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Affiliation(s)
- Alfred W Bronkhorst
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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48
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Bronkhorst AW, Miesen P, van Rij RP. Small RNAs tackle large viruses: RNA interference-based antiviral defense against DNA viruses in insects. Fly (Austin) 2013; 7:216-23. [PMID: 23974177 DOI: 10.4161/fly.25708] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The antiviral RNA interference (RNAi) pathway processes viral double-stranded RNA (dsRNA) into viral small interfering RNAs (vsiRNA) that guide the recognition and cleavage of complementary viral target RNAs. In RNA virus infections, viral replication intermediates, dsRNA genomes or viral structured RNAs have been implicated as Dicer-2 substrates. In a recent publication, we demonstrated that a double-stranded DNA virus, Invertebrate iridescent virus 6, is a target of the Drosophila RNAi machinery, and we proposed that overlapping converging transcripts base pair to form the dsRNA substrates for vsiRNA biogenesis. Here, we discuss the role of RNAi in antiviral defense to DNA viruses in Drosophila and other invertebrate model systems.
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Affiliation(s)
- Alfred W Bronkhorst
- Department of Medical Microbiology; Radboud University Nijmegen Medical Centre; Nijmegen Centre for Molecular Life Sciences; Nijmegen Institute for Infection, Inflammation and Immunity; Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology; Radboud University Nijmegen Medical Centre; Nijmegen Centre for Molecular Life Sciences; Nijmegen Institute for Infection, Inflammation and Immunity; Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology; Radboud University Nijmegen Medical Centre; Nijmegen Centre for Molecular Life Sciences; Nijmegen Institute for Infection, Inflammation and Immunity; Nijmegen, The Netherlands
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49
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van Cleef KWR, Overheul GJ, Thomassen MC, Kaptein SJF, Davidson AD, Jacobs M, Neyts J, van Kuppeveld FJM, van Rij RP. Identification of a new dengue virus inhibitor that targets the viral NS4B protein and restricts genomic RNA replication. Antiviral Res 2013; 99:165-71. [PMID: 23735301 DOI: 10.1016/j.antiviral.2013.05.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/19/2013] [Accepted: 05/24/2013] [Indexed: 11/15/2022]
Abstract
Dengue virus (DENV) is an important human arthropod-borne virus with a major impact on public health. Nevertheless, a licensed vaccine or specific treatment is still lacking. We therefore screened the NIH Clinical Collection (NCC), a library of drug-like small molecules, for inhibitors of DENV replication using a cell line that contains a stably replicating DENV serotype 2 (DENV2) subgenomic replicon. The most potent DENV inhibitor in the NCC was δ opioid receptor antagonist SDM25N. This compound showed antiviral activity against wild-type DENV2 in both Hela and BHK-21 cells, but not in the C6/36 cell line derived from the mosquito Aedes albopictus. The structurally related compound naltrindole also inhibited DENV replication, albeit less potently. Using a transient subgenomic replicon, we demonstrate that SDM25N restricts genomic RNA replication rather than translation of the viral genome. We identified a single amino acid substitution (F164L) in the NS4B protein that confers resistance to SDM25N. Remarkably, an NS4B amino acid substitution (P104L), which was previously shown to confer resistance to the DENV inhibitor NITD-618, also provided resistance to SDM25N. In conclusion, we have identified a new DENV inhibitor, SDM25N, which restricts genomic RNA replication by - directly or indirectly - targeting the viral NS4B protein.
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Affiliation(s)
- Koen W R van Cleef
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, Nijmegen Institute for Infection, Inflammation and Immunity, Nijmegen, The Netherlands
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Merkling SH, van Rij RP. Beyond RNAi: antiviral defense strategies in Drosophila and mosquito. J Insect Physiol 2013; 59:159-170. [PMID: 22824741 DOI: 10.1016/j.jinsphys.2012.07.004] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/11/2012] [Accepted: 07/12/2012] [Indexed: 06/01/2023]
Abstract
Virus transmission and spread by arthropods is a major economic and public health concern. The ongoing dissemination of arthropod-borne viruses by blood-feeding insects is an important incentive to study antiviral immunity in these animals. RNA interference is a major mechanism for antiviral defense in insects, including the fruit fly Drosophila melanogaster and several vector mosquitoes. However, recent data suggest that the evolutionary conserved Toll, Imd and Jak-Stat signaling pathways also contribute to antiviral immunity. Moreover, symbionts, such as the intracellular bacterium Wolbachia and the gut microflora, influence the course of virus infection in insects. These results add an additional level of complexity to antiviral immunity, but also provide novel opportunities to control the spread of arboviruses. In this review, we provide an overview of the current knowledge and recent developments in antiviral immunity in Dipteran insects, with a focus on non-RNAi mediated inducible responses.
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Affiliation(s)
- Sarah H Merkling
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
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