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Host innate immune responses to viral RNA

English title Host innate immune responses to viral RNA
Applicant Thiel Volker
Number 149784
Funding scheme Project funding (Div. I-III)
Research institution Institut für Virologie und Immunologie Depart. Infektionskrankheiten und Pathologie Universität Bern
Institution of higher education Cantonal hospital of St.Gallen - KSPSG
Main discipline Molecular Biology
Start/End 01.04.2014 - 31.08.2017
Approved amount 711'216.00
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All Disciplines (4)

Discipline
Molecular Biology
Cellular Biology, Cytology
Biochemistry
Immunology, Immunopathology

Keywords (9)

localization of viral RNA; innate immunity; type I interferon; non-self RNA sensing; reverse genetics; RNA virus; viral RNA synthesis; Coronavirus; RNA modification

Lay Summary (German)

Lead
Angeborene Immunantwort gegen virale RNAIn diesem Projekt soll die Frage "wie, wo and wann wird viral RNA während einer Virusinfektion in der Zelle erkannt" bearbeitet werden.
Lay summary

Viren die sich im Zytoplasma der Wirtszellen vermehren benutzen Membranstrukturen der Wirtszelle um ein spezialisiertes Kompartiment zu schaffen das einerseits eine notwendige Konzentrierung von viralen und Wirtzellfaktoren für die Genomvermehrung sicher stellt und andererseits den Ort der Virusvermehrung vor antiviralen Wirtzellmechanismen schützt. Trotzdem können Virus-infizierte Zellen erkennen, dass sie infiziert sind und mittels der angeborenen Immunität antivirale Mechnismen in Gang setzen.

In diesem Projekt sind wir an der Frage interessiert wie, wann und wo virale RNA während einer Virusinfektion von der Wirtszelle erkannt wird. Um dies zu bearbeiten werden wir Infektionsmodelle mit humanen und murinen Coronaviren verwenden, die uns ermöglichen sowohl die Viren als auch die Wirtszellen genetisch zu modifizieren. Wir werden auch einen Inhibitor der coronaviralen Replikation verwenden der die Membranstrukturen an denen die coronavirale Genomvermehrung stattfindet gezielt angreift. Mithilfe dieser Werkzeuge werden wir unter anderem mittels confokaler Laserscanning- und Elektronen-Mikroskopie eine detailierte Ansicht der Kinetik und Qualität der Wirtszellantworten unter genau definierten experimentellen Bedingungen erarbeiten. Unser Ziel ist es ein räumliches und zeitliches Verständnis der grundlegenden Prinzipien der Erkennung von viraler RNA und der antiviralen Wirtszellmechanismen im Rahmen der angeborenen Immunität zu schaffen. Diese generellen Aspekte der Biologie der RNA Erkennung und antiviralen Effektormechanismen haben auch über die Cornavirusinfektionen hinaus grosse Bedeutung.

Direct link to Lay Summary Last update: 05.11.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Immune protection against reinfection with nonprimate hepacivirus
Pfaender Stephanie, Walter Stephanie, Grabski Elena, Todt Daniel, Bruening Janina, Romero-Brey Inés, Gather Theresa, Brown Richard J. P., Hahn Kerstin, Puff Christina, Pfankuche Vanessa M., Hansmann Florian, Postel Alexander, Becher Paul, Thiel Volker, Kalinke Ulrich, Wagner Bettina, Bartenschlager Ralf, Baumgärtner Wolfgang, Feige Karsten, Pietschmann Thomas, Cavalleri Jessika M. V., Steinmann Eike (2017), Immune protection against reinfection with nonprimate hepacivirus, in Proceedings of the National Academy of Sciences, 114(12), E2430-E2439.
Virucidal Activity of World Health Organization–Recommended Formulations Against Enveloped Viruses, Including Zika, Ebola, and Emerging Coronaviruses
Siddharta Anindya, Pfaender Stephanie, Vielle Nathalie Jane, Dijkman Ronald, Friesland Martina, Becker Britta, Yang Jaewon, Engelmann Michael, Todt Daniel, Windisch Marc P., Brill Florian H., Steinmann Joerg, Steinmann Jochen, Becker Stephan, Alves Marco P., Pietschmann Thomas, Eickmann Markus, Thiel Volker, Steinmann Eike (2017), Virucidal Activity of World Health Organization–Recommended Formulations Against Enveloped Viruses, Including Zika, Ebola, and Emerging Coronaviruses, in The Journal of Infectious Diseases, 215(6), 902-906.
Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication
Kindler Eveline, Gil-Cruz Cristina, Spanier Julia, Li Yize, Wilhelm Jochen, Rabouw Huib H., Züst Roland, Hwang Mihyun, V’kovski Philip, Stalder Hanspeter, Marti Sabrina, Habjan Matthias, Cervantes-Barragan Luisa, Elliot Ruth, Karl Nadja, Gaughan Christina, van Kuppeveld Frank J. M., Silverman Robert H., Keller Markus, Ludewig Burkhard, Bergmann Cornelia C., Ziebuhr John, Weiss Susan R., Kalinke Ulrich, et al. (2017), Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication, in PLOS Pathogens, 13(2), e1006195-e1006195.
Inactivation of Zika virus in human breast milk by prolonged storage or pasteurization
Pfaender Stephanie, Vielle Nathalie J., Ebert Nadine, Steinmann Eike, Alves Marco P., Thiel Volker (2017), Inactivation of Zika virus in human breast milk by prolonged storage or pasteurization, in Virus Research, 228, 58-60.
The differentiated airway epithelium infected by influenza viruses maintains the barrier function despite a dramatic loss of ciliated cells
Wu Nai-Huei, Yang Wei, Beineke Andreas, Dijkman Ronald, Matrosovich Mikhail, Baumgärtner Wolfgang, Thiel Volker, Valentin-Weigand Peter, Meng Fandan, Herrler Georg (2016), The differentiated airway epithelium infected by influenza viruses maintains the barrier function despite a dramatic loss of ciliated cells, in Scientific Reports, 6(1), 39668-39668.
The Swiss Society of Microbiology: Small Bugs, Big Questions and Cool Answers
Greub Gilbert, Holliger Christof, Sanglard Dominique, Schrenzel Jacques, Thiel Volker, Viollier Patrick (2016), The Swiss Society of Microbiology: Small Bugs, Big Questions and Cool Answers, in CHIMIA International Journal for Chemistry, 70(12), 874-877.
Systems biology of viral infection
Kaderali Lars, Thiel Volker (2016), Systems biology of viral infection, in Virus Research, 218, 1-1.
SARS-CoV and IFN: Too Little, Too Late
Kindler Eveline, Thiel Volker (2016), SARS-CoV and IFN: Too Little, Too Late, in Cell Host & Microbe, 19(2), 139-141.
Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response
Kindler E., Thiel V., Weber F. (2016), Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response, in Ziebuhr John (ed.), Elsevier, this is wasting my time, 219-243.
Murine Coronavirus Ubiquitin-Like Domain Is Important for Papain-Like Protease Stability and Viral Pathogenesis
Mielech Anna M., Deng Xufang, Chen Yafang, Kindler Eveline, Wheeler Dorthea L., Mesecar Andrew D., Thiel Volker, Perlman Stanley, Baker Susan C. (2015), Murine Coronavirus Ubiquitin-Like Domain Is Important for Papain-Like Protease Stability and Viral Pathogenesis, in Journal of Virology, 89(9), 4907-4917.
New insights on the role of paired membrane structures in coronavirus replication
V’kovski Philip, Al-Mulla Hawaa, Thiel Volker, Neuman Benjamin W. (2015), New insights on the role of paired membrane structures in coronavirus replication, in Virus Research, 202, 33-40.
To sense or not to sense viral RNA—essentials of coronavirus innate immune evasion
Kindler Eveline, Thiel Volker (2014), To sense or not to sense viral RNA—essentials of coronavirus innate immune evasion, in Current Opinion in Microbiology, 20, 69-75.
Targeting Membrane-Bound Viral RNA Synthesis Reveals Potent Inhibition of Diverse Coronaviruses Including the Middle East Respiratory Syndrome Virus
Lundin Anna, Dijkman Ronald, Bergström Tomas, Kann Nina, Adamiak Beata, Hannoun Charles, Kindler Eveline, Jónsdóttir Hulda R., Muth Doreen, Kint Joeri, Forlenza Maria, Müller Marcel A., Drosten Christian, Thiel Volker, Trybala Edward (2014), Targeting Membrane-Bound Viral RNA Synthesis Reveals Potent Inhibition of Diverse Coronaviruses Including the Middle East Respiratory Syndrome Virus, in PLoS Pathogens, 10(5), e1004166-e1004166.
Competitive Fitness in Coronaviruses Is Not Correlated with Size or Number of Double-Membrane Vesicles under Reduced-Temperature Growth Conditions
Al-Mulla H. M. N., Turrell L., Smith N. M., Payne L., Baliji S., Zust R., Thiel V., Baker S. C., Siddell S. G., Neuman B. W. (2014), Competitive Fitness in Coronaviruses Is Not Correlated with Size or Number of Double-Membrane Vesicles under Reduced-Temperature Growth Conditions, in mBio, 5(2), e01107-13-e01107-13.

Collaboration

Group / person Country
Types of collaboration
Prof. Friedemann Weber, Institute for Virology, University of Freiburg Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Edward Trybala Sweden (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. S.G. Siddell, Department of Cellular and Molecular Medicine, University of Bristol Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof John Ziebuhr Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Eric Snijder Netherlands (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events



Self-organised

Title Date Place
XIVth International Nidovirus Symposium 04.06.2017 Kansas City, United States of America

Communication with the public

Communication Title Media Place Year
Other activities Swiss Society for Microbiology; member of section lay communication Rhaeto-Romanic Switzerland Italian-speaking Switzerland Western Switzerland German-speaking Switzerland 2017

Associated projects

Number Title Start Funding scheme
173085 Host innate immune responses to viral RNA 01.09.2017 Project funding (Div. I-III)
128786 Laser scanning confocal microscope for in vivo and in situ imaging 01.12.2009 R'EQUIP
173085 Host innate immune responses to viral RNA 01.09.2017 Project funding (Div. I-III)
132898 Impact of RNA modification on coronavirus-induced innate immune responses 01.10.2010 Project funding (Div. I-III)
160780 Viral Plasticity Underlying Tropism And Pathogenesis/ Innate Immune Evasion Of Emerging Viruses 01.11.2015 Sinergia

Abstract

"Host innate immune responses to viral RNA"1. Project summaryBackground: Coronaviruses are RNA viruses of both veterinary and medical importance. The SARS-CoV epidemic 2002/2003, and the recent emergence of the novel human coronavirus EMC, exemplified the zoonotic potential of coronaviruses and their ability to seriously impact on human health. Notably, in most cell types neither high nor low pathogenic coronaviruses elicit pronounced innate immune responses, such as type-I interferons (IFNs), during the early phase of viral infection, suggesting that coronaviruses counteract sensing of viral nucleic acid. During our previous SNF-funded projects we have uncovered a link between Mda5-mediated sensing of coronaviral RNA and ribose 2’O-methylation, suggesting that RNA modifications such as 2’O-methylation provide a molecular signature for discrimination of self and non-self mRNA. More recently, by assessing a coronaviral inhibitor targeting membrane-bound RNA synthesis, we found that inhibitor-resistant viruses can efficiently replicate without inducing double-membrane vesicles (DMVs). These DMVs are a hallmark of coronavirus replication and harbor dsRNA. Therefore, these inhibitor-resistant viruses represent an excellent tool to study sensing of viral RNA and antiviral effector mechanisms under conditions where dsRNA is not shielded by DMVs but accessible to binding by host cell cytosolic RNA sensors.Working hypothesis and aims: We hypothesize that induction of innate immune responses to viral RNA and restriction of RNA virus replication is dependent on (i) modification of viral mRNA, such as 2’O-methylation, and (ii) localization of viral RNA in the host cell. Furthermore, innate immune responses and restriction of RNA virus replication appears to be very different in particular cell types, depending on which particular innate immune pathways and antiviral mechanisms dominate. The reverse genetic systems for the mouse hepatitis virus (MHV) and human coronavirus 229E (HCoV-229E) in combination with murine and human models of infection that are amenable to genetic modification will allow us to dissect key steps and key molecules involved in host innate immune responses on the molecular level. It will be important to analyze the molecular interactions within infected primary target cells with a particular focus on interactions between pathogen recognition receptors, antiviral effector proteins, dsRNA, and the viral replicase-transcriptase complex. To do this we will generate a number of recombinant murine and human coronaviruses that are deficient in 2’O-methylation, contain inhibitor-resistant mutations and combinations thereof. Using these novel tools we will then assess innate immune responses in primary human and murine cells in order to obtain a detailed view on kinetics and quality of innate immune responses under well-defined conditions. These studies will provide spatial and temporal view of basic principles of RNA recognition and antiviral innate immune mechanisms in different primary cell types following virus infection. Expected significance: The proposed studies will provide general insights into the biology of viral RNA sensing and antiviral effector mechanisms that are highly relevant also beyond coronavirus infections. We expect to identify key mediators of viral RNA sensing and the “antiviral state” that are apparently counteracted by many RNA viruses through methylation of viral mRNA and shielding of dsRNA by host cell membranes. Therefore, a better understanding of these fundamental aspects of innate immune responses to RNA virus infection will facilitate the development of novel strategies to interfere with viral RNA replication during the early phase of infections.
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