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Viruses are obligate intracellular parasites, which depend on the host cellular machineries to replicate their genome and complete their infectious cycle. Long double stranded (ds)RNA is a common viral by-product originating during RNA virus replication and is universally sensed as a danger signal to trigger the antiviral response. As a result, viruses hide dsRNA intermediates into viral replication factories and have evolved strategies to hijack cellular proteins for their benefit. The characterization of the host factors associated to viral dsRNA and involved in viral replication remains a major challenge to develop new antiviral drugs against RNA viruses. Here, we performed anti-dsRNA immunoprecipitation followed by mass spectrometry to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human HCT116 cells. Among the validated factors, we characterized SFPQ (Splicing factor, proline-glutamine rich) as a new dsRNA-associated factor upon SINV infection. We proved that SFPQ is able to directly bind to dsRNAs in vitro, that its association to dsRNA is independent of single-stranded (ss)RNA flanking regions in vivo and that it is able to bind to the viral genome upon infection. Furthermore, we showed that both knock-down and knock-out of SFPQ reduce SINV infection in human HCT116 and SK-N-BE(2) cells, suggesting that SFPQ could enhance viral replication. Overall, this study not only represents a resource to further study SINV dsRNA-associated factors upon infection but also identifies SFPQ as a new proviral dsRNA binding protein.
Erika Girardi; Mélanie Messmer; Paula Lopez; Aurélie Fender; Johana Chicher; Béatrice Chane-Woon-Ming; Philippe Hammann; Sébastien Pfeffer. Determination of dsRNA interactome upon Sindbis virus infection in human cells identifies SFPQ as a critical proviral factor. 2021, 1 .
AMA StyleErika Girardi, Mélanie Messmer, Paula Lopez, Aurélie Fender, Johana Chicher, Béatrice Chane-Woon-Ming, Philippe Hammann, Sébastien Pfeffer. Determination of dsRNA interactome upon Sindbis virus infection in human cells identifies SFPQ as a critical proviral factor. . 2021; ():1.
Chicago/Turabian StyleErika Girardi; Mélanie Messmer; Paula Lopez; Aurélie Fender; Johana Chicher; Béatrice Chane-Woon-Ming; Philippe Hammann; Sébastien Pfeffer. 2021. "Determination of dsRNA interactome upon Sindbis virus infection in human cells identifies SFPQ as a critical proviral factor." , no. : 1.
When facing a viral infection, the organism has to put in place a number of defense mechanisms in order to clear the pathogen from the cell. At the early phase of this preparation for fighting against the invader, the innate immune response is triggered by the sensing of danger signals. Among those molecular cues, double-stranded RNA (dsRNA) is a very potent inducer of different reactions at the cellular level that can ultimately lead to cell death. Using a genome-wide screening approach, we set to identify genes involved in dsRNA entry, sensing, and apoptosis induction in human cells. This allowed us to determine that the heparan sulfate pathway and the conserved oligomeric Golgi complex are key determinants allowing entry of both dsRNA and viral nucleic acid leading to cell death.
Olivier Petitjean; Erika Girardi; Richard Patryk Ngondo; Vladimir Lupashin; Sébastien Pfeffer. Genome-Wide CRISPR-Cas9 Screen Reveals the Importance of the Heparan Sulfate Pathway and the Conserved Oligomeric Golgi Complex for Synthetic Double-Stranded RNA Uptake and Sindbis Virus Infection. mSphere 2020, 5, 1 .
AMA StyleOlivier Petitjean, Erika Girardi, Richard Patryk Ngondo, Vladimir Lupashin, Sébastien Pfeffer. Genome-Wide CRISPR-Cas9 Screen Reveals the Importance of the Heparan Sulfate Pathway and the Conserved Oligomeric Golgi Complex for Synthetic Double-Stranded RNA Uptake and Sindbis Virus Infection. mSphere. 2020; 5 (6):1.
Chicago/Turabian StyleOlivier Petitjean; Erika Girardi; Richard Patryk Ngondo; Vladimir Lupashin; Sébastien Pfeffer. 2020. "Genome-Wide CRISPR-Cas9 Screen Reveals the Importance of the Heparan Sulfate Pathway and the Conserved Oligomeric Golgi Complex for Synthetic Double-Stranded RNA Uptake and Sindbis Virus Infection." mSphere 5, no. 6: 1.
Double stranded RNA (dsRNA) is the hallmark of many viral infections. dsRNA is produced either by RNA viruses during replication or by DNA viruses upon convergent transcription. Synthetic dsRNA is also able to mimic viral-induced activation of innate immune response and cell death. In this study, we employed a genome-wide CRISPR-Cas9 loss of function screen based on cell survival in order to identify genes implicated in the host response to dsRNA. By challenging HCT116 human cells with either synthetic dsRNA or Sindbis virus (SINV), we identified the heparan sulfate (HS) pathway as a crucial factor for dsRNA entry and we validated SINV dependency on HS. Interestingly, we uncovered a novel role for COG4, a component of the Conserved Oligomeric Golgi (COG) complex, as a factor involved in cell survival to both dsRNA and SINV in human cells. We showed that COG4 knock-out led to a decrease of extracellular HS, specifically affected dsRNA transfection efficiency and reduced viral production, explaining the increased cell survival of these mutants.
Olivier Petitjean; Erika Girardi; Richard P Ngondo; Vladimir V. Lupashin; Sebastien Pfeffer. Genome-wide CRISPR-Cas9 screen reveals the importance of the heparane sulphate pathway and the conserved oligomeric golgi complex for synthetic dsRNA uptake and Sindbis virus infection. 2020, 1 .
AMA StyleOlivier Petitjean, Erika Girardi, Richard P Ngondo, Vladimir V. Lupashin, Sebastien Pfeffer. Genome-wide CRISPR-Cas9 screen reveals the importance of the heparane sulphate pathway and the conserved oligomeric golgi complex for synthetic dsRNA uptake and Sindbis virus infection. . 2020; ():1.
Chicago/Turabian StyleOlivier Petitjean; Erika Girardi; Richard P Ngondo; Vladimir V. Lupashin; Sebastien Pfeffer. 2020. "Genome-wide CRISPR-Cas9 screen reveals the importance of the heparane sulphate pathway and the conserved oligomeric golgi complex for synthetic dsRNA uptake and Sindbis virus infection." , no. : 1.
The antiviral innate immune response mainly involves type I interferon (IFN) in mammalian cells. The contribution of the RNA silencing machinery remains to be established, but several recent studies indicate that the ribonuclease DICER can generate viral siRNAs in specific conditions. It has also been proposed that type I IFN and RNA silencing could be mutually exclusive antiviral responses. In order to decipher the implication of DICER during infection of human cells with the Sindbis virus, we determined its interactome by proteomics analysis. We show that DICER specifically interacts with several double-stranded RNA binding proteins and RNA helicases during viral infection. In particular, proteins such as DHX9, ADAR-1 and the protein kinase RNA-activated (PKR) are enriched with DICER in virus-infected cells. We demonstrate the importance of DICER helicase domain in its interaction with PKR and showed that it has functional consequences for the cellular response to viral infection.
Thomas C Montavon; Morgane Baldaccini; Mathieu Lefevre; Erika Girardi; Beatrice Chane-Woon-Ming; Melanie Messmer; Philippe Hammann; Johana Chicher; Sebastien Pfeffer. Human Dicer helicase domain recruits PKR and dsRNA binding proteins during viral infection. 2020, 1 .
AMA StyleThomas C Montavon, Morgane Baldaccini, Mathieu Lefevre, Erika Girardi, Beatrice Chane-Woon-Ming, Melanie Messmer, Philippe Hammann, Johana Chicher, Sebastien Pfeffer. Human Dicer helicase domain recruits PKR and dsRNA binding proteins during viral infection. . 2020; ():1.
Chicago/Turabian StyleThomas C Montavon; Morgane Baldaccini; Mathieu Lefevre; Erika Girardi; Beatrice Chane-Woon-Ming; Melanie Messmer; Philippe Hammann; Johana Chicher; Sebastien Pfeffer. 2020. "Human Dicer helicase domain recruits PKR and dsRNA binding proteins during viral infection." , no. : 1.
Arthropod-borne (arbo) viruses are part of a class of pathogens that are transmitted to their final hosts by insects. Because of climate change, the habitat of some of these insects, such as mosquitoes, is shifting, thereby facilitating the emergence of viral epidemics. Among the pathologies associated with arbovirus infection, neurological diseases such as meningitis and encephalitis represent a significant health burden. Using a genome-wide miRNA screen, we identified neuronal miR-124 as a positive regulator of the Sindbis and chikungunya alphaviruses. We also showed that this effect was in part direct, thereby opening novel avenues to treat alphavirus infections.
Paula López; Erika Girardi; Bryan C. Mounce; Amélie Weiss; Béatrice Chane-Woon-Ming; Mélanie Messmer; Pasi Kaukinen; Arnaud Kopp; Diane Bortolamiol-Becet; Ali Fendri; Marco Vignuzzi; Laurent Brino; Sébastien Pfeffer. High-Throughput Fluorescence-Based Screen Identifies the Neuronal MicroRNA miR-124 as a Positive Regulator of Alphavirus Infection. Journal of Virology 2020, 94, 1 .
AMA StylePaula López, Erika Girardi, Bryan C. Mounce, Amélie Weiss, Béatrice Chane-Woon-Ming, Mélanie Messmer, Pasi Kaukinen, Arnaud Kopp, Diane Bortolamiol-Becet, Ali Fendri, Marco Vignuzzi, Laurent Brino, Sébastien Pfeffer. High-Throughput Fluorescence-Based Screen Identifies the Neuronal MicroRNA miR-124 as a Positive Regulator of Alphavirus Infection. Journal of Virology. 2020; 94 (9):1.
Chicago/Turabian StylePaula López; Erika Girardi; Bryan C. Mounce; Amélie Weiss; Béatrice Chane-Woon-Ming; Mélanie Messmer; Pasi Kaukinen; Arnaud Kopp; Diane Bortolamiol-Becet; Ali Fendri; Marco Vignuzzi; Laurent Brino; Sébastien Pfeffer. 2020. "High-Throughput Fluorescence-Based Screen Identifies the Neuronal MicroRNA miR-124 as a Positive Regulator of Alphavirus Infection." Journal of Virology 94, no. 9: 1.
Micro (mi)RNAs are small regulatory RNAs, which act as guide for the RISC complex to modulate the expression of target genes. In addition to their role in maintaining essential physiological functions in the cell, miRNAs can also regulate viral infections. They can do so directly by targeting RNAs of viral origin or indirectly by targeting RNAs from the host and this can result in a positive or negative outcome for the virus. Here, we performed a miRNA genome-wide screen in order to identify cellular miRNAs involved in the regulation of arbovirus infection in human cells. We identified sixteen miRNAs showing a positive effect on the virus, among which a number of neuron-specific ones such as miR-124. We confirmed that overexpression of miR-124 increases Sindbis virus (SINV) viral production and that this effect is mediated by its seed sequence. We further demonstrated that the SINV genome possesses a binding site for miR-124-3p. Both inhibition of miR-124-3p or silent mutations to disrupt this binding site in the viral RNA abolished the positive regulation. We also proved that miR-124 inhibition reduces SINV infection in human differentiated neuronal cells. Finally, we showed that the proviral effect of miR-124 is conserved for other medically relevant alphaviruses. Indeed, inhibition of miR-124 expression reduces chikungunya virus (CHIKV) viral production in human cells. Altogether, our work expands the panel of positive regulation of the viral cycle by direct binding of host miRNAs to the viral RNA and provides new insights into the role of cellular miRNAs as regulators of alphavirus infection.SIGNIFICANCE STATEMENTArthropod-borne (arbo) viruses are part of a class of pathogens that are transmitted to their final hosts by insects. Because of climate change, the habitat of some of these insects, such as mosquitoes, is shifting, thereby facilitating the emergence of viral epidemics. Among the pathologies associated with arboviruses infection, neurological diseases like meningitis or encephalitis represent a significant health burden. Using a genome-wide miRNA screen, we identified the neuronal miR-124 as a positive regulator of the Sindbis and chikungunya alphaviruses. We also showed that this effect was in part direct, thereby opening novel avenues to treat alphaviruses infection.
Paula Lopez; Erika Girardi; Bryan C. Mounce; Amelie Weiss; Beatrice Chane-Woon-Ming; Melanie Messmer; Pasi Kaukinen; Arnaud Kopp; Diane Bortolamiol-Becet; Ali Fendri; Marco Vignuzzi; Laurent Brino; Sebastien Pfeffer. High-throughput fluorescence-based screen identifies the neuronal microRNA miR-124 as a positive regulator of alphavirus infection. 2019, 758201 .
AMA StylePaula Lopez, Erika Girardi, Bryan C. Mounce, Amelie Weiss, Beatrice Chane-Woon-Ming, Melanie Messmer, Pasi Kaukinen, Arnaud Kopp, Diane Bortolamiol-Becet, Ali Fendri, Marco Vignuzzi, Laurent Brino, Sebastien Pfeffer. High-throughput fluorescence-based screen identifies the neuronal microRNA miR-124 as a positive regulator of alphavirus infection. . 2019; ():758201.
Chicago/Turabian StylePaula Lopez; Erika Girardi; Bryan C. Mounce; Amelie Weiss; Beatrice Chane-Woon-Ming; Melanie Messmer; Pasi Kaukinen; Arnaud Kopp; Diane Bortolamiol-Becet; Ali Fendri; Marco Vignuzzi; Laurent Brino; Sebastien Pfeffer. 2019. "High-throughput fluorescence-based screen identifies the neuronal microRNA miR-124 as a positive regulator of alphavirus infection." , no. : 758201.
Parasites intracellulaires obligatoires, les virus dépendent d’un grand nombre de facteurs cellulaires pour accomplir leur cycle de multiplication. Parmi ceux-ci, les microARN (miARN) ont récemment émergé comme d’importants modulateurs des infections virales. Ces petites molécules régulatrices agissent comme des répresseurs de l’expression des gènes. Au cours de l’infection, ils peuvent agir sur des ARN cibles d’origine cellulaire mais aussi virale. Cette synthèse fait le point sur les différents mécanismes, directs et indirects, impliquant ces miARN dans la régulation des virus et aborde les possibles applications thérapeutiques qui peuvent en découler.
Paula López; Erika Girardi; Sébastien Pfeffer. Importance des microARN cellulaires dans la régulation des infections virales. médecine/sciences 2019, 35, 667 -673.
AMA StylePaula López, Erika Girardi, Sébastien Pfeffer. Importance des microARN cellulaires dans la régulation des infections virales. médecine/sciences. 2019; 35 (8-9):667-673.
Chicago/Turabian StylePaula López; Erika Girardi; Sébastien Pfeffer. 2019. "Importance des microARN cellulaires dans la régulation des infections virales." médecine/sciences 35, no. 8-9: 667-673.
Every living organism has to constantly face threats from the environment and deal with a large number of pathogens against which it has to defend itself to survive. Among those, viruses represent a large class of obligatory intracellular parasites, which rely on their host machinery to multiply and propagate. As a result, viruses and their hosts have engaged in an ever-evolving arms race to be able to maintain their existence. The role played by micro (mi)RNAs in this ongoing battle has been extensively studied in the past 15 years and will be the subject of this review article. We will mainly focus on cellular miRNAs and their implication during viral infection in mammals. Thus, we will describe current techniques that can be used to identify miRNAs involved in the modulation of viral infection and to characterize their targets and mode of action. We will also present different reported examples of miRNA-mediated regulation of viruses, which can have a positive outcome either for the host or for the virus. In addition, the mode of action is also of a dual nature, depending on the target of the miRNA. Indeed, the regulatory small RNA can either directly guide an Argonaute protein on a viral transcript, or target a cellular mRNA involved in the host antiviral response. We will then see whether and how viruses respond to miRNA-mediated targeting. Finally, we will discuss how our knowledge of viral targeting by miRNA can be exploited for developing new antiviral therapeutic approaches.
Erika Girardi; Paula López; Sébastien Pfeffer. On the Importance of Host MicroRNAs During Viral Infection. Frontiers in Genetics 2018, 9, 439 .
AMA StyleErika Girardi, Paula López, Sébastien Pfeffer. On the Importance of Host MicroRNAs During Viral Infection. Frontiers in Genetics. 2018; 9 ():439.
Chicago/Turabian StyleErika Girardi; Paula López; Sébastien Pfeffer. 2018. "On the Importance of Host MicroRNAs During Viral Infection." Frontiers in Genetics 9, no. : 439.
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.
Erika Girardi; Pascal Miesen; Bas Pennings; Lionel Frangeul; Maria-Carla Saleh; Ronald P. Van Rij. Histone-derived piRNA biogenesis depends on the ping-pong partners Piwi5 and Ago3 inAedes aegypti. Nucleic Acids Research 2017, 45, 4881 -4892.
AMA StyleErika Girardi, Pascal Miesen, Bas Pennings, Lionel Frangeul, Maria-Carla Saleh, Ronald P. Van Rij. Histone-derived piRNA biogenesis depends on the ping-pong partners Piwi5 and Ago3 inAedes aegypti. Nucleic Acids Research. 2017; 45 (8):4881-4892.
Chicago/Turabian StyleErika Girardi; Pascal Miesen; Bas Pennings; Lionel Frangeul; Maria-Carla Saleh; Ronald P. Van Rij. 2017. "Histone-derived piRNA biogenesis depends on the ping-pong partners Piwi5 and Ago3 inAedes aegypti." Nucleic Acids Research 45, no. 8: 4881-4892.
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.
Pascal Miesen; Erika Girardi; Ronald P. van Rij. Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs inAedes aegyptimosquito cells. Nucleic Acids Research 2015, 43, 6545 -6556.
AMA StylePascal Miesen, Erika Girardi, Ronald P. van Rij. Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs inAedes aegyptimosquito cells. Nucleic Acids Research. 2015; 43 (13):6545-6556.
Chicago/Turabian StylePascal Miesen; Erika Girardi; Ronald P. van Rij. 2015. "Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs inAedes aegyptimosquito cells." Nucleic Acids Research 43, no. 13: 6545-6556.
In plants and invertebrates RNA silencing is a major defense mechanism against virus infections. The first event in RNA silencing is dicing of long double stranded RNAs into small interfering RNAs (siRNAs). The Dicer proteins involved in this process are phylogenetically conserved and have the same domain organization. Accordingly, the production of viral derived siRNAs has also been observed in the mouse, but only in restricted cell types. To gain insight on this restriction, we compare the dicing activity of human Dicer and fly Dicer-2 in the context of Sindbis virus (SINV) infection. Expression of human Dicer in flies inefficiently rescues the production of viral siRNAs but confers some protection against SINV. Conversely, expression of Dicer-2 in human cells allows the production of viral 21 nt small RNAs. However, this does not confer resistance to viral infection, but on the contrary results in stronger accumulation of viral RNA. We further show that Dicer-2 expression in human cells perturbs interferon (IFN) signaling pathways and antagonizes protein kinase R (PKR)-mediated antiviral immunity. Overall, our data suggest that a functional incompatibility between the Dicer and IFN pathways explains the predominance of the IFN response in mammalian somatic cells.
Erika Girardi; Mathieu Lefèvre; Béatrice Chane-Woon-Ming; Simona Paro; Bill Claydon; Jean-Luc Imler; Carine Meignin; Sébastien Pfeffer. Cross-species comparative analysis of Dicer proteins during Sindbis virus infection. Scientific Reports 2015, 5, 10693 .
AMA StyleErika Girardi, Mathieu Lefèvre, Béatrice Chane-Woon-Ming, Simona Paro, Bill Claydon, Jean-Luc Imler, Carine Meignin, Sébastien Pfeffer. Cross-species comparative analysis of Dicer proteins during Sindbis virus infection. Scientific Reports. 2015; 5 (1):10693.
Chicago/Turabian StyleErika Girardi; Mathieu Lefèvre; Béatrice Chane-Woon-Ming; Simona Paro; Bill Claydon; Jean-Luc Imler; Carine Meignin; Sébastien Pfeffer. 2015. "Cross-species comparative analysis of Dicer proteins during Sindbis virus infection." Scientific Reports 5, no. 1: 10693.
Hepatitis C virus (HCV) infection is a leading cause of liver cirrhosis and cancer. Cell entry of HCV and other pathogens is mediated by tight junction (TJ) proteins, but successful therapeutic targeting of TJ proteins has not been reported yet. Using a human liver-chimeric mouse model, we show that a monoclonal antibody specific for the TJ protein claudin-1 (ref. 7) eliminates chronic HCV infection without detectable toxicity. This antibody inhibits HCV entry, cell-cell transmission and virus-induced signaling events. Antibody treatment reduces the number of HCV-infected hepatocytes in vivo, highlighting the need for de novo infection by means of host entry factors to maintain chronic infection. In summary, we demonstrate that an antibody targeting a virus receptor can cure chronic viral infection and uncover TJ proteins as targets for antiviral therapy.
Laurent Mailly; Fei Xiao; Joachim Lupberger; Garrick K Wilson; Philippe Aubert; Hong Tuan Francois Duong; Diego Calabrese; Céline Leboeuf; Isabel Fofana; Christine Thumann; Simonetta Bandiera; Marc Lütgehetmann; Tassilo Volz; Christopher Davis; Helen J Harris; Christopher Mee; Erika Girardi; Béatrice Chane-Woon-Ming; Robinet Eric; Nicola Fletcher; Ralf Bartenschlager; Patrick Pessaux; Koen Vercauteren; Philip Meuleman; Pascal Villa; Lars Kaderali; Sébastien Pfeffer; Markus H Heim; Michel Neunlist; Mirjam B Zeisel; Maura Dandri; Jane McKeating; Eric Robinet; Thomas F Baumert. Clearance of persistent hepatitis C virus infection in humanized mice using a claudin-1-targeting monoclonal antibody. Nature Biotechnology 2015, 33, 549 -554.
AMA StyleLaurent Mailly, Fei Xiao, Joachim Lupberger, Garrick K Wilson, Philippe Aubert, Hong Tuan Francois Duong, Diego Calabrese, Céline Leboeuf, Isabel Fofana, Christine Thumann, Simonetta Bandiera, Marc Lütgehetmann, Tassilo Volz, Christopher Davis, Helen J Harris, Christopher Mee, Erika Girardi, Béatrice Chane-Woon-Ming, Robinet Eric, Nicola Fletcher, Ralf Bartenschlager, Patrick Pessaux, Koen Vercauteren, Philip Meuleman, Pascal Villa, Lars Kaderali, Sébastien Pfeffer, Markus H Heim, Michel Neunlist, Mirjam B Zeisel, Maura Dandri, Jane McKeating, Eric Robinet, Thomas F Baumert. Clearance of persistent hepatitis C virus infection in humanized mice using a claudin-1-targeting monoclonal antibody. Nature Biotechnology. 2015; 33 (5):549-554.
Chicago/Turabian StyleLaurent Mailly; Fei Xiao; Joachim Lupberger; Garrick K Wilson; Philippe Aubert; Hong Tuan Francois Duong; Diego Calabrese; Céline Leboeuf; Isabel Fofana; Christine Thumann; Simonetta Bandiera; Marc Lütgehetmann; Tassilo Volz; Christopher Davis; Helen J Harris; Christopher Mee; Erika Girardi; Béatrice Chane-Woon-Ming; Robinet Eric; Nicola Fletcher; Ralf Bartenschlager; Patrick Pessaux; Koen Vercauteren; Philip Meuleman; Pascal Villa; Lars Kaderali; Sébastien Pfeffer; Markus H Heim; Michel Neunlist; Mirjam B Zeisel; Maura Dandri; Jane McKeating; Eric Robinet; Thomas F Baumert. 2015. "Clearance of persistent hepatitis C virus infection in humanized mice using a claudin-1-targeting monoclonal antibody." Nature Biotechnology 33, no. 5: 549-554.
Small RNAs play a critical role in host-pathogen interaction. Indeed, small RNA-mediated silencing or RNA interference (RNAi) is one of the earliest forms of antiviral immunity. Although it represents the main defense system against viruses in many organisms, the antiviral role of RNAi has not been clearly proven in higher vertebrates. However, it is well established that their response to viral infection relies on the recognition of viral RNAs by host pattern recognition receptors (PRRs) to trigger activation of the interferon pathway. In the present work, we report the existence of a novel small noncoding RNA population produced in mammalian cells upon RNA virus infection. Using Sindbis virus (SINV) as a prototypic arbovirus model, we profiled the small RNA population of infected cells in both human and African green monkey cell lines. Here, we provide evidence for the presence of discrete small RNAs of viral origin that are not associated with the RNA-induced silencing complex (RISC), that are highly expressed and detected by Northern blot analysis, and that accumulate as 21- to 28-nucleotide (nt) species during infection. We report that the cellular antiviral endoribonuclease RNase L cleaves the viral genome, producing in turn the small RNAs. Surprisingly, we uncovered the presence of a modification on the 3′-end nucleotide of SINV-derived viral small RNAs (SvsRNAs) that might be at the origin of their stability. Altogether, our findings show that stable modified small viral RNAs could represent a novel way to modulate host-virus interaction upon SINV infection. IMPORTANCE In a continuous arms race, viruses have to deal with host antiviral responses in order to successfully establish an infection. In mammalian cells, the host defense mechanism relies on the recognition of viral RNAs, resulting in the activation of type I interferons (IFNs). In turn, the expression of many interferon-stimulated genes (ISGs) is induced to inhibit viral replication. Here we report that the cytoplasmic, interferon-induced, cellular endoribonuclease RNase L is involved in the accumulation of a novel small RNA population of viral origin. These small RNAs are produced upon SINV infection of mammalian cells and are stabilized by a 3′-end modification. Altogether, our findings indicate that in our system RNA silencing is not active against Sindbis virus (SINV) and might open the way to a better understanding of the antiviral response mediated by a novel class of small RNAs.
Erika Girardi; Béatrice Chane-Woon-Ming; Mélanie Messmer; Pasi Kaukinen; Sébastien Pfeffer. Identification of RNase L-Dependent, 3′-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells. mBio 2013, 4, e00698-13 -13.
AMA StyleErika Girardi, Béatrice Chane-Woon-Ming, Mélanie Messmer, Pasi Kaukinen, Sébastien Pfeffer. Identification of RNase L-Dependent, 3′-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells. mBio. 2013; 4 (6):e00698-13-13.
Chicago/Turabian StyleErika Girardi; Béatrice Chane-Woon-Ming; Mélanie Messmer; Pasi Kaukinen; Sébastien Pfeffer. 2013. "Identification of RNase L-Dependent, 3′-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells." mBio 4, no. 6: e00698-13-13.
International audienceHepatitis C virus (HCV) is a human hepatotropic virus, yet the relevant host factors restricting HCV infection to hepatocytes are only partially understood. We demonstrate that exogenous expression of defined host factors reconstituted the entire HCV life cycle in human non-hepatic 293T cells. This study shows robust HCV entry, RNA replication, and production of infectious virus in human non-hepatic cells, and highlights key host factors required for liver tropism of HCV
Daniel Da Costa; Marine Turek; Daniel J. Felmlee; Erika Girardi; Sébastien Pfeffer; Gang Long; Ralf Bartenschlager; Mirjam B. Zeisel; Thomas F. Baumert. Reconstitution of the Entire Hepatitis C Virus Life Cycle in Nonhepatic Cells. Journal of Virology 2012, 86, 11919 -11925.
AMA StyleDaniel Da Costa, Marine Turek, Daniel J. Felmlee, Erika Girardi, Sébastien Pfeffer, Gang Long, Ralf Bartenschlager, Mirjam B. Zeisel, Thomas F. Baumert. Reconstitution of the Entire Hepatitis C Virus Life Cycle in Nonhepatic Cells. Journal of Virology. 2012; 86 (21):11919-11925.
Chicago/Turabian StyleDaniel Da Costa; Marine Turek; Daniel J. Felmlee; Erika Girardi; Sébastien Pfeffer; Gang Long; Ralf Bartenschlager; Mirjam B. Zeisel; Thomas F. Baumert. 2012. "Reconstitution of the Entire Hepatitis C Virus Life Cycle in Nonhepatic Cells." Journal of Virology 86, no. 21: 11919-11925.
Summary In Duchenne muscular dystrophy (DMD) the absence of dystrophin at the sarcolemma delocalizes and downregulates nitric oxide synthase (nNOS); this alters S-nitrosylation of HDAC2 and its chromatin association. We show that the differential HDAC2 nitrosylation state in Duchenne versus wild-type conditions deregulates the expression of a specific subset of microRNA genes. Several circuitries controlled by the identified microRNAs, such as the one linking miR-1 to the G6PD enzyme and the redox state of cell, or miR-29 to extracellular proteins and the fibrotic process, explain some of the DMD pathogenetic traits. We also show that, at variance with other myomiRs, miR-206 escapes from the dystrophin-nNOS control being produced in activated satellite cells before dystrophin expression; in these cells, it contributes to muscle regeneration through repression of the satellite specific factor, Pax7. We conclude that the pathway activated by dystrophin/nNOS controls several important circuitries increasing the robustness of the muscle differentiation program.
Davide Cacchiarelli; Julie Martone; Erika Girardi; Marcella Cesana; Tania Incitti; Mariangela Morlando; Carmine Nicoletti; Tiziana Santini; Olga Sthandier; Laura Barberi; Alberto Auricchio; Antonio Musarò; Irene Bozzoni. MicroRNAs Involved in Molecular Circuitries Relevant for the Duchenne Muscular Dystrophy Pathogenesis Are Controlled by the Dystrophin/nNOS Pathway. Cell Metabolism 2010, 12, 341 -351.
AMA StyleDavide Cacchiarelli, Julie Martone, Erika Girardi, Marcella Cesana, Tania Incitti, Mariangela Morlando, Carmine Nicoletti, Tiziana Santini, Olga Sthandier, Laura Barberi, Alberto Auricchio, Antonio Musarò, Irene Bozzoni. MicroRNAs Involved in Molecular Circuitries Relevant for the Duchenne Muscular Dystrophy Pathogenesis Are Controlled by the Dystrophin/nNOS Pathway. Cell Metabolism. 2010; 12 (4):341-351.
Chicago/Turabian StyleDavide Cacchiarelli; Julie Martone; Erika Girardi; Marcella Cesana; Tania Incitti; Mariangela Morlando; Carmine Nicoletti; Tiziana Santini; Olga Sthandier; Laura Barberi; Alberto Auricchio; Antonio Musarò; Irene Bozzoni. 2010. "MicroRNAs Involved in Molecular Circuitries Relevant for the Duchenne Muscular Dystrophy Pathogenesis Are Controlled by the Dystrophin/nNOS Pathway." Cell Metabolism 12, no. 4: 341-351.
The first step in microRNA (miRNA) biogenesis occurs in the nucleus and is mediated by the Microprocessor complex containing the RNase III-like enzyme Drosha and its cofactor DGCR8. Here we show that the 5′→3′ exonuclease Xrn2 associates with independently transcribed miRNAs and, in combination with Drosha processing, attenuates transcription in downstream regions. We suggest that, after Drosha cleavage, a torpedo-like mechanism acts on nascent long precursor miRNAs, whereby Xrn2 exonuclease degrades the RNA polymerase II-associated transcripts inducing its release from the template. While involved in primary transcript termination, this attenuation effect does not restrict clustered miRNA expression, which, in the majority of cases, is separated by short spacers. We also show that transcripts originating from a miRNA promoter are retained on the chromatin template and are more efficiently processed than those produced from mRNA or snRNA Pol II-dependent promoters. These data imply that coupling between transcription and processing promotes efficient expression of independently transcribed miRNAs.
Monica Ballarino; Francesca Pagano; Erika Girardi; Mariangela Morlando; Davide Cacchiarelli; Marcella Marchioni; Nicholas J. Proudfoot; Irene Bozzoni. Coupled RNA Processing and Transcription of Intergenic Primary MicroRNAs. Molecular and Cellular Biology 2009, 29, 5632 -5638.
AMA StyleMonica Ballarino, Francesca Pagano, Erika Girardi, Mariangela Morlando, Davide Cacchiarelli, Marcella Marchioni, Nicholas J. Proudfoot, Irene Bozzoni. Coupled RNA Processing and Transcription of Intergenic Primary MicroRNAs. Molecular and Cellular Biology. 2009; 29 (20):5632-5638.
Chicago/Turabian StyleMonica Ballarino; Francesca Pagano; Erika Girardi; Mariangela Morlando; Davide Cacchiarelli; Marcella Marchioni; Nicholas J. Proudfoot; Irene Bozzoni. 2009. "Coupled RNA Processing and Transcription of Intergenic Primary MicroRNAs." Molecular and Cellular Biology 29, no. 20: 5632-5638.