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2024
Gaucherand Léa, Baldaccini Morgane, Pfeffer Sébastien
In: Bioessays, pp. e2400173, 2024, ISSN: 1521-1878.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{pmid39248656,
title = {Beyond RNAi: How the Dicer protein modulates the antiviral innate immune response in mammalian cells: Mammalian Dicer could regulate the innate immune response in an RNAi-independent manner as a result of losing long dsRNA processive activity},
author = {Léa Gaucherand and Morgane Baldaccini and Sébastien Pfeffer},
doi = {10.1002/bies.202400173},
issn = {1521-1878},
year = {2024},
date = {2024-09-01},
urldate = {2024-09-01},
journal = {Bioessays},
pages = {e2400173},
abstract = {While Dicer plays an important antiviral role through the RNAi pathway in plants and invertebrates, its contribution to antiviral immunity in vertebrates and more specifically mammals is more controversial. The apparent limited RNAi activity in mammalian cells has been attributed to the reduced long dsRNA processive activity of mammalian Dicer, as well as a functional incompatibility between the RNAi and IFN pathways. Why Dicer has lost this antiviral activity in the profit of the IFN pathway is still unclear. We propose that the primary direct antiviral activity of Dicer has been functionally replaced by other sensors in the IFN pathway, leading to its specialization toward microRNA maturation. As a result, Dicer can regulate the innate immune response and prevent basal activation of the IFN pathway in mammals. Here, we discuss this hypothesis, highlighting how the adaptation of the helicase domain of mammalian Dicer may be key to this process.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
While Dicer plays an important antiviral role through the RNAi pathway in plants and invertebrates, its contribution to antiviral immunity in vertebrates and more specifically mammals is more controversial. The apparent limited RNAi activity in mammalian cells has been attributed to the reduced long dsRNA processive activity of mammalian Dicer, as well as a functional incompatibility between the RNAi and IFN pathways. Why Dicer has lost this antiviral activity in the profit of the IFN pathway is still unclear. We propose that the primary direct antiviral activity of Dicer has been functionally replaced by other sensors in the IFN pathway, leading to its specialization toward microRNA maturation. As a result, Dicer can regulate the innate immune response and prevent basal activation of the IFN pathway in mammals. Here, we discuss this hypothesis, highlighting how the adaptation of the helicase domain of mammalian Dicer may be key to this process.
Silva Elisabete Cruz Da, Gaki Paraskevi, Flieg Fabien, Messmer Melanie, Gucciardi Floriane, Markovska Yevheniia, Reisch Andreas, Fafi-Kremer Samira, Pfeffer Sébastien, Klymchenko Andrey S
Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads Journal Article
In: Small, pp. e2404167, 2024, ISSN: 1613-6829.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{pmid39011971,
title = {Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads},
author = {Elisabete Cruz Da Silva and Paraskevi Gaki and Fabien Flieg and Melanie Messmer and Floriane Gucciardi and Yevheniia Markovska and Andreas Reisch and Samira Fafi-Kremer and Sébastien Pfeffer and Andrey S Klymchenko},
doi = {10.1002/smll.202404167},
issn = {1613-6829},
year = {2024},
date = {2024-07-01},
urldate = {2024-07-01},
journal = {Small},
pages = {e2404167},
abstract = {Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.
Messmer Mélanie, Pierson Louison, Pasquier Charline, Djordjevic Nikola, Chicher Johana, Hammann Philippe, Pfeffer Sébastien, Girardi Erika
DEAD box RNA helicase 5 is a new pro-viral host factor for Sindbis virus infection Journal Article
In: Virol J, vol. 21, no. 1, pp. 76, 2024, ISSN: 1743-422X.
Abstract | Links | BibTeX | Tags: PFEFFER, PPSE, Unité ARN
@article{pmid38553727,
title = {DEAD box RNA helicase 5 is a new pro-viral host factor for Sindbis virus infection},
author = {Mélanie Messmer and Louison Pierson and Charline Pasquier and Nikola Djordjevic and Johana Chicher and Philippe Hammann and Sébastien Pfeffer and Erika Girardi},
doi = {10.1186/s12985-024-02349-3},
issn = {1743-422X},
year = {2024},
date = {2024-03-01},
urldate = {2024-03-01},
journal = {Virol J},
volume = {21},
number = {1},
pages = {76},
abstract = {BACKGROUND: RNA helicases are emerging as key factors regulating host-virus interactions. The DEAD-box ATP-dependent RNA helicase DDX5, which plays an important role in many aspects of cellular RNA biology, was also found to either promote or inhibit viral replication upon infection with several RNA viruses. Here, our aim is to examine the impact of DDX5 on Sindbis virus (SINV) infection.nnMETHODS: We analysed the interaction between DDX5 and the viral RNA using imaging and RNA-immunoprecipitation approaches. The interactome of DDX5 in mock- and SINV-infected cells was determined by mass spectrometry. We validated the interaction between DDX17 and the viral capsid by co- immunoprecipitation in the presence or absence of an RNase treatment. We determined the subcellular localization of DDX5, its cofactor DDX17 and the viral capsid protein by co-immunofluorescence. Finally, we investigated the impact of DDX5 depletion and overexpression on SINV infection at the viral protein, RNA and infectious particle accumulation level. The contribution of DDX17 was also tested by knockdown experiments.nnRESULTS: In this study we demonstrate that DDX5 interacts with the SINV RNA during infection. Furthermore, the proteomic analysis of the DDX5 interactome in mock and SINV-infected HCT116 cells identified new cellular and viral partners and confirmed the interaction between DDX5 and DDX17. Both DDX5 and DDX17 re-localize from the nucleus to the cytoplasm upon SINV infection and interact with the viral capsid protein. We also show that DDX5 depletion negatively impacts the viral replication cycle, while its overexpression has a pro-viral effect. Finally, we observed that DDX17 depletion reduces SINV infection, an effect which is even more pronounced in a DDX5-depleted background, suggesting a synergistic pro-viral effect of the DDX5 and DDX17 proteins on SINV.nnCONCLUSIONS: These results not only shed light on DDX5 as a novel and important host factor to the SINV life cycle, but also expand our understanding of the roles played by DDX5 and DDX17 as regulators of viral infections.},
keywords = {PFEFFER, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: RNA helicases are emerging as key factors regulating host-virus interactions. The DEAD-box ATP-dependent RNA helicase DDX5, which plays an important role in many aspects of cellular RNA biology, was also found to either promote or inhibit viral replication upon infection with several RNA viruses. Here, our aim is to examine the impact of DDX5 on Sindbis virus (SINV) infection.nnMETHODS: We analysed the interaction between DDX5 and the viral RNA using imaging and RNA-immunoprecipitation approaches. The interactome of DDX5 in mock- and SINV-infected cells was determined by mass spectrometry. We validated the interaction between DDX17 and the viral capsid by co- immunoprecipitation in the presence or absence of an RNase treatment. We determined the subcellular localization of DDX5, its cofactor DDX17 and the viral capsid protein by co-immunofluorescence. Finally, we investigated the impact of DDX5 depletion and overexpression on SINV infection at the viral protein, RNA and infectious particle accumulation level. The contribution of DDX17 was also tested by knockdown experiments.nnRESULTS: In this study we demonstrate that DDX5 interacts with the SINV RNA during infection. Furthermore, the proteomic analysis of the DDX5 interactome in mock and SINV-infected HCT116 cells identified new cellular and viral partners and confirmed the interaction between DDX5 and DDX17. Both DDX5 and DDX17 re-localize from the nucleus to the cytoplasm upon SINV infection and interact with the viral capsid protein. We also show that DDX5 depletion negatively impacts the viral replication cycle, while its overexpression has a pro-viral effect. Finally, we observed that DDX17 depletion reduces SINV infection, an effect which is even more pronounced in a DDX5-depleted background, suggesting a synergistic pro-viral effect of the DDX5 and DDX17 proteins on SINV.nnCONCLUSIONS: These results not only shed light on DDX5 as a novel and important host factor to the SINV life cycle, but also expand our understanding of the roles played by DDX5 and DDX17 as regulators of viral infections.
Baldaccini Morgane, Gaucherand Léa, Chane-Woon-Ming Béatrice, Messmer Mélanie, Gucciardi Floriane, Pfeffer Sébastien
The helicase domain of human Dicer prevents RNAi-independent activation of antiviral and inflammatory pathways Journal Article
In: EMBO J, 2024, ISSN: 1460-2075.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{pmid38287188,
title = {The helicase domain of human Dicer prevents RNAi-independent activation of antiviral and inflammatory pathways},
author = {Morgane Baldaccini and Léa Gaucherand and Béatrice Chane-Woon-Ming and Mélanie Messmer and Floriane Gucciardi and Sébastien Pfeffer},
doi = {10.1038/s44318-024-00035-2},
issn = {1460-2075},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {EMBO J},
abstract = {In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. All deletion mutants display a PKR-dependent antiviral phenotype against certain viruses, and one of them, Dicer N1, acts in a completely RNAi-independent manner. Transcriptomic analyses show that many genes from the interferon and inflammatory response pathways are upregulated in Dicer N1 expressing cells. We show that some of these genes are controlled by NF-kB and that blocking this pathway abrogates the antiviral phenotype of Dicer N1. Our findings highlight the crosstalk between Dicer, PKR, and the NF-kB pathway, and suggest that human Dicer may have repurposed its helicase domain to prevent basal activation of antiviral and inflammatory pathways.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. All deletion mutants display a PKR-dependent antiviral phenotype against certain viruses, and one of them, Dicer N1, acts in a completely RNAi-independent manner. Transcriptomic analyses show that many genes from the interferon and inflammatory response pathways are upregulated in Dicer N1 expressing cells. We show that some of these genes are controlled by NF-kB and that blocking this pathway abrogates the antiviral phenotype of Dicer N1. Our findings highlight the crosstalk between Dicer, PKR, and the NF-kB pathway, and suggest that human Dicer may have repurposed its helicase domain to prevent basal activation of antiviral and inflammatory pathways.
2023
Gaucherand Lea, Iyer Amrita, Gilabert Isabel, Rycroft Chris H, Gaglia Marta M
Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs Journal Article
In: Nat Microbiol, 2023, ISSN: 2058-5276.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{pmid37349586,
title = {Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs},
author = {Lea Gaucherand and Amrita Iyer and Isabel Gilabert and Chris H Rycroft and Marta M Gaglia},
doi = {10.1038/s41564-023-01409-8},
issn = {2058-5276},
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
journal = {Nat Microbiol},
abstract = {Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases. However, viruses also need to ensure expression of their own genes. The influenza A virus endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for viral replication. To understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5' rapid amplification of complementary DNA ends coupled to high-throughput sequencing. This analysis, along with RNA structure predictions and validation experiments using reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs in a manner reminiscent of cellular self versus non-self discrimination.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases. However, viruses also need to ensure expression of their own genes. The influenza A virus endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for viral replication. To understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5' rapid amplification of complementary DNA ends coupled to high-throughput sequencing. This analysis, along with RNA structure predictions and validation experiments using reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs in a manner reminiscent of cellular self versus non-self discrimination.
Girardi Erika, Messmer Mélanie, Lopez Paula, Fender Aurélie, Chicher Johana, Chane-Woon-Ming Béatrice, Hammann Philippe, Pfeffer Sébastien
Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection Journal Article
In: RNA, vol. 29, no. 3, pp. 361–375, 2023, ISSN: 1469-9001.
Abstract | Links | BibTeX | Tags: PFEFFER, PPSE, Unité ARN
@article{pmid36617674b,
title = {Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection},
author = {Erika Girardi and Mélanie Messmer and Paula Lopez and Aurélie Fender and Johana Chicher and Béatrice Chane-Woon-Ming and Philippe Hammann and Sébastien Pfeffer},
doi = {10.1261/rna.079270.122},
issn = {1469-9001},
year = {2023},
date = {2023-03-01},
urldate = {2023-03-01},
journal = {RNA},
volume = {29},
number = {3},
pages = {361--375},
abstract = {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 with 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 analysis to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human cells. Among the identified proteins, we characterized SFPQ (splicing factor, proline-glutamine rich) as a new dsRNA-associated proviral factor upon SINV infection. We showed that SFPQ depletion reduces SINV infection in human HCT116 and SK-N-BE(2) cells, suggesting that SFPQ enhances viral production. We demonstrated that the cytoplasmic fraction of SFPQ partially colocalizes with dsRNA upon SINV infection. In agreement, we proved by RNA-IP that SFPQ can bind dsRNA and viral RNA. Furthermore, we showed that overexpression of a wild-type, but not an RNA binding mutant SFPQ, increased viral infection, suggesting that RNA binding is essential for its positive effect on the virus. Overall, this study provides the community with a compendium of dsRNA-associated factors during viral infection and identifies SFPQ as a new proviral dsRNA binding protein.},
keywords = {PFEFFER, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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 with 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 analysis to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human cells. Among the identified proteins, we characterized SFPQ (splicing factor, proline-glutamine rich) as a new dsRNA-associated proviral factor upon SINV infection. We showed that SFPQ depletion reduces SINV infection in human HCT116 and SK-N-BE(2) cells, suggesting that SFPQ enhances viral production. We demonstrated that the cytoplasmic fraction of SFPQ partially colocalizes with dsRNA upon SINV infection. In agreement, we proved by RNA-IP that SFPQ can bind dsRNA and viral RNA. Furthermore, we showed that overexpression of a wild-type, but not an RNA binding mutant SFPQ, increased viral infection, suggesting that RNA binding is essential for its positive effect on the virus. Overall, this study provides the community with a compendium of dsRNA-associated factors during viral infection and identifies SFPQ as a new proviral dsRNA binding protein.
Lee Seungjae, Jee David, Srivastava Sid, Yang Acong, Ramidi Abhinav, Shang Renfu, Bortolamiol-Becet Diane, Pfeffer Sébastien, Gu Shuo, Wen Jiayu, Lai Eric C
Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals Journal Article
In: Cell Rep, vol. 42, no. 2, pp. 112111, 2023, ISSN: 2211-1247.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{pmid36800291,
title = {Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals},
author = {Seungjae Lee and David Jee and Sid Srivastava and Acong Yang and Abhinav Ramidi and Renfu Shang and Diane Bortolamiol-Becet and Sébastien Pfeffer and Shuo Gu and Jiayu Wen and Eric C Lai},
doi = {10.1016/j.celrep.2023.112111},
issn = {2211-1247},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {Cell Rep},
volume = {42},
number = {2},
pages = {112111},
abstract = {Canonical microRNA (miRNA) hairpins are processed by the RNase III enzymes Drosha and Dicer into ∼22 nt RNAs loaded into an Argonaute (Ago) effector. In addition, splicing generates numerous intronic hairpins that bypass Drosha (mirtrons) to yield mature miRNAs. Here, we identify hundreds of previously unannotated, splicing-derived hairpins in intermediate-length (∼50-100 nt) but not small (20-30 nt) RNA data. Since we originally defined mirtrons from small RNA duplexes, we term this larger set as structured splicing-derived RNAs (ssdRNAs). These associate with Dicer and/or Ago complexes, but generally accumulate modestly and are poorly conserved. We propose they contaminate the canonical miRNA pathway, which consequently requires defense against the siege of splicing-derived substrates. Accordingly, ssdRNAs/mirtrons comprise dominant hairpin substrates for 3' tailing by multiple terminal nucleotidyltransferases, notably TUT4/7 and TENT2. Overall, the rampant proliferation of young mammalian mirtrons/ssdRNAs, coupled with an inhibitory molecular defense, comprises a Red Queen's race of intragenomic conflict.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Canonical microRNA (miRNA) hairpins are processed by the RNase III enzymes Drosha and Dicer into ∼22 nt RNAs loaded into an Argonaute (Ago) effector. In addition, splicing generates numerous intronic hairpins that bypass Drosha (mirtrons) to yield mature miRNAs. Here, we identify hundreds of previously unannotated, splicing-derived hairpins in intermediate-length (∼50-100 nt) but not small (20-30 nt) RNA data. Since we originally defined mirtrons from small RNA duplexes, we term this larger set as structured splicing-derived RNAs (ssdRNAs). These associate with Dicer and/or Ago complexes, but generally accumulate modestly and are poorly conserved. We propose they contaminate the canonical miRNA pathway, which consequently requires defense against the siege of splicing-derived substrates. Accordingly, ssdRNAs/mirtrons comprise dominant hairpin substrates for 3' tailing by multiple terminal nucleotidyltransferases, notably TUT4/7 and TENT2. Overall, the rampant proliferation of young mammalian mirtrons/ssdRNAs, coupled with an inhibitory molecular defense, comprises a Red Queen's race of intragenomic conflict.
2022
Girardi Erika, Messmer Melanie, Lopez Paula, Fender Aurelie, Chicher Johana, Chane-Woon-Ming Beatrice, Hammann Philippe, Pfeffer Sebastien
Proteomics-based determination of double stranded RNA interactome reveals known and new factors involved in Sindbis virus infection Journal Article
In: RNA, vol. 29, iss. 3, pp. 361-375, 2022, ISSN: 1469-9001.
Abstract | Links | BibTeX | Tags: PFEFFER, PPSE, Unité ARN
@article{pmid36617674,
title = {Proteomics-based determination of double stranded RNA interactome reveals known and new factors involved in Sindbis virus infection},
author = {Erika Girardi and Melanie Messmer and Paula Lopez and Aurelie Fender and Johana Chicher and Beatrice Chane-Woon-Ming and Philippe Hammann and Sebastien Pfeffer},
doi = {10.1261/rna.079270.122},
issn = {1469-9001},
year = {2022},
date = {2022-12-01},
urldate = {2022-12-01},
journal = {RNA},
volume = {29},
issue = {3},
pages = {361-375},
abstract = {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 with 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 analysis to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human cells. Among the identified proteins, we characterized SFPQ (Splicing factor, proline-glutamine rich) as a new dsRNA-associated proviral factor upon SINV infection. We showed that SFPQ depletion reduces SINV infection in human HCT116 and SK-N-BE(2) cells, suggesting that SFPQ enhances viral production. We demonstrated that the cytoplasmic fraction of SFPQ partially colocalizes with dsRNA upon SINV infection. In agreement, we proved by RNA-IP that SFPQ can bind dsRNA and viral RNA. Furthermore, we showed that overexpression of a wild type, but not an RNA binding mutant SFPQ, increased viral infection, suggesting that RNA binding is essential for its positive effect on the virus. Overall, this study provides the community with a compendium of dsRNA-associated factors during viral infection and identifies SFPQ as a new proviral dsRNA binding protein.},
keywords = {PFEFFER, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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 with 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 analysis to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human cells. Among the identified proteins, we characterized SFPQ (Splicing factor, proline-glutamine rich) as a new dsRNA-associated proviral factor upon SINV infection. We showed that SFPQ depletion reduces SINV infection in human HCT116 and SK-N-BE(2) cells, suggesting that SFPQ enhances viral production. We demonstrated that the cytoplasmic fraction of SFPQ partially colocalizes with dsRNA upon SINV infection. In agreement, we proved by RNA-IP that SFPQ can bind dsRNA and viral RNA. Furthermore, we showed that overexpression of a wild type, but not an RNA binding mutant SFPQ, increased viral infection, suggesting that RNA binding is essential for its positive effect on the virus. Overall, this study provides the community with a compendium of dsRNA-associated factors during viral infection and identifies SFPQ as a new proviral dsRNA binding protein.
Vilimova Monika, Pfeffer Sébastien
Post-transcriptional regulation of polycistronic microRNAs Journal Article
In: Wiley Interdiscip Rev RNA, vol. 14, iss. 2, pp. e1749, 2022, ISSN: 1757-7012.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{pmid35702737,
title = {Post-transcriptional regulation of polycistronic microRNAs},
author = {Monika Vilimova and Sébastien Pfeffer},
doi = {10.1002/wrna.1749},
issn = {1757-7012},
year = {2022},
date = {2022-06-01},
urldate = {2022-06-01},
journal = {Wiley Interdiscip Rev RNA},
volume = {14},
issue = {2},
pages = {e1749},
abstract = {An important proportion of microRNA (miRNA) genes tend to lie close to each other within animal genomes. Such genomic organization is generally referred to as miRNA clusters. Even though many miRNA clusters have been greatly studied, most attention has been usually focused on functional impacts of clustered miRNA co-expression. However, there is also another compelling aspect about these miRNA clusters, their polycistronic nature. Being transcribed on a single RNA precursor, polycistronic miRNAs benefit from common transcriptional regulation allowing their coordinated expression. And yet, numerous reports have revealed striking discrepancies in the accumulation of mature miRNAs produced from the same cluster. Indeed, the larger polycistronic transcripts can act as platforms providing unforeseen post-transcriptional regulatory mechanisms controlling individual miRNA processing, thus leading to differential miRNA expression, and sometimes even challenging the general assumption that polycistronic miRNAs are co-expressed. In this review, we aim to address the current knowledge about how miRNA polycistrons are post-transcriptionally regulated. In particular, we will focus on the mechanisms occurring at the level of the primary transcript, which are highly relevant for individual miRNA processing and as such have a direct repercussion on miRNA function within the cell. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
An important proportion of microRNA (miRNA) genes tend to lie close to each other within animal genomes. Such genomic organization is generally referred to as miRNA clusters. Even though many miRNA clusters have been greatly studied, most attention has been usually focused on functional impacts of clustered miRNA co-expression. However, there is also another compelling aspect about these miRNA clusters, their polycistronic nature. Being transcribed on a single RNA precursor, polycistronic miRNAs benefit from common transcriptional regulation allowing their coordinated expression. And yet, numerous reports have revealed striking discrepancies in the accumulation of mature miRNAs produced from the same cluster. Indeed, the larger polycistronic transcripts can act as platforms providing unforeseen post-transcriptional regulatory mechanisms controlling individual miRNA processing, thus leading to differential miRNA expression, and sometimes even challenging the general assumption that polycistronic miRNAs are co-expressed. In this review, we aim to address the current knowledge about how miRNA polycistrons are post-transcriptionally regulated. In particular, we will focus on the mechanisms occurring at the level of the primary transcript, which are highly relevant for individual miRNA processing and as such have a direct repercussion on miRNA function within the cell. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
Camara A., Lavanant A. C., Abe J., Desforges H. L., Alexandre Y. O., Girardi E., Igamberdieva Z., Asano K., Tanaka M., Hehlgans T., Pfeffer K., Pfeffer S., Mueller S. N., Stein J. V., Mueller C. G.
CD169(+) macrophages in lymph node and spleen critically depend on dual RANK and LTbetaR signaling Journal Article
In: Proc Natl Acad Sci U S A, vol. 119, no. 3, pp. e2108540119, 2022, ISBN: 35031565, (1091-6490 (Electronic) 0027-8424 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: PFEFFER, Team-Mueller, Unité ARN
@article{nokey,
title = {CD169(+) macrophages in lymph node and spleen critically depend on dual RANK and LTbetaR signaling},
author = {A. Camara and A. C. Lavanant and J. Abe and H. L. Desforges and Y. O. Alexandre and E. Girardi and Z. Igamberdieva and K. Asano and M. Tanaka and T. Hehlgans and K. Pfeffer and S. Pfeffer and S. N. Mueller and J. V. Stein and C. G. Mueller},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35031565},
isbn = {35031565},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {119},
number = {3},
pages = {e2108540119},
abstract = {CD169(+) macrophages reside in lymph node (LN) and spleen and play an important role in the immune defense against pathogens. As resident macrophages, they are responsive to environmental cues to shape their tissue-specific identity. We have previously shown that LN CD169(+) macrophages require RANKL for formation of their niche and their differentiation. Here, we demonstrate that they are also dependent on direct lymphotoxin beta (LTbeta) receptor (R) signaling. In the absence or the reduced expression of either RANK or LTbetaR, their differentiation is perturbed, generating myeloid cells expressing SIGN-R1 in LNs. Conditions of combined haploinsufficiencies of RANK and LTbetaR revealed that both receptors contribute equally to LN CD169(+) macrophage differentiation. In the spleen, the Cd169-directed ablation of either receptor results in a selective loss of marginal metallophilic macrophages (MMMs). Using a RANKL reporter mouse, we identify splenic marginal zone stromal cells as a source of RANKL and demonstrate that it participates in MMM differentiation. The loss of MMMs had no effect on the splenic B cell compartments but compromised viral capture and the expansion of virus-specific CD8(+) T cells. Taken together, the data provide evidence that CD169(+) macrophage differentiation in LN and spleen requires dual signals from LTbetaR and RANK with implications for the immune response.},
note = {1091-6490 (Electronic)
0027-8424 (Linking)
Journal Article},
keywords = {PFEFFER, Team-Mueller, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
CD169(+) macrophages reside in lymph node (LN) and spleen and play an important role in the immune defense against pathogens. As resident macrophages, they are responsive to environmental cues to shape their tissue-specific identity. We have previously shown that LN CD169(+) macrophages require RANKL for formation of their niche and their differentiation. Here, we demonstrate that they are also dependent on direct lymphotoxin beta (LTbeta) receptor (R) signaling. In the absence or the reduced expression of either RANK or LTbetaR, their differentiation is perturbed, generating myeloid cells expressing SIGN-R1 in LNs. Conditions of combined haploinsufficiencies of RANK and LTbetaR revealed that both receptors contribute equally to LN CD169(+) macrophage differentiation. In the spleen, the Cd169-directed ablation of either receptor results in a selective loss of marginal metallophilic macrophages (MMMs). Using a RANKL reporter mouse, we identify splenic marginal zone stromal cells as a source of RANKL and demonstrate that it participates in MMM differentiation. The loss of MMMs had no effect on the splenic B cell compartments but compromised viral capture and the expansion of virus-specific CD8(+) T cells. Taken together, the data provide evidence that CD169(+) macrophage differentiation in LN and spleen requires dual signals from LTbetaR and RANK with implications for the immune response.
Brugier A., Hafirrassou M. L., Pourcelot M., Baldaccini M., Kril V., Couture L., Kummerer B. M., Gallois-Montbrun S., Bonnet-Madin L., Vidalain P. O., Delaugerre C., Pfeffer S., Meertens L., Amara A.
RACK1 Associates with RNA-Binding Proteins Vigilin and SERBP1 to Facilitate Dengue Virus Replication Journal Article
In: J Virol, vol. 96, iss. 7, pp. e0196221, 2022, ISBN: 35266803, (1098-5514 (Electronic) 0022-538X (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{nokey,
title = {RACK1 Associates with RNA-Binding Proteins Vigilin and SERBP1 to Facilitate Dengue Virus Replication},
author = {A. Brugier and M. L. Hafirrassou and M. Pourcelot and M. Baldaccini and V. Kril and L. Couture and B. M. Kummerer and S. Gallois-Montbrun and L. Bonnet-Madin and P. O. Vidalain and C. Delaugerre and S. Pfeffer and L. Meertens and A. Amara},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35266803},
doi = {10.1128/jvi.01962-21},
isbn = {35266803},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {J Virol},
volume = {96},
issue = {7},
pages = {e0196221},
abstract = {Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no effective treatment is available. DENV relies heavily on the host cellular machinery for productive infection. Here, we show that the scaffold protein RACK1, which is part of the DENV replication complex, mediates infection by binding to the 40S ribosomal subunit. Mass spectrometry analysis of RACK1 partners coupled to an RNA interference screen-identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV genome. Genetic ablation of Vigilin or SERBP1 rendered cells poorly susceptible to DENV, as well as related flaviviruses, by hampering the translation and replication steps. Finally, we established that a Vigilin or SERBP1 mutant lacking RACK1 binding but still interacting with the viral RNA is unable to mediate DENV infection. We propose that RACK1 recruits Vigilin and SERBP1, linking the DENV genome to the translation machinery for efficient infection. IMPORTANCE We recently identified the scaffolding RACK1 protein as an important host-dependency factor for dengue virus (DENV), a positive-stranded RNA virus responsible for the most prevalent mosquito-borne viral disease worldwide. Here, we have performed the first RACK1 interactome in human cells and identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV RNA to regulate viral replication. Importantly, Vigilin and SERBP1 interact with RACK1 and the DENV viral RNA (vRNA) to mediate viral replication. Overall, our results suggest that RACK1 acts as a binding platform at the surface of the 40S ribosomal subunit to recruit Vigilin and SERBP1, which may therefore function as linkers between the viral RNA and the translation machinery to facilitate infection.},
note = {1098-5514 (Electronic)
0022-538X (Linking)
Journal Article},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no effective treatment is available. DENV relies heavily on the host cellular machinery for productive infection. Here, we show that the scaffold protein RACK1, which is part of the DENV replication complex, mediates infection by binding to the 40S ribosomal subunit. Mass spectrometry analysis of RACK1 partners coupled to an RNA interference screen-identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV genome. Genetic ablation of Vigilin or SERBP1 rendered cells poorly susceptible to DENV, as well as related flaviviruses, by hampering the translation and replication steps. Finally, we established that a Vigilin or SERBP1 mutant lacking RACK1 binding but still interacting with the viral RNA is unable to mediate DENV infection. We propose that RACK1 recruits Vigilin and SERBP1, linking the DENV genome to the translation machinery for efficient infection. IMPORTANCE We recently identified the scaffolding RACK1 protein as an important host-dependency factor for dengue virus (DENV), a positive-stranded RNA virus responsible for the most prevalent mosquito-borne viral disease worldwide. Here, we have performed the first RACK1 interactome in human cells and identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV RNA to regulate viral replication. Importantly, Vigilin and SERBP1 interact with RACK1 and the DENV viral RNA (vRNA) to mediate viral replication. Overall, our results suggest that RACK1 acts as a binding platform at the surface of the 40S ribosomal subunit to recruit Vigilin and SERBP1, which may therefore function as linkers between the viral RNA and the translation machinery to facilitate infection.
2021
Vilimova Monika, Contrant Maud, Randrianjafy Ramy, Dumas Philippe, Elbasani Endrit, Ojala Päivi M, Pfeffer Sébastien, Fender Aurélie
Correction to 'Cis regulation within a cluster of viral microRNAs' Miscellaneous
2021, ISSN: 1362-4962.
Links | BibTeX | Tags: PFEFFER, Unité ARN
@misc{pmid34520556,
title = {Correction to 'Cis regulation within a cluster of viral microRNAs'},
author = {Monika Vilimova and Maud Contrant and Ramy Randrianjafy and Philippe Dumas and Endrit Elbasani and Päivi M Ojala and Sébastien Pfeffer and Aurélie Fender},
doi = {10.1093/nar/gkab806},
issn = {1362-4962},
year = {2021},
date = {2021-10-01},
urldate = {2021-10-01},
journal = {Nucleic Acids Res},
volume = {49},
number = {18},
pages = {10804--10805},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {misc}
}
Montavon T C, Baldaccini M, Lefevre M, Girardi E, Chane-Woon-Ming B, Messmer M, Hammann P, Chicher J, Pfeffer S
Human DICER helicase domain recruits PKR and modulates its antiviral activity Journal Article
In: PLoS Pathog, vol. 17, no. 5, pp. e1009549, 2021, ISBN: 33984068, (1553-7374 (Electronic) 1553-7366 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: PFEFFER, PPSE, Unité ARN
@article{Montavon2021,
title = {Human DICER helicase domain recruits PKR and modulates its antiviral activity},
author = {T C Montavon and M Baldaccini and M Lefevre and E Girardi and B Chane-Woon-Ming and M Messmer and P Hammann and J Chicher and S Pfeffer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33984068},
doi = {0.1371/journal.ppat.1009549},
isbn = {33984068},
year = {2021},
date = {2021-01-01},
journal = {PLoS Pathog},
volume = {17},
number = {5},
pages = {e1009549},
abstract = {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 alphaviruses such as the Sindbis virus and Semliki forest 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 that the helicase domain of DICER is essential for this interaction and that its deletion confers antiviral properties to this protein in an RNAi-independent, PKR-dependent, manner.},
note = {1553-7374 (Electronic)
1553-7366 (Linking)
Journal Article},
keywords = {PFEFFER, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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 alphaviruses such as the Sindbis virus and Semliki forest 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 that the helicase domain of DICER is essential for this interaction and that its deletion confers antiviral properties to this protein in an RNAi-independent, PKR-dependent, manner.
Vilimova M, Contrant M, Randrianjafy R, Dumas P, Elbasani E, Ojala P M, Pfeffer S, Fender A
Cis regulation within a cluster of viral microRNAs Journal Article
In: Nucleic Acids Res, 2021, ISBN: 34417603, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{Vilimova2021,
title = {Cis regulation within a cluster of viral microRNAs},
author = {M Vilimova and M Contrant and R Randrianjafy and P Dumas and E Elbasani and P M Ojala and S Pfeffer and A Fender},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34417603},
doi = {10.1093/nar/gkab806},
isbn = {34417603},
year = {2021},
date = {2021-01-01},
journal = {Nucleic Acids Res},
abstract = {MicroRNAs (miRNAs) are small regulatory RNAs involved in virtually all biological processes. Although many of them are co-expressed from clusters, little is known regarding the impact of this organization on the regulation of their accumulation. In this study, we set to decipher a regulatory mechanism controlling the expression of the ten clustered pre-miRNAs from Kaposi's sarcoma associated herpesvirus (KSHV). We measured in vitro the efficiency of cleavage of each individual pre-miRNA by the Microprocessor and found that pre-miR-K1 and -K3 were the most efficiently cleaved pre-miRNAs. A mutational analysis showed that, in addition to producing mature miRNAs, they are also important for the optimal expression of the whole set of miRNAs. We showed that this feature depends on the presence of a canonical pre-miRNA at this location since we could functionally replace pre-miR-K1 by a heterologous pre-miRNA. Further in vitro processing analysis suggests that the two stem-loops act in cis and that the cluster is cleaved in a sequential manner. Finally, we exploited this characteristic of the cluster to inhibit the expression of the whole set of miRNAs by targeting the pre-miR-K1 with LNA-based antisense oligonucleotides in cells either expressing a synthetic construct or latently infected with KSHV.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
MicroRNAs (miRNAs) are small regulatory RNAs involved in virtually all biological processes. Although many of them are co-expressed from clusters, little is known regarding the impact of this organization on the regulation of their accumulation. In this study, we set to decipher a regulatory mechanism controlling the expression of the ten clustered pre-miRNAs from Kaposi's sarcoma associated herpesvirus (KSHV). We measured in vitro the efficiency of cleavage of each individual pre-miRNA by the Microprocessor and found that pre-miR-K1 and -K3 were the most efficiently cleaved pre-miRNAs. A mutational analysis showed that, in addition to producing mature miRNAs, they are also important for the optimal expression of the whole set of miRNAs. We showed that this feature depends on the presence of a canonical pre-miRNA at this location since we could functionally replace pre-miR-K1 by a heterologous pre-miRNA. Further in vitro processing analysis suggests that the two stem-loops act in cis and that the cluster is cleaved in a sequential manner. Finally, we exploited this characteristic of the cluster to inhibit the expression of the whole set of miRNAs by targeting the pre-miR-K1 with LNA-based antisense oligonucleotides in cells either expressing a synthetic construct or latently infected with KSHV.
Baldaccini M., Pfeffer S.
Untangling the roles of RNA helicases in antiviral innate immunity Journal Article
In: PLoS Pathog, vol. 17, no. 12, pp. e1010072, 2021, ISBN: 34882751, (1553-7374 (Electronic) 1553-7366 (Linking) Journal Article Review).
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{nokey,
title = {Untangling the roles of RNA helicases in antiviral innate immunity},
author = {M. Baldaccini and S. Pfeffer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34882751},
doi = {10.1371/journal.ppat.1010072},
isbn = {34882751},
year = {2021},
date = {2021-01-01},
journal = {PLoS Pathog},
volume = {17},
number = {12},
pages = {e1010072},
abstract = {One of the first layers of protection that metazoans put in place to defend themselves against viruses rely on the use of proteins containing DExD/H-box helicase domains. These members of the duplex RNA-activated ATPase (DRA) family act as sensors of double-stranded RNA (dsRNA) molecules, a universal marker of viral infections. DRAs can be classified into 2 subgroups based on their mode of action: They can either act directly on the dsRNA, or they can trigger a signaling cascade. In the first group, the type III ribonuclease Dicer plays a key role to activate the antiviral RNA interference (RNAi) pathway by cleaving the viral dsRNA into small interfering RNAs (siRNAs). This represents the main innate antiviral immune mechanism in arthropods and nematodes. Even though Dicer is present and functional in mammals, the second group of DRAs, containing the RIG-I-like RNA helicases, appears to have functionally replaced RNAi and activate type I interferon (IFN) response upon dsRNA sensing. However, recent findings tend to blur the frontier between these 2 mechanisms, thereby highlighting the crucial and diverse roles played by RNA helicases in antiviral innate immunity. Here, we will review our current knowledge of the importance of these key proteins in viral infection, with a special focus on the interplay between the 2 main types of response that are activated by dsRNA.},
note = {1553-7374 (Electronic)
1553-7366 (Linking)
Journal Article
Review},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
One of the first layers of protection that metazoans put in place to defend themselves against viruses rely on the use of proteins containing DExD/H-box helicase domains. These members of the duplex RNA-activated ATPase (DRA) family act as sensors of double-stranded RNA (dsRNA) molecules, a universal marker of viral infections. DRAs can be classified into 2 subgroups based on their mode of action: They can either act directly on the dsRNA, or they can trigger a signaling cascade. In the first group, the type III ribonuclease Dicer plays a key role to activate the antiviral RNA interference (RNAi) pathway by cleaving the viral dsRNA into small interfering RNAs (siRNAs). This represents the main innate antiviral immune mechanism in arthropods and nematodes. Even though Dicer is present and functional in mammals, the second group of DRAs, containing the RIG-I-like RNA helicases, appears to have functionally replaced RNAi and activate type I interferon (IFN) response upon dsRNA sensing. However, recent findings tend to blur the frontier between these 2 mechanisms, thereby highlighting the crucial and diverse roles played by RNA helicases in antiviral innate immunity. Here, we will review our current knowledge of the importance of these key proteins in viral infection, with a special focus on the interplay between the 2 main types of response that are activated by dsRNA.
2020
Petitjean O, Girardi E, Ngondon RP, Lupashin V, Pfeffer S
In: mSphere, vol. 5, no. 6, pp. e00914-20, 2020.
Abstract | Links | BibTeX | Tags: complex oligomeric Golgi complex, CRISPR-Cas9 screen, double-stranded RNA, heparan-sulfate, PFEFFER, Transfection, Unité ARN, virus
@article{Petitjean2020,
title = {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 },
author = {O Petitjean and E Girardi and RP Ngondon and V Lupashin and S Pfeffer
},
url = {https://pubmed.ncbi.nlm.nih.gov/33177215/},
doi = {10.1128/mSphere.00914-20 },
year = {2020},
date = {2020-11-01},
journal = { mSphere},
volume = {5},
number = {6},
pages = {e00914-20},
abstract = {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 knockout led to a decrease of extracellular HS that specifically affected dsRNA transfection efficiency and reduced viral production, which explains the increased cell survival of these mutants.IMPORTANCE 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. },
keywords = {complex oligomeric Golgi complex, CRISPR-Cas9 screen, double-stranded RNA, heparan-sulfate, PFEFFER, Transfection, Unité ARN, virus},
pubstate = {published},
tppubtype = {article}
}
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 knockout led to a decrease of extracellular HS that specifically affected dsRNA transfection efficiency and reduced viral production, which explains the increased cell survival of these mutants.IMPORTANCE 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.
Lopez P, Girardi E, Mounce B C, Weiss A, Chane-Woon-Ming B, Messmer M, Kaukinen P, Kopp A, Bortolamiol-Becet D, Fendri A, Vignuzzi M, Brino L, Pfeffer S
High-throughput Fluorescence-Based Screen Identifies the Neuronal microRNA miR-124 as a Positive Regulator of Alphavirus Infection Journal Article
In: J Virol, vol. 94, no. 9, pp. e02145-02119, 2020, ISBN: 32102877.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{,
title = {High-throughput Fluorescence-Based Screen Identifies the Neuronal microRNA miR-124 as a Positive Regulator of Alphavirus Infection},
author = {P Lopez and E Girardi and B C Mounce and A Weiss and B Chane-Woon-Ming and M Messmer and P Kaukinen and A Kopp and D Bortolamiol-Becet and A Fendri and M Vignuzzi and L Brino and S Pfeffer},
url = {https://pubmed.ncbi.nlm.nih.gov/32102877},
doi = {10.1128/JVI.02145-19},
isbn = {32102877},
year = {2020},
date = {2020-01-01},
journal = {J Virol},
volume = {94},
number = {9},
pages = {e02145-02119},
abstract = {Micro (mi)RNAs are small regulatory RNAs, which act by modulating 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 host mRNAs and this can result in a positive or negative outcome for the virus. Here, we performed a fluorescence-based 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 Sindbis virus (SINV) expressing GFP, among which a number of neuron-specific ones such as miR-124. We confirmed that overexpression of miR-124 increases both SINV structural protein translation and 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. Both inhibition of miR-124 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 alphaviruses as its inhibition 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.IMPORTANCEArthropod-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.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Micro (mi)RNAs are small regulatory RNAs, which act by modulating 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 host mRNAs and this can result in a positive or negative outcome for the virus. Here, we performed a fluorescence-based 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 Sindbis virus (SINV) expressing GFP, among which a number of neuron-specific ones such as miR-124. We confirmed that overexpression of miR-124 increases both SINV structural protein translation and 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. Both inhibition of miR-124 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 alphaviruses as its inhibition 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.IMPORTANCEArthropod-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.
Herzog K, Bandiera S, Pernot S, Fauvelle C, Jühling F, Weiss A, Bull A, Durand S C, Chane-Woon-Ming B, Pfeffer S, Mercey M, Lerat H, Meunier J C, Raffelsberger W, Brino L, Baumert T F, Zeisel M B
In: Gut, vol. 69, no. 2, pp. 380-392, 2020, ISBN: 31076402.
Abstract | Links | BibTeX | Tags: HCV hepatitis C hepatocyte molecular mechanisms, PFEFFER, Unité ARN
@article{,
title = {Functional microRNA screen uncovers O-linked N-acetylglucosamine transferase as a host factor modulating hepatitis C virus morphogenesis and infectivity},
author = {K Herzog and S Bandiera and S Pernot and C Fauvelle and F Jühling and A Weiss and A Bull and S C Durand and B Chane-Woon-Ming and S Pfeffer and M Mercey and H Lerat and J C Meunier and W Raffelsberger and L Brino and T F Baumert and M B Zeisel},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31076402?dopt=Abstract},
doi = {10.1136/gutjnl-2018-317423},
isbn = {31076402},
year = {2020},
date = {2020-01-01},
journal = {Gut},
volume = {69},
number = {2},
pages = {380-392},
abstract = {OBJECTIVE:
Infection of human hepatocytes by the hepatitis C virus (HCV) is a multistep process involving both viral and host factors. microRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Given that miRNAs were indicated to regulate between 30% and 75% of all human genes, we aimed to investigate the functional and regulatory role of miRNAs for the HCV life cycle.
DESIGN:
To systematically reveal human miRNAs affecting the HCV life cycle, we performed a two-step functional high-throughput miRNA mimic screen in Huh7.5.1 cells infected with recombinant cell culture-derived HCV. miRNA targeting was then assessed using a combination of computational and functional approaches.
RESULTS:
We uncovered miR-501-3p and miR-619-3p as novel modulators of HCV assembly/release. We discovered that these miRNAs regulate O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) protein expression and identified OGT and O-GlcNAcylation as regulators of HCV morphogenesis and infectivity. Furthermore, increased OGT expression in patient-derived liver tissue was associated with HCV-induced liver disease and cancer.
CONCLUSION:
miR-501-3p and miR-619-3p and their target OGT are previously undiscovered regulatory host factors for HCV assembly and infectivity. In addition to its effect on HCV morphogenesis, OGT may play a role in HCV-induced liver disease and hepatocarcinogenesis.},
keywords = {HCV hepatitis C hepatocyte molecular mechanisms, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
OBJECTIVE:
Infection of human hepatocytes by the hepatitis C virus (HCV) is a multistep process involving both viral and host factors. microRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Given that miRNAs were indicated to regulate between 30% and 75% of all human genes, we aimed to investigate the functional and regulatory role of miRNAs for the HCV life cycle.
DESIGN:
To systematically reveal human miRNAs affecting the HCV life cycle, we performed a two-step functional high-throughput miRNA mimic screen in Huh7.5.1 cells infected with recombinant cell culture-derived HCV. miRNA targeting was then assessed using a combination of computational and functional approaches.
RESULTS:
We uncovered miR-501-3p and miR-619-3p as novel modulators of HCV assembly/release. We discovered that these miRNAs regulate O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) protein expression and identified OGT and O-GlcNAcylation as regulators of HCV morphogenesis and infectivity. Furthermore, increased OGT expression in patient-derived liver tissue was associated with HCV-induced liver disease and cancer.
CONCLUSION:
miR-501-3p and miR-619-3p and their target OGT are previously undiscovered regulatory host factors for HCV assembly and infectivity. In addition to its effect on HCV morphogenesis, OGT may play a role in HCV-induced liver disease and hepatocarcinogenesis.
Infection of human hepatocytes by the hepatitis C virus (HCV) is a multistep process involving both viral and host factors. microRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Given that miRNAs were indicated to regulate between 30% and 75% of all human genes, we aimed to investigate the functional and regulatory role of miRNAs for the HCV life cycle.
DESIGN:
To systematically reveal human miRNAs affecting the HCV life cycle, we performed a two-step functional high-throughput miRNA mimic screen in Huh7.5.1 cells infected with recombinant cell culture-derived HCV. miRNA targeting was then assessed using a combination of computational and functional approaches.
RESULTS:
We uncovered miR-501-3p and miR-619-3p as novel modulators of HCV assembly/release. We discovered that these miRNAs regulate O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) protein expression and identified OGT and O-GlcNAcylation as regulators of HCV morphogenesis and infectivity. Furthermore, increased OGT expression in patient-derived liver tissue was associated with HCV-induced liver disease and cancer.
CONCLUSION:
miR-501-3p and miR-619-3p and their target OGT are previously undiscovered regulatory host factors for HCV assembly and infectivity. In addition to its effect on HCV morphogenesis, OGT may play a role in HCV-induced liver disease and hepatocarcinogenesis.
Girardi E, Pfeffer S, Baumert T F, Majzoub K
Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell Journal Article
In: Semin Cell Dev Biol, vol. S1084-9521, no. 20, pp. 30091-4, 2020, ISBN: 32847707.
Abstract | Links | BibTeX | Tags: Innate Immunity RNA biology RNA viruses Technology Viral RNA sensing Viral Translation Virology., PFEFFER, Unité ARN
@article{,
title = {Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell},
author = {E Girardi and S Pfeffer and T F Baumert and K Majzoub},
url = {https://pubmed.ncbi.nlm.nih.gov/32847707/},
doi = {10.1016/j.semcdb.2020.08.006},
isbn = {32847707},
year = {2020},
date = {2020-01-01},
journal = {Semin Cell Dev Biol},
volume = {S1084-9521},
number = {20},
pages = {30091-4},
abstract = {As obligate intracellular parasites with limited coding capacity, RNA viruses rely on host cells to complete their multiplication cycle. Viral RNAs (vRNAs) are central to infection. They carry all the necessary information for a virus to synthesize its proteins, replicate and spread and could also play essential non-coding roles. Regardless of its origin or tropism, vRNA has by definition evolved in the presence of host RNA Binding Proteins (RBPs), which resulted in intricate and complicated interactions with these factors. While on one hand some host RBPs recognize vRNA as non-self and mobilize host antiviral defenses, vRNA must also co-opt other host RBPs to promote viral infection. Focusing on pathogenic RNA viruses, we will review important scenarios of RBP-vRNA interactions during which host RBPs recognize, modify or degrade vRNAs. We will then focus on how vRNA hijacks the largest ribonucleoprotein complex (RNP) in the cell, the ribosome, to selectively promote the synthesis of its proteins. We will finally reflect on how novel technologies are helping in deepening our understanding of vRNA-host RBPs interactions, which can be ultimately leveraged to combat everlasting viral threats.},
keywords = {Innate Immunity RNA biology RNA viruses Technology Viral RNA sensing Viral Translation Virology., PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
As obligate intracellular parasites with limited coding capacity, RNA viruses rely on host cells to complete their multiplication cycle. Viral RNAs (vRNAs) are central to infection. They carry all the necessary information for a virus to synthesize its proteins, replicate and spread and could also play essential non-coding roles. Regardless of its origin or tropism, vRNA has by definition evolved in the presence of host RNA Binding Proteins (RBPs), which resulted in intricate and complicated interactions with these factors. While on one hand some host RBPs recognize vRNA as non-self and mobilize host antiviral defenses, vRNA must also co-opt other host RBPs to promote viral infection. Focusing on pathogenic RNA viruses, we will review important scenarios of RBP-vRNA interactions during which host RBPs recognize, modify or degrade vRNAs. We will then focus on how vRNA hijacks the largest ribonucleoprotein complex (RNP) in the cell, the ribosome, to selectively promote the synthesis of its proteins. We will finally reflect on how novel technologies are helping in deepening our understanding of vRNA-host RBPs interactions, which can be ultimately leveraged to combat everlasting viral threats.
Ghosh S, Guimaraes J C, Lanzafame M, Schmidt A, Syed A P, Dimitriades B, Börsch A, Ghosh S, Mittal N, Montavon T, Correia A L, Danner J, Meister G, Terracciano L M, Pfeffer S, Piscuoglio S, Zavolan M
Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation Journal Article
In: EMBO J, pp. in press, 2020, ISBN: 32812257.
Abstract | Links | BibTeX | Tags: Argonaute 1 breast cancer endogenous dsRNA interferon response translation readthrough, PFEFFER, Unité ARN
@article{,
title = {Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation},
author = {S Ghosh and J C Guimaraes and M Lanzafame and A Schmidt and A P Syed and B Dimitriades and A Börsch and S Ghosh and N Mittal and T Montavon and A L Correia and J Danner and G Meister and L M Terracciano and S Pfeffer and S Piscuoglio and M Zavolan},
url = {https://pubmed.ncbi.nlm.nih.gov/32812257/},
doi = {10.15252/embj.2019103922},
isbn = {32812257},
year = {2020},
date = {2020-01-01},
journal = {EMBO J},
pages = {in press},
abstract = {Translational readthrough, i.e., elongation of polypeptide chains beyond the stop codon, was initially reported for viral RNA, but later found also on eukaryotic transcripts, resulting in proteome diversification and protein-level modulation. Here, we report that AGO1x, an evolutionarily conserved translational readthrough isoform of Argonaute 1, is generated in highly proliferative breast cancer cells, where it curbs accumulation of double-stranded RNAs (dsRNAs) and consequent induction of interferon responses and apoptosis. In contrast to other mammalian Argonaute protein family members with primarily cytoplasmic functions, AGO1x exhibits nuclear localization in the vicinity of nucleoli. We identify AGO1x interaction with the polyribonucleotide nucleotidyltransferase 1 (PNPT1) and show that the depletion of this protein further augments dsRNA accumulation. Our study thus uncovers a novel function of an Argonaute protein in buffering the endogenous dsRNA-induced interferon responses, different than the canonical function of AGO proteins in the miRNA effector pathway. As AGO1x expression is tightly linked to breast cancer cell proliferation, our study thus suggests a new direction for limiting tumor growth.},
keywords = {Argonaute 1 breast cancer endogenous dsRNA interferon response translation readthrough, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Translational readthrough, i.e., elongation of polypeptide chains beyond the stop codon, was initially reported for viral RNA, but later found also on eukaryotic transcripts, resulting in proteome diversification and protein-level modulation. Here, we report that AGO1x, an evolutionarily conserved translational readthrough isoform of Argonaute 1, is generated in highly proliferative breast cancer cells, where it curbs accumulation of double-stranded RNAs (dsRNAs) and consequent induction of interferon responses and apoptosis. In contrast to other mammalian Argonaute protein family members with primarily cytoplasmic functions, AGO1x exhibits nuclear localization in the vicinity of nucleoli. We identify AGO1x interaction with the polyribonucleotide nucleotidyltransferase 1 (PNPT1) and show that the depletion of this protein further augments dsRNA accumulation. Our study thus uncovers a novel function of an Argonaute protein in buffering the endogenous dsRNA-induced interferon responses, different than the canonical function of AGO proteins in the miRNA effector pathway. As AGO1x expression is tightly linked to breast cancer cell proliferation, our study thus suggests a new direction for limiting tumor growth.
2019
Spaety M E, Gries A, Badie A, Venkatasamy A, Romain B, Orvain C, Yanagihara K, Okamoto K, Jung A C, Mellitzer G, Pfeffer S, Gaiddon C
HDAC4 Levels Control Sensibility toward Cisplatin in Gastric Cancer via the p53-p73/BIK Pathway Journal Article
In: Cancers (Basel), vol. 11, no. 11, pp. 1747, 2019, ISBN: 31703394.
Abstract | Links | BibTeX | Tags: BIK HDAC4 cisplatin gastric cancer miR-140 p53 p73, PFEFFER, Unité ARN
@article{,
title = {HDAC4 Levels Control Sensibility toward Cisplatin in Gastric Cancer via the p53-p73/BIK Pathway},
author = {M E Spaety and A Gries and A Badie and A Venkatasamy and B Romain and C Orvain and K Yanagihara and K Okamoto and A C Jung and G Mellitzer and S Pfeffer and C Gaiddon},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31703394},
doi = {10.3390/cancers11111747},
isbn = {31703394},
year = {2019},
date = {2019-01-01},
journal = {Cancers (Basel)},
volume = {11},
number = {11},
pages = {1747},
abstract = {Gastric cancer (GC) remains a health issue due to the low efficiency of therapies, such as cisplatin. This unsatisfactory situation highlights the necessity of finding factors impacting GC sensibility to therapies. We analyzed the cisplatin pangenomic response in cancer cells and found HDAC4 as a major epigenetic regulator being inhibited. HDAC4 mRNA repression was partly mediated by the cisplatin-induced expression of miR-140. At a functional level, HDAC4 inhibition favored cisplatin cytotoxicity and reduced tumor growth. Inversely, overexpression of HDAC4 inhibits cisplatin cytotoxicity. Importantly, HDAC4 expression was found to be elevated in gastric tumors compared to healthy tissues, and in particular in specific molecular subgroups. Furthermore, mutations in HDAC4 correlate with good prognosis. Pathway analysis of genes whose expression in patients correlated strongly with HDAC4 highlighted DNA damage, p53 stabilization, and apoptosis as processes downregulated by HDAC4. This was further confirmed by silencing of HDAC4, which favored cisplatin-induced apoptosis characterized by cleavage of caspase 3 and induction of proapoptotic genes, such as BIK, in part via a p53-dependent mechanism. Altogether, these results reveal HDAC4 as a resistance factor for cisplatin in GC cells that impacts on patients' survival.},
keywords = {BIK HDAC4 cisplatin gastric cancer miR-140 p53 p73, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gastric cancer (GC) remains a health issue due to the low efficiency of therapies, such as cisplatin. This unsatisfactory situation highlights the necessity of finding factors impacting GC sensibility to therapies. We analyzed the cisplatin pangenomic response in cancer cells and found HDAC4 as a major epigenetic regulator being inhibited. HDAC4 mRNA repression was partly mediated by the cisplatin-induced expression of miR-140. At a functional level, HDAC4 inhibition favored cisplatin cytotoxicity and reduced tumor growth. Inversely, overexpression of HDAC4 inhibits cisplatin cytotoxicity. Importantly, HDAC4 expression was found to be elevated in gastric tumors compared to healthy tissues, and in particular in specific molecular subgroups. Furthermore, mutations in HDAC4 correlate with good prognosis. Pathway analysis of genes whose expression in patients correlated strongly with HDAC4 highlighted DNA damage, p53 stabilization, and apoptosis as processes downregulated by HDAC4. This was further confirmed by silencing of HDAC4, which favored cisplatin-induced apoptosis characterized by cleavage of caspase 3 and induction of proapoptotic genes, such as BIK, in part via a p53-dependent mechanism. Altogether, these results reveal HDAC4 as a resistance factor for cisplatin in GC cells that impacts on patients' survival.
Lopez P, Girardi E, Pfeffer S
[Importance of cellular microRNAs in the regulation of viral infections] Journal Article
In: Med Sci (Paris), vol. 35, no. 8-9, pp. 667-673, 2019, ISBN: 31532379.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{,
title = {[Importance of cellular microRNAs in the regulation of viral infections]},
author = {P Lopez and E Girardi and S Pfeffer},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31532379},
doi = {10.1051/medsci/2019130},
isbn = {31532379},
year = {2019},
date = {2019-01-01},
journal = {Med Sci (Paris)},
volume = {35},
number = {8-9},
pages = {667-673},
abstract = {Viruses are obligatory intracellular parasites that rely on a wide range of cellular factors to successfully accomplish their infectious cycle. Among those, micro (mi)RNAs have recently emerged as important modulators of viral infections. These small regulatory molecules act as repressors of gene expression. During infection, miRNAs can function by targeting either cellular or viral RNAs. In this review, we will recapitulate what has been reported to date on this interplay between cellular miRNAs and viruses and the effect on the infection. Furthermore, we will briefly discuss the possibilities of interfering with the infection through the modulation of this pathway to develop novel antiviral therapies.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Viruses are obligatory intracellular parasites that rely on a wide range of cellular factors to successfully accomplish their infectious cycle. Among those, micro (mi)RNAs have recently emerged as important modulators of viral infections. These small regulatory molecules act as repressors of gene expression. During infection, miRNAs can function by targeting either cellular or viral RNAs. In this review, we will recapitulate what has been reported to date on this interplay between cellular miRNAs and viruses and the effect on the infection. Furthermore, we will briefly discuss the possibilities of interfering with the infection through the modulation of this pathway to develop novel antiviral therapies.
2018
Olivier Petitjean Thomas Montavon, Pfeffer Sébastien
To have and have not, RNA interference as an antiviral defense system in mammals Journal Article
In: Virologie (Montrouge), vol. 22, no. 5, pp. 251-260, 2018, ISSN: 33111686 .
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{Petitjean2018,
title = {To have and have not, RNA interference as an antiviral defense system in mammals },
author = {Olivier Petitjean, Thomas Montavon and Sébastien Pfeffer},
url = {https://pubmed.ncbi.nlm.nih.gov/33111686/},
doi = { 10.1684/vir.2018.0748 },
issn = {33111686 },
year = {2018},
date = {2018-10-01},
journal = {Virologie (Montrouge)},
volume = {22},
number = {5},
pages = {251-260},
abstract = {RNA silencing is a small RNA based mechanism regulating gene expression and involved in many biological processes in most eukaryotes. In plants, nematodes and arthropods, this mechanism participates to antiviral defense. In mammals, although the RNA silencing machinery is present and needed for the microRNA pathway, its importance as an antiviral defense is still debated. In recent years, several studies have attempted to answer to the question of whether RNA silencing as an antiviral pathway is retained in mammals. However, these studies did not provide a clear answer yet. In this review, we will present the arguments for and against a relevant antiviral role of RNA interference (RNAi) in mammals, by discussing examples of active and functional mammalian antiviral RNAi in specific cell types and/or in specific conditions. },
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RNA silencing is a small RNA based mechanism regulating gene expression and involved in many biological processes in most eukaryotes. In plants, nematodes and arthropods, this mechanism participates to antiviral defense. In mammals, although the RNA silencing machinery is present and needed for the microRNA pathway, its importance as an antiviral defense is still debated. In recent years, several studies have attempted to answer to the question of whether RNA silencing as an antiviral pathway is retained in mammals. However, these studies did not provide a clear answer yet. In this review, we will present the arguments for and against a relevant antiviral role of RNA interference (RNAi) in mammals, by discussing examples of active and functional mammalian antiviral RNAi in specific cell types and/or in specific conditions.
Girardi E, López P, Pfeffer S
On the Importance of Host MicroRNAs During Viral Infection Journal Article
In: Front Genet, vol. 9, pp. 439, 2018, ISBN: 30333857.
Abstract | Links | BibTeX | Tags: defense mechanism hostpathogen interaction microRNA post-transcriptional regulation virus, PFEFFER, Unité ARN
@article{,
title = {On the Importance of Host MicroRNAs During Viral Infection},
author = {E Girardi and P López and S Pfeffer},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30333857?dopt=Abstract},
doi = {10.3389/fgene.2018.00439},
isbn = {30333857},
year = {2018},
date = {2018-01-01},
journal = {Front Genet},
volume = {9},
pages = {439},
abstract = {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.},
keywords = {defense mechanism hostpathogen interaction microRNA post-transcriptional regulation virus, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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.
Creugny A, Fender A, Pfeffer S
Regulation of primary-microRNA processing Journal Article
In: FEBS Lett, vol. 592, no. 12, pp. 1980-1996, 2018, ISBN: 29683487.
Abstract | Links | BibTeX | Tags: Drosha biogenesis microRNA regulation, PFEFFER, Unité ARN
@article{,
title = {Regulation of primary-microRNA processing},
author = {A Creugny and A Fender and S Pfeffer},
url = {https://www.ncbi.nlm.nih.gov/pubmed/29683487?dopt=Abstract},
doi = {10.1002/1873-3468.13067},
isbn = {29683487},
year = {2018},
date = {2018-01-01},
journal = {FEBS Lett},
volume = {592},
number = {12},
pages = {1980-1996},
abstract = {MicroRNAs (miRNAs) are evolutionarily conserved small regulatory RNAs that participate in the fine-tuning of many, if not all, fundamental biological processes. Molecular mechanisms involved in miRNA biogenesis and mode of action have been elucidated in the past two decades. Similar to many cellular pathways, miRNA processing and function can be globally or specifically regulated at several levels and by numerous proteins and RNAs. Given their role as fine-tuning molecules, it is essential for miRNA expression to be tightly regulated in order to maintain cellular homeostasis. Here, we review our current knowledge of the first step of their maturation occurring in the nucleus and how it can be specifically and dynamically modulated. This article is protected by copyright. All rights reserved.},
keywords = {Drosha biogenesis microRNA regulation, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
MicroRNAs (miRNAs) are evolutionarily conserved small regulatory RNAs that participate in the fine-tuning of many, if not all, fundamental biological processes. Molecular mechanisms involved in miRNA biogenesis and mode of action have been elucidated in the past two decades. Similar to many cellular pathways, miRNA processing and function can be globally or specifically regulated at several levels and by numerous proteins and RNAs. Given their role as fine-tuning molecules, it is essential for miRNA expression to be tightly regulated in order to maintain cellular homeostasis. Here, we review our current knowledge of the first step of their maturation occurring in the nucleus and how it can be specifically and dynamically modulated. This article is protected by copyright. All rights reserved.
Bortolamiol-Bécet D, Monsion B, Chapuis S, Hleibieh K, Scheidecker D, Alioua A, Bogaert F, Revers F, Brault V, Ziegler-Graff V
Phloem-Triggered Virus-Induced Gene Silencing Using a Recombinant Polerovirus Journal Article
In: Front Microbiol, vol. 9, pp. 2449, 2018, ISBN: 30405546.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN, VIGS phloem polerovirus suppressor of RNA silencing visual monitoring of infection
@article{,
title = {Phloem-Triggered Virus-Induced Gene Silencing Using a Recombinant Polerovirus},
author = {D Bortolamiol-Bécet and B Monsion and S Chapuis and K Hleibieh and D Scheidecker and A Alioua and F Bogaert and F Revers and V Brault and V Ziegler-Graff},
url = {https://www.ncbi.nlm.nih.gov/pubmed/30405546?dopt=Abstract},
doi = {10.3389/fmicb.2018.02449},
isbn = {30405546},
year = {2018},
date = {2018-01-01},
journal = {Front Microbiol},
volume = {9},
pages = {2449},
abstract = {The phloem-limited poleroviruses infect Arabidopsis thaliana without causing noticeable disease symptoms. In order to facilitate visual infection identification, we developed virus-induced gene silencing (VIGS) vectors derived from Turnip yellows virus (TuYV). Short sequences from the host gene AtCHLI1 required for chlorophyll biosynthesis [42 nucleotides in sense or antisense orientation or as an inverted-repeat (IR), or an 81 nucleotide sense fragment] were inserted into the 3' non-coding region of the TuYV genome to screen for the most efficient and robust silencing vector. All recombinant viruses produced a clear vein chlorosis phenotype on infected Arabidopsis plants due to the expression inhibition of the AtCHLI1 gene. The introduction of a sense-oriented sequence into TuYV genome resulted in a virus exhibiting a more sustainable chlorosis than the virus containing an IR of the same length. This observation was correlated with a higher stability of the sense sequence insertion in the viral genome. In order to evaluate the impact of the TuYV silencing suppressor P0 in the VIGS mechanism a P0 knock-out mutation was introduced into the recombinant TuYV viruses. They induced a similar but milder vein clearing phenotype due to lower viral accumulation. This indicates that P0 does not hinder the performances of the TuYV silencing effect and confirms that in the viral infection context, P0 has no major impact on the production, propagation and action of the short distance silencing signal in phloem cells. Finally, we showed that TuYV can be used to strongly silence the phloem specific AtRTM1 gene. The TuYV-derived VIGS vectors therefore represent powerful tools to easily detect and monitor TuYV in infected plants and conduct functional analysis of phloem-restricted genes. Moreover this example indicates the potential of poleroviruses for use in functional genomic studies of agronomic plants.},
keywords = {PFEFFER, Unité ARN, VIGS phloem polerovirus suppressor of RNA silencing visual monitoring of infection},
pubstate = {published},
tppubtype = {article}
}
The phloem-limited poleroviruses infect Arabidopsis thaliana without causing noticeable disease symptoms. In order to facilitate visual infection identification, we developed virus-induced gene silencing (VIGS) vectors derived from Turnip yellows virus (TuYV). Short sequences from the host gene AtCHLI1 required for chlorophyll biosynthesis [42 nucleotides in sense or antisense orientation or as an inverted-repeat (IR), or an 81 nucleotide sense fragment] were inserted into the 3' non-coding region of the TuYV genome to screen for the most efficient and robust silencing vector. All recombinant viruses produced a clear vein chlorosis phenotype on infected Arabidopsis plants due to the expression inhibition of the AtCHLI1 gene. The introduction of a sense-oriented sequence into TuYV genome resulted in a virus exhibiting a more sustainable chlorosis than the virus containing an IR of the same length. This observation was correlated with a higher stability of the sense sequence insertion in the viral genome. In order to evaluate the impact of the TuYV silencing suppressor P0 in the VIGS mechanism a P0 knock-out mutation was introduced into the recombinant TuYV viruses. They induced a similar but milder vein clearing phenotype due to lower viral accumulation. This indicates that P0 does not hinder the performances of the TuYV silencing effect and confirms that in the viral infection context, P0 has no major impact on the production, propagation and action of the short distance silencing signal in phloem cells. Finally, we showed that TuYV can be used to strongly silence the phloem specific AtRTM1 gene. The TuYV-derived VIGS vectors therefore represent powerful tools to easily detect and monitor TuYV in infected plants and conduct functional analysis of phloem-restricted genes. Moreover this example indicates the potential of poleroviruses for use in functional genomic studies of agronomic plants.
2016
Alsaleh G, Nehmar R, Blüml S, Schleiss C, Ostermann E, Dillenseger J P, Sayeh A, Choquet P, Dembele D, Francois A, Salmon J H, Paul N, Schabbauer G, Bierry G, Meyer A, Gottenberg J E, Haas G, Pfeffer S, Vallat L, Sibilia J, Bahram S, Georgel P
Reduced DICER1 expression bestows rheumatoid arthritis synoviocytes proinflammatory properties and resistance to apoptotic stimuli. Journal Article
In: Arthritis Rheumatol, vol. 68, no. 8, pp. 1839-1848, 2016, ISBN: 26882526.
Abstract | Links | BibTeX | Tags: DICER1 inflammation microRNA rheumatoid arthritis, PFEFFER, Unité ARN
@article{,
title = {Reduced DICER1 expression bestows rheumatoid arthritis synoviocytes proinflammatory properties and resistance to apoptotic stimuli.},
author = {G Alsaleh and R Nehmar and S Blüml and C Schleiss and E Ostermann and J P Dillenseger and A Sayeh and P Choquet and D Dembele and A Francois and J H Salmon and N Paul and G Schabbauer and G Bierry and A Meyer and J E Gottenberg and G Haas and S Pfeffer and L Vallat and J Sibilia and S Bahram and P Georgel},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26882526},
doi = {10.1002/art.39641},
isbn = {26882526},
year = {2016},
date = {2016-01-01},
journal = {Arthritis Rheumatol},
volume = {68},
number = {8},
pages = {1839-1848},
abstract = {Objectives While the regulatory role of individual microRNAs in rheumatoid arthritis is well established, the role of DICER1 in the pathogenesis of the disease has not yet been investigated. Here, we analyze the expression of factors involved in miRNA biogenesis in synoviocytes (FLS) from RA patients and monitored arthritis triggered by K/BxN serum transfer in Dicer-deficient mice. Methods Genes and precursor miRNAs expression was quantified by RT-qPCR. miRNAs macroarray profiling was monitored by RT-qPCR. Cytokines were quantified by ELISA. Experimental arthritis in mice was achieved by serum transfer from K/BxN donors. Apoptosis was quantified using an ELISA assay. Results Here we report decreased DICER1 and mature miRNA expression in synovial fibroblasts isolated from rheumatoid arthritis (RA) patients. These cells are hyperresponsive to LPS, as evidenced by increased IL-6 secretion upon stimulation. Experimental serum transfer arthritis in Dicer mouse mutants confirmed that unbalanced miRNAs biogenesis correlates with enhanced inflammatory response. Finally, synoviocytes from both RA patients and from Dicer mutant mouse exhibit increased resistance to apoptotic stimuli. Conclusion Our work further substantiates the important role of DICER1 in the maintenance of homeostasis and the regulation of inflammatory responses. This article is protected by copyright. All rights reserved.},
keywords = {DICER1 inflammation microRNA rheumatoid arthritis, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Objectives While the regulatory role of individual microRNAs in rheumatoid arthritis is well established, the role of DICER1 in the pathogenesis of the disease has not yet been investigated. Here, we analyze the expression of factors involved in miRNA biogenesis in synoviocytes (FLS) from RA patients and monitored arthritis triggered by K/BxN serum transfer in Dicer-deficient mice. Methods Genes and precursor miRNAs expression was quantified by RT-qPCR. miRNAs macroarray profiling was monitored by RT-qPCR. Cytokines were quantified by ELISA. Experimental arthritis in mice was achieved by serum transfer from K/BxN donors. Apoptosis was quantified using an ELISA assay. Results Here we report decreased DICER1 and mature miRNA expression in synovial fibroblasts isolated from rheumatoid arthritis (RA) patients. These cells are hyperresponsive to LPS, as evidenced by increased IL-6 secretion upon stimulation. Experimental serum transfer arthritis in Dicer mouse mutants confirmed that unbalanced miRNAs biogenesis correlates with enhanced inflammatory response. Finally, synoviocytes from both RA patients and from Dicer mutant mouse exhibit increased resistance to apoptotic stimuli. Conclusion Our work further substantiates the important role of DICER1 in the maintenance of homeostasis and the regulation of inflammatory responses. This article is protected by copyright. All rights reserved.
Haas G, Cetin S, Messmer M, Chane-Woon-Ming B, Terenzi O, Chicher J, Kuhn L, Hammann P, Pfeffer S
Identification of factors involved in target RNA-directed microRNA degradation. Journal Article
In: Nucleic Acids Res, vol. 44, no. 6, pp. 2873-2887, 2016, ISBN: 26809675.
Abstract | Links | BibTeX | Tags: PFEFFER, PPSE, Unité ARN
@article{,
title = {Identification of factors involved in target RNA-directed microRNA degradation.},
author = {G Haas and S Cetin and M Messmer and B Chane-Woon-Ming and O Terenzi and J Chicher and L Kuhn and P Hammann and S Pfeffer},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26809675?dopt=Abstract},
doi = {10.1093/nar/gkw040},
isbn = {26809675},
year = {2016},
date = {2016-01-01},
journal = {Nucleic Acids Res},
volume = {44},
number = {6},
pages = {2873-2887},
abstract = {The mechanism by which micro (mi)RNAs control their target gene expression is now well understood. It is however less clear how the level of miRNAs themselves is regulated. Under specific conditions, abundant and highly complementary target RNA can trigger miRNA degradation by a mechanism involving nucleotide addition and exonucleolytic degradation. One such mechanism has been previously observed to occur naturally during viral infection. To date, the molecular details of this phenomenon are not known. We report here that both the degree of complementarity and the ratio of miRNA/target abundance are crucial for the efficient decay of the small RNA. Using a proteomic approach based on the transfection of biotinylated antimiRNA oligonucleotides, we set to identify the factors involved in target-mediated miRNA degradation. Among the retrieved proteins, we identified members of the RNA-induced silencing complex, but also RNA modifying and degradation enzymes. We further validate and characterize the importance of one of these, the Perlman Syndrome 3'-5' exonuclease DIS3L2. We show that this protein interacts with Argonaute 2 and functionally validate its role in target-directed miRNA degradation both by artificial targets and in the context of mouse cytomegalovirus infection},
keywords = {PFEFFER, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The mechanism by which micro (mi)RNAs control their target gene expression is now well understood. It is however less clear how the level of miRNAs themselves is regulated. Under specific conditions, abundant and highly complementary target RNA can trigger miRNA degradation by a mechanism involving nucleotide addition and exonucleolytic degradation. One such mechanism has been previously observed to occur naturally during viral infection. To date, the molecular details of this phenomenon are not known. We report here that both the degree of complementarity and the ratio of miRNA/target abundance are crucial for the efficient decay of the small RNA. Using a proteomic approach based on the transfection of biotinylated antimiRNA oligonucleotides, we set to identify the factors involved in target-mediated miRNA degradation. Among the retrieved proteins, we identified members of the RNA-induced silencing complex, but also RNA modifying and degradation enzymes. We further validate and characterize the importance of one of these, the Perlman Syndrome 3'-5' exonuclease DIS3L2. We show that this protein interacts with Argonaute 2 and functionally validate its role in target-directed miRNA degradation both by artificial targets and in the context of mouse cytomegalovirus infection
Haar J, Contrant M, Bernhardt K, Feederle R, Diederichs S, Pfeffer S, Delecluse H J
The expression of a viral microRNA is regulated by clustering to allow optimal B cell transformation. Journal Article
In: Nucleic Acids Res, vol. 44, no. 3, pp. 1326-1341, 2016, ISBN: 26635399.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{,
title = {The expression of a viral microRNA is regulated by clustering to allow optimal B cell transformation.},
author = {J Haar and M Contrant and K Bernhardt and R Feederle and S Diederichs and S Pfeffer and H J Delecluse},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26635399?dopt=Abstract},
doi = {10.1093/nar/gkv1330},
isbn = {26635399},
year = {2016},
date = {2016-01-01},
journal = {Nucleic Acids Res},
volume = {44},
number = {3},
pages = {1326-1341},
abstract = {The Epstein-Barr virus (EBV) transforms B cells by expressing latent proteins and the BHRF1 microRNA cluster. MiR-BHRF1-3, its most transforming member, belongs to the recently identified group of weakly expressed microRNAs. We show here that miR-BHRF1-3 displays an unusually low propensity to form a stem-loop structure, an effect potentiated by miR-BHRF1-3's proximity to the BHRF1 polyA site. Cloning miR-BHRF1-2 or a cellular microRNA, but not a ribozyme, 5' of miR-BHRF1-3 markedly enhanced its expression. However, a virus carrying mutated miR-BHRF1-2 seed regions expressed miR-BHRF1-3 at normal levels and was fully transforming. Therefore, miR-BHRF1-2's role during transformation is independent of its seed regions, revealing a new microRNA function. Increasing the distance between miR-BHRF1-2 and miR-BHRF1-3 in EBV enhanced miR-BHRF1-3's expression but decreased its transforming potential. Thus, the expression of some microRNAs must be restricted to a narrow range, as achieved by placing miR-BHRF1-3 under the control of miR-BHRF1-2.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The Epstein-Barr virus (EBV) transforms B cells by expressing latent proteins and the BHRF1 microRNA cluster. MiR-BHRF1-3, its most transforming member, belongs to the recently identified group of weakly expressed microRNAs. We show here that miR-BHRF1-3 displays an unusually low propensity to form a stem-loop structure, an effect potentiated by miR-BHRF1-3's proximity to the BHRF1 polyA site. Cloning miR-BHRF1-2 or a cellular microRNA, but not a ribozyme, 5' of miR-BHRF1-3 markedly enhanced its expression. However, a virus carrying mutated miR-BHRF1-2 seed regions expressed miR-BHRF1-3 at normal levels and was fully transforming. Therefore, miR-BHRF1-2's role during transformation is independent of its seed regions, revealing a new microRNA function. Increasing the distance between miR-BHRF1-2 and miR-BHRF1-3 in EBV enhanced miR-BHRF1-3's expression but decreased its transforming potential. Thus, the expression of some microRNAs must be restricted to a narrow range, as achieved by placing miR-BHRF1-3 under the control of miR-BHRF1-2.
2015
Sorel O, Tuddenham L, Myster F, Palmeira L, Kerkhofs P, Pfeffer S, Vanderplasschen A, Dewals B G
Small RNA deep sequencing identifies viral microRNAs during malignant catarrhal fever induced by alcelaphine herpesvirus 1. Journal Article
In: J Gen Virol, vol. 96, no. 11, pp. 3360-3372, 2015, ISBN: 26329753.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{,
title = {Small RNA deep sequencing identifies viral microRNAs during malignant catarrhal fever induced by alcelaphine herpesvirus 1.},
author = {O Sorel and L Tuddenham and F Myster and L Palmeira and P Kerkhofs and S Pfeffer and A Vanderplasschen and B G Dewals},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26329753},
doi = {10.1099/jgv.0.000272},
isbn = {26329753},
year = {2015},
date = {2015-01-01},
journal = {J Gen Virol},
volume = {96},
number = {11},
pages = {3360-3372},
abstract = {Alcelaphine herpesvirus 1 (AlHV-1) is a γ-herpesvirus (γ-HV) carried asymptomatically by wildebeest. Upon cross-species transmission, AlHV-1 induces a fatal lymphoproliferative disease named malignant catarrhal fever (MCF) in many ruminants, including cattle and the rabbit model. Latency has been shown to be essential for MCF induction. However, the mechanisms causing the activation and proliferation of infected CD8+ T cells are unknown. Many γ-HVs express microRNAs (miRNAs). These small noncoding RNAs can regulate expression of host or viral target genes involved in various pathways and are thought to facilitate viral infection and/or mediate activation and proliferation of infected lymphocytes. AlHV-1 genome has been predicted to encode a large number of miRNAs. However, their precise contribution in viral infection and pathogenesis in vivo remains unknown. Here, using small RNAs cloning and sequencing we identified 36 potential miRNAs expressed in a lymphoblastoid cell line propagated from a calf infected with AlHV-1 and developing MCF. Among the sequenced candidate miRNAs, 32 were expressed on the reverse strand of the genome in two main clusters. The expression of these 32 viral miRNAs was further validated using northern blot and qRT-PCR in lymphoid organs of MCF-developing calves or rabbits. To determine the concerted contribution in MCF of 28 viral miRNAs clustered in the non-protein-coding region of the AlHV-1 genome, a recombinant virus was produced. The absence of these 28 miRNAs did not affect viral growth in vitro or MCF induction in rabbits, indicating that the AlHV-1 miRNAs clustered in this non-protein-coding genomic region are dispensable MCF induction.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Alcelaphine herpesvirus 1 (AlHV-1) is a γ-herpesvirus (γ-HV) carried asymptomatically by wildebeest. Upon cross-species transmission, AlHV-1 induces a fatal lymphoproliferative disease named malignant catarrhal fever (MCF) in many ruminants, including cattle and the rabbit model. Latency has been shown to be essential for MCF induction. However, the mechanisms causing the activation and proliferation of infected CD8+ T cells are unknown. Many γ-HVs express microRNAs (miRNAs). These small noncoding RNAs can regulate expression of host or viral target genes involved in various pathways and are thought to facilitate viral infection and/or mediate activation and proliferation of infected lymphocytes. AlHV-1 genome has been predicted to encode a large number of miRNAs. However, their precise contribution in viral infection and pathogenesis in vivo remains unknown. Here, using small RNAs cloning and sequencing we identified 36 potential miRNAs expressed in a lymphoblastoid cell line propagated from a calf infected with AlHV-1 and developing MCF. Among the sequenced candidate miRNAs, 32 were expressed on the reverse strand of the genome in two main clusters. The expression of these 32 viral miRNAs was further validated using northern blot and qRT-PCR in lymphoid organs of MCF-developing calves or rabbits. To determine the concerted contribution in MCF of 28 viral miRNAs clustered in the non-protein-coding region of the AlHV-1 genome, a recombinant virus was produced. The absence of these 28 miRNAs did not affect viral growth in vitro or MCF induction in rabbits, indicating that the AlHV-1 miRNAs clustered in this non-protein-coding genomic region are dispensable MCF induction.
Oussaief L, Fendri A, Chane-Woon-Ming B, Poirey R, Delecluse H J, Joab I, Pfeffer S
Modulation of the microRNA cluster miR-183-96-182 expression by the Epstein-Barr virus latent membrane protein 1. Journal Article
In: J Virol, vol. 89, no. 23, pp. 12178-12188, 2015, ISBN: 26401047.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{,
title = {Modulation of the microRNA cluster miR-183-96-182 expression by the Epstein-Barr virus latent membrane protein 1.},
author = {L Oussaief and A Fendri and B Chane-Woon-Ming and R Poirey and H J Delecluse and I Joab and S Pfeffer},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26401047?dopt=Abstract},
doi = {10.1128/JVI.01757-15},
isbn = {26401047},
year = {2015},
date = {2015-01-01},
journal = {J Virol},
volume = {89},
number = {23},
pages = {12178-12188},
abstract = {Epstein-Barr virus (EBV) is an oncogenic human herpesvirus involved in the pathogenesis of Burkitt's lymphoma (BL) and various other lymphoproliferative disorders. In BL, EBV protein expression is restricted to the EBNA1, but small non-coding RNAs such as the EBERs and micro (mi)RNAs can also be detected. miRNAs play major roles in crucial processes such as proliferation, differentiation and cell death. It has recently become clear that alteration in the expression profile of miRNAs contribute to the pathogenesis of a number of malignancies. During latent infection, EBV expresses 25 viral pre-miRNAs and modulates the expression of specific cellular miRNAs, such as miR-155 and miR-146, which potentially play a role in oncogenesis. Here, we established the small RNA expression profiles of three BL cell lines. Using large-scale sequencing coupled to northern blot and real-time RT-PCR analysis validation, we demonstrated the differential expression of some cellular and viral miRNAs. High-level expression of the miR-183-96-182 cluster and EBV miR-BART cluster was significantly associated with EBV type I latency. This expression was not affected by viral reactivation since TGF-β1 stimulation did not significantly change the miRNA profiles. However, using several approaches, including de novo infection with a mutant virus, we present evidence that the expression of latent membrane protein (LMP) 1 triggered down-regulation of the expression of the miR-183-96-182 cluster. We further show that this effect involves the Akt signaling pathway.
IMPORTANCE:
In addition to expressing their own miRNAs, herpesviruses also impact the expression levels of cellular miRNAs. This regulation can be either positive or negative and usually results in the perturbation of pathways to create a cellular environment that is more "virus-friendly". For example, EBV induces the expression of miR-155, a well-characterized oncomiR, which leads to increased cell proliferation and decreased cell death. Here, we show that EBV-encoded LMP-1 protein is also involved in the down-regulation of a cluster of three miRNAs, miR-183, -96 and -182, which are known to be also repressed in several cancers. We therefore identify yet another potential player in EBV-induced oncogenesis.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Epstein-Barr virus (EBV) is an oncogenic human herpesvirus involved in the pathogenesis of Burkitt's lymphoma (BL) and various other lymphoproliferative disorders. In BL, EBV protein expression is restricted to the EBNA1, but small non-coding RNAs such as the EBERs and micro (mi)RNAs can also be detected. miRNAs play major roles in crucial processes such as proliferation, differentiation and cell death. It has recently become clear that alteration in the expression profile of miRNAs contribute to the pathogenesis of a number of malignancies. During latent infection, EBV expresses 25 viral pre-miRNAs and modulates the expression of specific cellular miRNAs, such as miR-155 and miR-146, which potentially play a role in oncogenesis. Here, we established the small RNA expression profiles of three BL cell lines. Using large-scale sequencing coupled to northern blot and real-time RT-PCR analysis validation, we demonstrated the differential expression of some cellular and viral miRNAs. High-level expression of the miR-183-96-182 cluster and EBV miR-BART cluster was significantly associated with EBV type I latency. This expression was not affected by viral reactivation since TGF-β1 stimulation did not significantly change the miRNA profiles. However, using several approaches, including de novo infection with a mutant virus, we present evidence that the expression of latent membrane protein (LMP) 1 triggered down-regulation of the expression of the miR-183-96-182 cluster. We further show that this effect involves the Akt signaling pathway.
IMPORTANCE:
In addition to expressing their own miRNAs, herpesviruses also impact the expression levels of cellular miRNAs. This regulation can be either positive or negative and usually results in the perturbation of pathways to create a cellular environment that is more "virus-friendly". For example, EBV induces the expression of miR-155, a well-characterized oncomiR, which leads to increased cell proliferation and decreased cell death. Here, we show that EBV-encoded LMP-1 protein is also involved in the down-regulation of a cluster of three miRNAs, miR-183, -96 and -182, which are known to be also repressed in several cancers. We therefore identify yet another potential player in EBV-induced oncogenesis.
IMPORTANCE:
In addition to expressing their own miRNAs, herpesviruses also impact the expression levels of cellular miRNAs. This regulation can be either positive or negative and usually results in the perturbation of pathways to create a cellular environment that is more "virus-friendly". For example, EBV induces the expression of miR-155, a well-characterized oncomiR, which leads to increased cell proliferation and decreased cell death. Here, we show that EBV-encoded LMP-1 protein is also involved in the down-regulation of a cluster of three miRNAs, miR-183, -96 and -182, which are known to be also repressed in several cancers. We therefore identify yet another potential player in EBV-induced oncogenesis.
Mailly L, Xiao F, Lupberger J, Wilson G K, Aubert P, Duong F H, Calabrese D, Leboeuf C, Fofana I, Thumann C, Bandiera S, Lütgehetmann M, Volz T, Davis C, Harris H J, Mee C J, Girardi E, Chane-Woon-Ming B, Ericsson M, Fletcher N, Bartenschlager R, Pessaux P, Vercauteren K, Meuleman P, Villa P, Kaderali L, Pfeffer S, Heim M H, Neunlist M, Zeisel M B, Dandri M, McKeating J A, Robinet E, Baumert T F
Clearance of persistent hepatitis C virus infection in humanized mice using a claudin-1-targeting monoclonal antibody. Journal Article
In: Nat Biotechnol, vol. 33, no. 5, pp. 549-554, 2015, ISBN: 25798937.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{,
title = {Clearance of persistent hepatitis C virus infection in humanized mice using a claudin-1-targeting monoclonal antibody.},
author = {L Mailly and F Xiao and J Lupberger and G K Wilson and P Aubert and F H Duong and D Calabrese and C Leboeuf and I Fofana and C Thumann and S Bandiera and M Lütgehetmann and T Volz and C Davis and H J Harris and C J Mee and E Girardi and B Chane-Woon-Ming and M Ericsson and N Fletcher and R Bartenschlager and P Pessaux and K Vercauteren and P Meuleman and P Villa and L Kaderali and S Pfeffer and M H Heim and M Neunlist and M B Zeisel and M Dandri and J A McKeating and E Robinet and T F Baumert},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25798937?dopt=Abstract},
doi = {10.1038/nbt.3179},
isbn = {25798937},
year = {2015},
date = {2015-01-01},
journal = {Nat Biotechnol},
volume = {33},
number = {5},
pages = {549-554},
abstract = {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.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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.
Girardi E, Lefèvre M, Chane-Woon-Ming B, Paro S, Claydon B, Imler JL, Meignin C, Pfeffer S
Cross-species comparative analysis of Dicer proteins during Sindbis virus infection. Journal Article
In: Sci Rep, vol. 5, pp. 10693, 2015, ISBN: 26024431.
Abstract | Links | BibTeX | Tags: meignin, PFEFFER, Unité ARN
@article{,
title = {Cross-species comparative analysis of Dicer proteins during Sindbis virus infection.},
author = {E Girardi and M Lefèvre and B Chane-Woon-Ming and S Paro and B Claydon and JL Imler and C Meignin and S Pfeffer},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26024431?dopt=Abstract},
doi = {10.1038/srep10693},
isbn = {26024431},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
journal = {Sci Rep},
volume = {5},
pages = {10693},
abstract = {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.},
keywords = {meignin, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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.
Bandiera S, Pfeffer S, Baumert T F, Zeisel M B
miR-122 - a key factor and therapeutic target in liver disease. Journal Article
In: J Hepatol, vol. 62, no. 2, pp. 448-457, 2015, ISBN: 25308172.
Abstract | Links | BibTeX | Tags: HBV HCC HCV Hepatitis Liver disease pathogenesis miR-122, PFEFFER, Unité ARN
@article{,
title = {miR-122 - a key factor and therapeutic target in liver disease.},
author = {S Bandiera and S Pfeffer and T F Baumert and M B Zeisel},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25308172?dopt=Abstract},
doi = {10.1016/j.jhep.2014.10.004},
isbn = {25308172},
year = {2015},
date = {2015-01-01},
journal = {J Hepatol},
volume = {62},
number = {2},
pages = {448-457},
abstract = {Being the largest internal organ of the human body with the unique ability of self-regeneration, the liver is involved in a wide variety of vital functions that require highly orchestrated and controlled biochemical processes. Increasing evidence suggests that microRNA (miRNA) are essential for the regulation of liver development, regeneration and metabolic functions. Hence, alterations in intrahepatic miRNA networks have been associated with liver disease including hepatitis, steatosis, cirrhosis and hepatocellular carcinoma (HCC). miR-122 is the most frequent miRNA in the adult liver, and a central player in liver biology and disease. Furthermore, miR-122 has been shown to be an essential host factor for hepatitis C virus (HCV) infection and an antiviral target complementary to standard of care using direct-acting antivirals or interferon-based treatment. This review summarizes our current understanding of the key role of miR-122 in liver physiology and disease highlighting its role in HCC and viral hepatitis. We also discuss the perspectives of miRNA-based therapeutic approaches for viral hepatitis and liver disease.},
keywords = {HBV HCC HCV Hepatitis Liver disease pathogenesis miR-122, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Being the largest internal organ of the human body with the unique ability of self-regeneration, the liver is involved in a wide variety of vital functions that require highly orchestrated and controlled biochemical processes. Increasing evidence suggests that microRNA (miRNA) are essential for the regulation of liver development, regeneration and metabolic functions. Hence, alterations in intrahepatic miRNA networks have been associated with liver disease including hepatitis, steatosis, cirrhosis and hepatocellular carcinoma (HCC). miR-122 is the most frequent miRNA in the adult liver, and a central player in liver biology and disease. Furthermore, miR-122 has been shown to be an essential host factor for hepatitis C virus (HCV) infection and an antiviral target complementary to standard of care using direct-acting antivirals or interferon-based treatment. This review summarizes our current understanding of the key role of miR-122 in liver physiology and disease highlighting its role in HCC and viral hepatitis. We also discuss the perspectives of miRNA-based therapeutic approaches for viral hepatitis and liver disease.
2014
Stik G, Muylkens B, Coupeau D, Laurent S, Dambrine G, Messmer M, Chane-Woon-Ming B, Pfeffer S, Rasschaert D
Small RNA cloning and sequencing strategy affects host and viral microRNA expression signatures Journal Article
In: J Biotechnol, vol. 181, pp. 35-44, 2014, ISBN: 24746587.
Abstract | Links | BibTeX | Tags: Marek's disease virus MicroRNA Small RNA cloning and sequencing Viral infection, PFEFFER, Unité ARN
@article{,
title = {Small RNA cloning and sequencing strategy affects host and viral microRNA expression signatures},
author = {G Stik and B Muylkens and D Coupeau and S Laurent and G Dambrine and M Messmer and B Chane-Woon-Ming and S Pfeffer and D Rasschaert},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24746587},
doi = {10.1016/j.jbiotec.2014.04.005},
isbn = {24746587},
year = {2014},
date = {2014-01-01},
journal = {J Biotechnol},
volume = {181},
pages = {35-44},
abstract = {The establishment of the microRNA (miRNA) expression signatures is the basic element to investigate the role played by these regulatory molecules in the biology of an organism. Marek's disease virus 1 (MDV-1) is an avian herpesvirus that naturally infects chicken and induces T cells lymphomas. During latency, MDV-1, like other herpesviruses, expresses a limited subset of transcripts. These include three miRNA clusters. Several studies identified the expression of virus and host encoded miRNAs from MDV-1 infected cell cultures and chickens. But a high discrepancy was observed when miRNA cloning frequencies obtained from different cloning and sequencing protocols were compared. Thus, we analyzed the effect of small RNA library preparation and sequencing on the miRNA frequencies obtained from the same RNA samples collected during MDV-1 infection of chicken at different steps of the oncoviral pathogenesis. Qualitative and quantitative variations were found in the data, depending on the strategy used. One of the mature miRNA derived from the latency-associated-transcript (LAT), mdv1-miR-M7-5p, showed the highest variation. Its cloning frequency was 50% of the viral miRNA counts when a small scale sequencing approach was used. Its frequency was 100 times less abundant when determined through the deep sequencing approach. Northern blot analysis showed a better correlation with the miRNA frequencies found by the small scale sequencing approach. By analyzing the cellular miRNA repertoire, we also found a gap between the two sequencing approaches. Collectively, our study indicates that next-generation sequencing data considered alone are limited for assessing the absolute copy number of transcripts. Thus, the quantification of small RNA should be addressed by compiling data obtained by using different techniques such as microarrays, qRT-PCR and NB analysis in support of high throughput sequencing data. These observations should be considered when miRNA variations are studied prior addressing functional studies.},
keywords = {Marek's disease virus MicroRNA Small RNA cloning and sequencing Viral infection, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The establishment of the microRNA (miRNA) expression signatures is the basic element to investigate the role played by these regulatory molecules in the biology of an organism. Marek's disease virus 1 (MDV-1) is an avian herpesvirus that naturally infects chicken and induces T cells lymphomas. During latency, MDV-1, like other herpesviruses, expresses a limited subset of transcripts. These include three miRNA clusters. Several studies identified the expression of virus and host encoded miRNAs from MDV-1 infected cell cultures and chickens. But a high discrepancy was observed when miRNA cloning frequencies obtained from different cloning and sequencing protocols were compared. Thus, we analyzed the effect of small RNA library preparation and sequencing on the miRNA frequencies obtained from the same RNA samples collected during MDV-1 infection of chicken at different steps of the oncoviral pathogenesis. Qualitative and quantitative variations were found in the data, depending on the strategy used. One of the mature miRNA derived from the latency-associated-transcript (LAT), mdv1-miR-M7-5p, showed the highest variation. Its cloning frequency was 50% of the viral miRNA counts when a small scale sequencing approach was used. Its frequency was 100 times less abundant when determined through the deep sequencing approach. Northern blot analysis showed a better correlation with the miRNA frequencies found by the small scale sequencing approach. By analyzing the cellular miRNA repertoire, we also found a gap between the two sequencing approaches. Collectively, our study indicates that next-generation sequencing data considered alone are limited for assessing the absolute copy number of transcripts. Thus, the quantification of small RNA should be addressed by compiling data obtained by using different techniques such as microarrays, qRT-PCR and NB analysis in support of high throughput sequencing data. These observations should be considered when miRNA variations are studied prior addressing functional studies.
Pfeffer S
Herpesviruses Encode Their Own MicroRNAs. Journal Article
In: Clin Chem, vol. 60, no. 5, pp. 791-792, 2014, ISBN: 24778302.
Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{,
title = {Herpesviruses Encode Their Own MicroRNAs.},
author = {S Pfeffer},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24778302?dopt=Abstract},
doi = {10.1373/clinchem.2013.216408},
isbn = {24778302},
year = {2014},
date = {2014-01-01},
journal = {Clin Chem},
volume = {60},
number = {5},
pages = {791-792},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2012
Tuddenham L, Jung J S, Chane-Woon-Ming B, Dölken L, Pfeffer S
Small RNA deep-sequencing identifies microRNAs and other small non-coding RNAs from human herpesvirus 6 (HHV-6B). Journal Article
In: J Virol, vol. 86, pp. 1638-1649, 2012, ISBN: 22114334, (Published ahead of print 23 November 2011).
Abstract | Links | BibTeX | Tags: MicroRNA Roseolovirus HHV-6 Sup-T-1 OriLyt, PFEFFER, Unité ARN
@article{,
title = {Small RNA deep-sequencing identifies microRNAs and other small non-coding RNAs from human herpesvirus 6 (HHV-6B).},
author = {L Tuddenham and J S Jung and B Chane-Woon-Ming and L Dölken and S Pfeffer},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22114334},
doi = {10.1128/ JVI.05911-11},
isbn = {22114334},
year = {2012},
date = {2012-01-01},
journal = {J Virol},
volume = {86},
pages = {1638-1649},
abstract = {Roseolovirus, or human herpesvirus 6 (HHV-6) is a ubiquitous human pathogen infecting over 95% of the population by the age of two years. As with other herpesviruses, reactivation of HHV-6 can present with severe complications in immunocompromised individuals. Recent studies have highlighted the importance of herpesvirus-derived micro (mi)RNAs in modulating both cellular and viral gene expression. An initial report, which computed the likelihood of various viruses to encode for miRNAs, did not predict HHV-6 miRNAs. To experimentally screen for small HHV-6 encoded RNAs, we conducted large-scale sequencing of Sup-T-1 cells lytically infected with a laboratory strain of HHV-6B. This revealed an abundant 60-65 nucleotide RNA of unknown function derived from the lytic origin of replication (OriLyt) that gave rise to smaller RNA species of 18-19 nucleotides in length. In addition, we identified four pre-miRNAs, whose mature forms accumulated in Argonaute 2. In contrast to other beta-herpesviruses, HHV-6B miRNAs are expressed from direct repeat regions (DR(L) and DR(R)) located at either side of the genome. All miRNAs are conserved in the closely related HHV-6A variant, and one of them is a seed ortholog of the human miR-582-5p. Similar to alpha-herpesvirus miRNAs, they are expressed antisense to immediate early ORFs and thus have the potential to regulate key viral regulators.},
note = {Published ahead of print 23 November 2011},
keywords = {MicroRNA Roseolovirus HHV-6 Sup-T-1 OriLyt, PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Roseolovirus, or human herpesvirus 6 (HHV-6) is a ubiquitous human pathogen infecting over 95% of the population by the age of two years. As with other herpesviruses, reactivation of HHV-6 can present with severe complications in immunocompromised individuals. Recent studies have highlighted the importance of herpesvirus-derived micro (mi)RNAs in modulating both cellular and viral gene expression. An initial report, which computed the likelihood of various viruses to encode for miRNAs, did not predict HHV-6 miRNAs. To experimentally screen for small HHV-6 encoded RNAs, we conducted large-scale sequencing of Sup-T-1 cells lytically infected with a laboratory strain of HHV-6B. This revealed an abundant 60-65 nucleotide RNA of unknown function derived fr