Characterization of two candidate genes, NCoA3 and IRF8, potentially involved in the control of HIV-1 latency

BACKGROUND: The persistence of latent HIV-1 reservoirs is the principal barrier preventing the eradication of HIV-1 infection in patients by current antiretroviral therapy. It is thus crucial to understand the molecular mechanisms involved in the establishment, maintenance and reactivation of HIV-1 latency. Since chromatin remodeling has been implicated in the transcriptional reactivation of the HIV-1 promoter, we assessed the role of the histone deacetylase inhibitor sodium butyrate (NaB) on two HIV-1 latently infected cell lines (U1 and ACH-2) gene expression. RESULTS: Analysis of microarrays data led us to select two candidate genes: NCoA3 (Nuclear Receptor Coactivator 3), a nuclear receptor coactivator and IRF8 (Interferon Regulatory Factor 8), an interferon regulatory factor. NCoA3 gene expression is upregulated following NaB treatment of latently infected cells whereas IRF8 gene expression is strongly downregulated in the promonocytic cell line following NaB treatment. Their differential expressions were confirmed at the transcriptional and translational levels. Moreover, NCoA3 gene expression was also upregulated after treatment of U1 and ACH-2 cells with phorbol myristyl acetate (PMA) but not trichostatin A (TSA) and after treatment with NaB of two others HIV-1 latently infected cell lines (OM10.1 and J1.1). IRF8 gene is only expressed in U1 cells and was also downregulated after treatment with PMA or TSA. Functional analyses confirmed that NCoA3 synergizes with Tat to enhance HIV-1 promoter transcription and that IRF8 represses the IRF1-mediated activation through the HIV-1 promoter Interferon-stimulated response element (ISRE). CONCLUSION: These results led us to postulate that NCoA3 could be involved in the transcriptional reactivation of the HIV-1 promoter from latency and that IRF8 may contribute to the maintenance of the latent state in the promonocytic cell line. Implication of these factors in the maintenance or reactivation of the viral latency may provide potential new targets to control HIV-1 replication in latent viral reservoirs

Interactions du VIH-1 avec ses cellules cibles : recherche de nouveaux réservoirs et analyse du contrôle de la latence

The identification of HIV cellular reservoirs and the understanding of the molecular mechanisms involved in the maintenance and reactivation of HIV latency are crucial to elaborate an efficient strategy to eliminate HIV from the body. My thesis project focused, on one hand, on the susceptibility of adipose tissue to HIV infection and its potential role as a new target tissue, and on the other hand, on the search for cellular candidates genes involved in the control of HIV latency.Firstly, we would like to determine whether the low viral production observed after infection of human adipose cells with HIV was due to low infection or replication efficiency. We showed that infection with viral particles pseudotyped with X4 and R5 envelope is restricted due to insufficient viral receptor co-expression levels in preadipocytes. These results suggested that adipose tissue is not a preferential target for HIV in vivo and could not be considered as a new reservoir for the virus.Secondly, we analysed differential gene expression on two HIV latently infected cell lines stimulated or not for the reactivation of latency by an histone deacetylase inhibitor. Analysis of microarrays data led us to select two candidate genes: NCoA3 and IRF8. We confirmed their differential expression at the transcriptional and translational levels and we analysed their functional role on HIV transcription. These results led us to postulate that NCoA3 and IRF8 could be involved respectively in the reactivation and maintenance of HIV latency.L'identification des réservoirs cellulaires du VIH ainsi que la compréhension des mécanismes moléculaires impliqués dans le maintien et la réactivation de la latence sont essentiels afin d'élaborer une stratégie efficace pour éliminer le virus de l'organisme. Mon travail de thèse a porté d'une part, sur l'étude de l'infection du tissu adipeux par le VIH et son rôle potentiel comme nouveau tissu cible, et d'autre part, sur la recherche de gènes cellulaires candidats impliqués dans le contrôle de la latence du VIH.Dans un premier temps, nous avons voulu déterminer si la faible production virale obtenue après infection des préadipocytes par le VIH est due à une faible efficacité d'infection ou de réplication. Nous avons montré que l'infection par les virus pseudotypés avec des glycoprotéines d'enveloppe de tropisme X4 et R5 est restreinte en raison d'une co-expression insuffisante des récepteurs viraux à la surface des préadipocytes. Cela suggère que le tissu adipeux n'est pas une cible privilégiée pour le virus in vivo et ne peut donc être considéré comme un nouveau réservoir pour le VIH.Dans un deuxième temps, nous avons analysé le transcriptome différentiel de lignées cellulaires infectées de façon latente par le VIH et stimulées ou non pour la réactivation de la latence par un inhibiteur d'histone déacétylase. Parmi les gènes caractérisés, deux nous ont paru particulièrement intéressants : NCoA3 et IRF8. Après avoir confirmé les modifications de l'expression de ces gènes, nous avons analysé leurs rôles fonctionnels sur la transcription du VIH. Les facteurs NCoA3 et IRF8 pourraient respectivement être impliqués dans la réactivation et le maintien de la latence virale

Interactions du VIH-1 avec ses cellules cibles (recherche de nouveaux réservoirs et analyse du contrôle de la latence)

PARIS7-Bibliothèque centrale (751132105) / SudocCACHAN-ENS (940162301) / SudocSudocFranceF

Experimental Approaches to Study Genome Packaging of Influenza A Viruses

International audienceThe genome of influenza A viruses (IAV) consists of eight single-stranded negative sense viral RNAs (vRNAs) encapsidated into viral ribonucleoproteins (vRNPs). It is now well established that genome packaging (i.e., the incorporation of a set of eight distinct vRNPs into budding viral particles), follows a specific pathway guided by segment-specific cis-acting packaging signals on each vRNA. However, the precise nature and function of the packaging signals, and the mechanisms underlying the assembly of vRNPs into sub-bundles in the cytoplasm and their selective packaging at the viral budding site, remain largely unknown. Here, we review the diverse and complementary methods currently being used to elucidate these aspects of the viral cycle. They range from conventional and competitive reverse genetics, single molecule imaging of vRNPs by fluorescence in situ hybridization (FISH) and high-resolution electron microscopy and tomography of budding viral particles, to solely in vitro approaches to investigate vRNA-vRNA interactions at the molecular level

Nuclear Import Defect of Human Immunodeficiency Virus Type 1 DNA Flap Mutants Is Not Dependent on the Viral Strain or Target Cell Type

We have previously established, using human immunodeficiency virus type 1 (HIV-1) strain LAI, that the HIV-1 central DNA Flap acts as a cis determinant of viral genome nuclear import. Although the impact of the DNA Flap on nuclear import has already found numerous independent confirmations in the context of lentivirus vectors, it has been claimed that it may be nonessential for infectious virus strains LAI, YU-2 (J. D. Dvorin et al., J. Virol. 76:12087-12096, 2002), HXB2, and NL4-3 (A. Limon et al., J. Virol. 76:12078-12086, 2002). We conducted a detailed analysis of virus infectivity using the provirus clones provided by the authors and analogous target cells. In contrast to published data, our results show that all cPPT mutant viruses exhibit reduced infectivity corresponding to a nuclear import defect irrespective of the viral genetic background or target cell

Influenza B Virus Infection Is Enhanced Upon Heterotypic Co-infection With Influenza A Virus

International audienceHomotypic co-infections with influenza viruses are described to increase genetic population diversity, to drive viral evolution and to allow genetic complementation. Less is known about heterotypic co-infections between influenza A (IAV) and influenza B (IBV) viruses. Previous publications showed that IAV replication was suppressed upon co-infection with IBV. However, the effect of heterotypic co-infections on IBV replication was not investigated. To do so, we produced by reverse genetics a pair of replication-competent recombinant IAV (A/WSN/33) and IBV (B/Brisbane/60/2008) expressing a GFP and mCherry fluorescent reporter, respectively. A549 cells were infected simultaneously or 1 h apart at a high MOI with IAV-GFP or IBV-mCherry and the fluorescence was measured at 6 h post-infection by flow cytometry. Unexpectedly, we observed that IBV-mCherry infection was enhanced upon co-infection with IAV-GFP, and more strongly so when IAV was added 1 h prior to IBV. The same effect was observed with wild-type viruses and with various strains of IAV. Using UV-inactivated IAV or type-specific antiviral compounds, we showed that the enhancing effect of IAV infection on IBV infection was dependent on transcription/replication of the IAV genome. Our results, taken with available data in the literature, support the hypothesis that the presence of IAV proteins can enhance IBV genome expression and/or complement IBV defective particles

Influenza virus infection induces widespread alterations of host cell splicing

Influenza A viruses (IAVs) use diverse mechanisms to interfere with cellular gene expression. Although many RNA-seq studies have documented IAV-induced changes in host mRNA abundance, few were designed to allow an accurate quantification of changes in host mRNA splicing. Here, we show that IAV infection of human lung cells induces widespread alterations of cellular splicing, with an overall increase in exon inclusion and decrease in intron retention. Over half of the mRNAs that show differential splicing undergo no significant changes in abundance or in their 3 ' end termination site, suggesting that IAVs can specifically manipulate cellular splicing. Among a randomly selected subset of 21 IAV-sensitive alternative splicing events, most are specific to IAV infection as they are not observed upon infection with VSV, induction of interferon expression or induction of an osmotic stress. Finally, the analysis of splicing changes in RED-depleted cells reveals a limited but significant overlap with the splicing changes in IAV-infected cells. This observation suggests that hijacking of RED by IAVs to promote splicing of the abundant viral NS1 mRNAs could partially divert RED from its target mRNAs. All our RNA-seq datasets and analyses are made accessible for browsing through a user-friendly Shiny interface (http://virhostnet.prabi.fr:3838/shinyapps/flu-splicing or https://github.com/cbenoitp/flu-splicing).Peer reviewe

Temperature-sensitive mutants in the influenza A virus RNA polymerase: alterations in the PA linker reduce nuclear targeting of the PB1-PA dimer and result in viral attenuation

International audienceThe influenza virus RNA-dependent RNA polymerase catalyzes genome replication and transcription within the cell nucleus. Efficient nuclear import and assembly of the polymerase subunits PB1, PB2, and PA are critical steps in the virus life cycle. We investigated the structure and function of the PA linker (residues 197 to 256), located between its N-terminal endonuclease domain and its C-terminal structured domain that binds PB1, the polymerase core. Circular dichroism experiments revealed that the PA linker by itself is structurally disordered. A large series of PA linker mutants exhibited a temperature-sensitive (ts) phenotype (reduced viral growth at 39.5 degrees C versus 37 degrees C/33 degrees C), suggesting an alteration of folding kinetic parameters. The ts phenotype was associated with a reduced efficiency of replication/transcription of a pseudoviral reporter RNA in a minireplicon assay. Using a fluorescent-tagged PB1, we observed that ts and lethal PA mutants did not efficiently recruit PB1 to reach the nucleus at 39.5 degrees C. A protein complementation assay using PA mutants, PB1, and beta-importin IPO5 tagged with fragments of the Gaussia princeps luciferase showed that increasing the temperature negatively modulated the PA-PB1 and the PA-PB1-IPO5 interactions or complex stability. The selection of revertant viruses allowed the identification of different types of compensatory mutations located in one or the other of the three polymerase subunits. Two ts mutants were shown to be attenuated and able to induce antibodies in mice. Taken together, our results identify a PA domain critical for PB1-PA nuclear import and that is a "hot spot" to engineer ts mutants that could be used to design novel attenuated vaccines