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Laboratory of Molecular Virology.

(Department Molecular Bases of Human Diseases)


Leader: Monsef BENKIRANE


Human Immunodeficiency Virus type 1 (HIV-1), the causative agent of AIDS, is a retrovirus that primarily infects cells of the immune system. The outcome of HIV-1 infection is the result of complex interactions between viral proteins and host cell factors. In most cases, HIV-1 successfully hijacks cellular pathways and bypasses cellular restriction factors for optimal replication, leading to continuous rounds of infection, replication and cell death. Ongoing viral replication causes the loss of CD4+ T cells and progression to immunodeficiency in infected individuals. However, in certain situations, the virus replication can be successfully controlled. First, HAART (Highly Active Anti-Retroviral Therapy) treatment revealed the existence of a pool of resting memory CD4+ T cells harboring integrated, but silent HIV-1 proviruses. Although this situation occurs in a small number of cells, it suggests that the intracellular defense mechanisms can be effective against HIV. This long lived viral reservoir is believed to be the major obstacle against HIV-1 eradication by HAART. Second, HIV-infected individuals, who can control the virus to undetectable levels for many years in the absence of any treatment, have been identified and referred to as Elite HIV Controllers, "EC". Again, this is a rare situation observed in 0.5% of infected patients. Still, it demonstrates that it is possible to naturally and effectively control HIV replication and disease progression. A common feature of these two situations is that viral replication is controlled at the gene expression level. A major challenge in the HIV field is to understand how, in these naturally occurring situations, the intracellular defense and/or immune response win the battle against HIV. Our main objectives are to identify the host factors and define the molecular mechanisms involved in the regulation of HIV-1 gene expression and to explore the involvement of cellular small non-coding RNAs in virus replication. We also use viruses as tools to understand important cellular processes, such as transcription and RNAi.

1- Understanding HIV-1 gene expression through the identification of key regulatory host factors involved in activating or repressing the viral promoter.
HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP (Sobhian et al. 2010. Mol Cell 38, 439-451). Studying the HIV-1 transcriptional activator Tat has led to important progress in our understanding of transcription elongation by RNAPII, a key regulatory step of gene expression. In this study, we purified HIV-1 Tat-associated factors from HeLa nuclear extracts and showed by biochemical analysis that HIV-1 Tat forms two distinct and stable complexes. The first one is Tatcom1, which consists of the core active P-TEFb, MLL-fusion partners involved in leukemia (AF9, AFF4, AFF1, ENL and ELL) and PAF1/CDC73. Importantly, Tatcom1 formation relies on Cyclin T1 and CDK9, while optimal CDK9 CTD-kinase activity depends on the presence of AF9. MLL-fusion partners and PAF1 are required for Tat-mediated transactivation of the HIV-1 promoter.

The second complex, Tatcom2, is composed of CDK9, Cyclin T1 and 7SK snRNP containing LARP7 and MEPCE. Tat remodels 7SK snRNP by interacting directly with 7SKRNA in vivo, leading to the formation of stress-resistant 7SK snRNP particles. Besides the identification of new factors that are important for P-TEFb function and are required for Tat transcriptional activity, our data show a coordinated control of RNAPII elongation by different classes of transcription elongation factors acting at the same promoter.

2- Understanding the crosstalk between HIV-1 replication and RNAi.
Suppression of HIV-1 replication by microRNA effectors (Chable-Bessia, Meziane et al. 2009. Retrovirology 6, 26). The rate of HIV-1 gene expression is a key step that determines the kinetics of virus spread and AIDS progression. Viral entry and gene expression are considered to be the key determinants for cell permissiveness to HIV. Recent reports highlighted the involvement of miRNAs in regulating HIV-1 replication post-transcriptionally. In this study we explored the role of cellular factors required for miRNA-mediated mRNA translational inhibition in regulating HIV-1 gene expression. We showed that HIV-1 mRNAs associate and co-localize with components of the RNA Induced Silencing Complex (RISC), and we characterized some of the proteins required for miRNA-mediated silencing (miRNA effectors). RCK/p54, GW182, LSm-1 and XRN1 negatively regulate HIV-1 gene expression by preventing viral mRNA association with polysomes. Interestingly, knockdown of RCK/p54 or DGCR8 resulted in virus reactivation in peripheral blood mononuclear cells (PBMCs) isolated from HIV-infected patients treated with suppressive HAART.
Competition between Dicer mRNA, pre-miRNA, viral RNA for Exportin-5 binding strikes a regulatory balance in cellular miRNA levels. (Bennasser et al. 2011. Nat Struct Mol Biol 18, 323-327).
microRNAs (miRNAs) are a class of small non-coding RNAs (sncRNAs) that function by regulating gene expression post-transcriptionally. Alterations in miRNA expression can dramatically influence cellular physiology and are associated with human diseases, including cancer. Here, we demonstrated cross-regulation between two components of the RNA interference machinery. Specific inhibition of Exportin-5, the karyopherin responsible for pre-miRNA export, down-regulates Dicer expression, the RNase III required for pre-miRNA maturation. This effect is post-transcriptional and results from increased nuclear localization of Dicer mRNA. In vitro assays and cellular RNA immunoprecipitation experiments showed that Exportin-5 directly interacts with Dicer mRNA. Titration of Exportin-5 by over-expressing either pre-miRNA or the adenoviral VA1 RNA resulted in loss of the Dicer mRNA/Exportin-5 interaction and reduction of Dicer level. This saturation also occurs during adenoviral infection and enhances viral replication. Our study reveals an important cross-regulatory mechanism between pre-miRNA or viral small RNAs and Dicer through XPO5.

3-Identification of host cell restriction factors.
Samhd1 is the dendritic and myeloid cell-specific HIV-1-restriction factor counteracted by Vpx. (Laguette et al. 2011. Nature http://dx.doi.org/10.1038/nature10117)
The primate lentivirus auxiliary protein Vpx counteracts an unknown restriction factor that renders human dendritic and myeloid cells largely refractory to HIV-1 infection. Here we identified Samhd1 as this restriction factor. Samhd1 is a protein involved in Aicardi-Goutière Syndrome (AGS), a genetic encephalopathy with symptoms mimicking congenital viral infections that has been proposed to act as a negative regulator of the interferon response 7. We show that Vpx induces proteasomal degradation of Samhd1. Silencing of Samhd1 in non-permissive cell lines alleviates HIV-1 restriction and is associated with a significant accumulation of viral DNA in infected cells. Concurrently, over-expression of Samhd1 in sensitive cells inhibits HIV-1 infection. The putative phosphohydrolase activity of Samhd1 is likely to be required for HIV-1 restriction. Vpx-mediated relief of restriction is abolished in Samhd1 negative cells. Finally, silencing of Samhd1 dramatically increases the susceptibility of monocytic-derived dendritic cells to infection. Altogether, our results demonstrate that Samhd1 is an anti-retroviral protein expressed in cells of the myeloid lineage that inhibits an early step of the viral life cycle. Our findings should be integrated in the development of DC-targeted vaccines against HIV/AIDS.



Group's News


News Just Published

On this cover (Mol. Cell vol 67, Issue 3, Aug.07, 2017): An artistic view of a novel role of the paraspeckle, a multi-subunit complex containing the protein HEXIM1 and NEAT1 long non-coding RNA. Morchikh and colleagues (pp. 387–399 - PMID: 28712728) report that paraspeckles are structures that sense foreign DNA in the nucleus and regulate DNA-mediated activation of innate immune response through the cGAS-STING pathway.
Painting by Fabrice Hyber, a French contemporary artist. ©Fabrice Hyber and Organoid-Pasteur, a database of images created by artists to represent scientific research.

News Découverte d'un marqueur du réservoir du VIH.

Des chercheurs français (dont l'équipe de Monsef Benkirane de l'IGH) ont identifié un marqueur qui permet de différencier les cellules « dormantes » infectées par le VIH des cellules saines. Cette découverte permettra d'isoler et d'analyser ces cellules réservoirs qui, en hébergeant silencieusement le virus, sont responsables de la persistance du virus même chez les patients sous traitements antirétroviraux, dont la charge virale est indétectable. Ces travaux s'inscrivent dans le cadre du programme stratégique de l'ANRS « Réservoirs du VIH ». Ils sont issus d'une collaboration entre le CNRS, l'Université de Montpellier, l'Inserm, l'Institut Pasteur, l'hôpital Henri-Mondor AP-HP de Créteil, l'hôpital Gui de Chauliac (CHU de Montpellier) et le VRI (Institut de recherche vaccinale), et font l'objet d'une publication dans la revue Nature le 15 mars 2017 : Descours, B. et al. Nature http://dx.doi.org/10.1038/nature21710 (2017). Un brevet, en propriété CNRS, a été déposé sur l'utilisation diagnostique et thérapeutique du marqueur identifié.
Illustration © Fabrice Hyber

[ Communiqué de presse ]

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News The HIT HIDDEN HIV website is now online!

Five organizations have decided to pool their resources in order to elaborate a stunning project funded by the European Commission: the Institute of Human Genetics (IGH), the Pasteur Institute, the University of Ulm, the Centre hospitalier universitaire vaudois and Pharis Biotec GmbH, a german firm, have launched HIT HIDDEN HIV in december 2012.

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Group's publications of the year (2017):

Descours B, Petitjean G, López-Zaragoza JL, Bruel T, Raffel R, Psomas C, Reynes J, Lacabaratz C, Levy Y, Schwartz O, Lelievre JD, Benkirane M..
CD32a is a marker of a CD4 T-cell HIV reservoir harbouring replication-competent proviruses
(2017), NATURE : 546(7660):686
Morchikh, M., Cribier, A., Raffel, R., Amraoui, S., Cau, J., Severac, D., Dubois, E., Schwartz, O., Bennasser, Y., Benkirane, M. .
HEXIM1 and NEAT1 lncRNA form a multi subunit complex that regulates DNA-mediated innate immune response
(2017), Mol. Cell : 37, 3, 387-399


All the publications of the group


Name / First name Room Phone status


BENKIRANE Monsef 009-010 9996 DR (CNRS) E-mail    Photo  
BENNASSER Yamina 130-131 9988 CR (INSERM) E-mail    Photo  
HANI El-Habib 132-133 9976 CR (CNRS) E-mail   
SOBHIAN Bijan 132 9976 CR (INSERM) E-mail    Photo  

   Engineer & Administrative

MALIRAT Nathalie 132-133 9976 AI (CNRS) E-mail    Photo  


CRIBIER Alexandra 130-131 9988 (CNRS) E-mail    Photo  
DESCOURS Benjamin 130-131 9988 (CNRS) E-mail    Photo  
DOYEN Cécile 132-133 9976 (CNRS) E-mail    Photo  
HOUSSIER Suzie 130-131 9988 (CNRS) E-mail    Photo  
PETITJEAN Gael 130-131 9988 (CNRS) E-mail    Photo  
RAHM Nadia 130-131 9988 (CNRS) E-mail    Photo  

   PhD students

GAYRAUD Thomas 132-133 9976 (Univ.Montp) E-mail    Photo  
RAFFEL Raoul 132 9976 (CNRS) E-mail    Photo  

   Fixed-term contract

BARCKMANN Bridlin S14 9549 IE (CNRS) E-mail    Photo  
MERITET Anais 130-131 9988 IE (CNRS) E-mail    Photo  

Laboratory of Molecular Virology. Group

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