Interaction hôte-pathogène lors de l’infection lentivirale

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prochainement sur vos écrans:

Axe de recherche 1 (PI, Andrea Cimarelli): Identification et caractérisation de facteurs cellulaires modulants la réplication du VIH et extrapolation à d’autres virus à ARN.

Axe de recherche 2 (PI, Lucie Etienne): Evolution des interactions virus-hôte et impact sur la transmission inter-espèces.


Axis 1 (PI: Andrea Cimarelli): Identification and characterization of cellular factors that modulate HIV replication and extrapolation to other RNA viruses

As all viruses, HIV is an intracellular parasite that relies on the cell to replicate and disseminate. The focus of this axis is to decipher the cell-virus interface through the study of the multitude of interactions established between cellular and viral proteins that allow, or in some instances impede, viral replication. Using HIV as a spearhead to uncover these interactions, we then extend our studies on model RNA viruses to determine whether they are important also for the replication of other viruses or whether they remain specific for HIV.

Some ongoing projects:

  • Antiviral Roles of the Interferon-Induced Transmembrane Family (IFITMs) in membrane fusogenicity

IFITMs are a family of broad antiviral factors targeting viruses as diverse as Ebola virus and

HIV. Also thanks to work of our lab, IFITMs are for the moment the sole antiviral factors capable of interfering with viral replication at two different steps: during viral entry, by sequestering incoming virions in endosomes and in infected cells by driving the production of virions of decreased infectivity (negative imprinting of virions). In both cases, IFITMs interfere with the process of fusion between the viral and the cellular membrane but how is unknown.
Here, we use omics and targeted approaches to identify: the cellular partners of IFITMs, the domains involved in their antiviral properties and the physical changes at the basis of the fusogenicity defects of membranes.

Our goal is to identify the underlying mechanism of IFITM inhibition which in the long run may pave the way for the development of novel and pan-viral strategies of viral control.

The figure presents the two mechanisms of viral inhibition by IFITMs.


Interferon-Sensitive protein 20 (ISG20) as a novel controller of viral translation.

The interferon- sensitive gene 20 (ISG20) is a member of the DEDD superfamily of RNA/DNA exonucleases that exhibits broad antiviral activities and that was thought to act uniquely by direct degradation of viral RNA. Using the Vesicular Stomatitis RhabdoVirus (VSV) as a model RNA virus, we have instead shown that ISG20 does not degrade viral RNA, but rather prevents its translation. This mechanism of translational control is distinct from previously described regulatory blocks at translation (IFITs, PKR), that discriminate RNAs based on their 5’ or on their requirement for different initiation factors.

At present, we are using different techniques to apprehend the exact mechanism of inhibition by ISG20 as well as its specificities Our long-term goal is to characterize a novel mechanism of viral control that could potentially give insights into novel strategies of viral modulation.

The figure presents cells either infected with a VSV-virus bearing a GFP reporter, or directly transfected with a GFP-coding plasmid both of which non-self genetic elements. The structure of ISG20 was determined in Horio et al, FEBS let. 2004. Residues that inactivate or not the protein’s functions have been colored in violet and yellow, respectively.

  • Identify novel modulators of the early phases of the life cycle of HIV

During infection, HIV injects its genome into the host cell cytoplasm as part of a tridimensional shell generally referred to as Core, Capsid, or viral nucleoprotein complex (VNC). This structure accompanies the viral genome through the major phases of the viral life cycle (reverse transcription, nuclear import…).
At present, we are using functional screens to identify cellular factors that affect the functional stability of viral cores, especially focusing on effectors of the type I interferon response.

Our long-term goal is to identify novel cellular factors that regulate HIV infection.

The figure presents a schematic and simplified view of the Early Phases of the life cycle of HIV.





Axis 2 (PI: Lucie Etienne): Evolution of virus-host interactions and impact on cross-species transmission

Using a combination of evolutionary and functional analyses, we want to understand what drives the species-specificity of viruses.

Cross-species transmissions of viruses from animals to humans are at the origin of major human pathogenic viruses. However, these zoonotic events are relatively rare, implying that molecular barriers among species actively contribute to the relative resistance of a given species to viral emergence. We suspect that species specific restriction factors, as well as receptors or other co-factors, may be of primary importance in blocking the cross-species transmission of viruses. In particular, we study the evolution of viral interacting proteins, and determine how these may shape the host species-specificity of viruses. We further characterize how viruses may adapt in a new species environment.

02_Equipe Cimarelli Andrea_webfig4

Here are some of our ongoing projects:

  • Understand what drives the species-specificity of primate lentiviruses

More than 40 primate species are infected by lentiviruses. Cross-species transmissions of simian lentiviruses are at the origin of the pathogenic HIV in humans. Here, we want to determine what governs the emergence of novel HIV. In particular, we want to elucidate what are the evolutionary and biological basis for host resistance to primate lentiviruses.

On one hand, we use phylogenetic and population genetics from great apes in combination with functional assays to characterize the evolution of “antiviral genes” and determine how these may shape the species-specificity of lentiviruses.

On the other hand, we perform viral in vitro evolution experiments to characterize how lentiviruses may adapt in a new species environment.

Identifying which proteins may protect a species against pathogenic viruses and how viruses interact and evolve in a restrictive environment will ultimately help to design novel antiviral “cure” therapies and evaluate risk of new viral emergence in humans.

02_Equipe Cimarelli Andrea_webfig5Phylogenetic analysis of the vif-vpr region of primate lentiviruses. (Etienne et al. Supplementary Figure, Cell Host Microbe, 2013)


  • Discover interferon-stimulated genes encoding for bona fide viral interacting proteins using a novel positive selection model in combination with virus-host functional assays.

Viruses replicate into the host cells and interact with multiple host proteins, also called viral interacting proteins. At the site of protein interactions with the pathogenic viruses, the host genes evolve very rapidly and signatures of episodic positive selection are left over evolutionary time. We propose to use this peculiar evolutive scheme to identify among the hundreds of interferon-stimulated genes, those that are in natura in direct relevant contact with a pathogenic virus and/or are potent relevant antiviral effectors. Here, we develop a novel positive selection model to identify these viral interacting proteins. We further use phylogenetic and in vitro functional approaches to determine the evolution and the mechanisms of these newly identified proteins.
Collaboration with Laurent Guéguen, LBBE, Lyon


  • Understand how pathogenic viruses and the host “life style” shape the bat’s genome

Here, we investigate how selected immune genes have evolved over millions of years during bat evolution. The originality of this project stems in the multidisciplinary approach using “indirect paleovirology” analyses with novel bat’s genome sequences and ecological data in combination with functional assays. In particular, we will explore how pathogenic viruses may have driven adaptation of the bat’s genome and how the life of bats in multi/mono-species assemblages may impact the immune gene’s diversity. By doing so, we hope to also decipher evolutionary determinants regulating cross-species transmission of bat’s viruses.
Collaboration with Dominique Pontier, LBBE, Lyon


  • On other projects, we also collaborate with:

– Michel Strubin Lab, University of Geneva, Switzerland

– Michael Emerman, Fred Hutch, Seattle, WA, USA

We also thank colleagues and genome sequencing centers for the public release of genomic sequences, as well as our colleagues for sharing crucial reagents/data (Guillaume Douay, Zoo de Lyon; Branka Horvat, Renaud Mahieux and Sandrine Alais, ENS de Lyon; Evan Eichler, UW).

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(in alphabetical order): amfAR, ANRS, CNRS, FINOVI, FRM, JoRISS, LabEx ECOFECT, Région Auvergne Rhône Alpes, Sidaction