Projets

1 – Host-pathogens interactions: use with occasional abuse, perversion that can lead to subversion?

Viruses are biological entities that rely on their abilities to manipulate the host components and machineries in order to replicate and spread. Viral manipulations of the host can be divided into two main categories depending on whether the targeted cellular functions are left intact or slightly modified (use with occasional abuse), altered (perverted) and even subverted (inducing great perturbations in the cellular functions). Our aims are to dissect and understand mechanisms by which viruses of different origins have evolved to establish productive infection at a cellular level but also at a population level. We are committed at enlightening virus-host interplays during the main steps of a virus replication cycle: virus attachment, penetration, uncoating, replication, assembly, and release of specific human pathogenic viruses as well as studying some immune escape mechanisms.

We focus on the biology of viral particles of specific pathogens, such as hepatitis viruses (HBV, HCV & HDV), orthonairoviruses, such as Crimean Congo Hemorrhagic Fever virus (CCHFV), and SARS-CoV-2, responsible of the current COVID-19 pandemic. These micro-organisms were selected first, as they are notorious human pathogens; second, as we have developed over the years strategic in vitro and in vivo experimental infectious models; and third, as they each provide fascinating research paradigms such as co-infections, intersections with lipid metabolism, or interaction with reservoirs/vectors.

Assembly & secretion of enveloped viral particles.

Viruses usurp several cellular pathways for assembling and releasing their virions and each virus developed some strategies to hijack the host functions for its own interest. Examples of viral perversion/subversion will be studied in depth for virus species for which this appears of specific interest in their fields. Key questions are to address:

• Host factors driving the organization of HCV pre-assembly steps and/or its assembly sites.
• Reorganization of membranes and pathways allowing assembly, envelopment and secretion of CCHFV.
• Mechanisms of envelopment of HDV ribonucleoprotein (RNP) by unconventional viruses.
• Mechanism of assembly of SARS-CoV-2 particles and interplay between viral structural proteins.

Dealing with the extracellular environment.

After having subverted and averted proviral and antiviral host factors, respectively, during production in infected cells, viruses face specific challenges to allow the secretion of their viral particles in the extracellular medium, an environment that contains many antiviral weapons, such as e.g., neutralizing antibodies, and adapt appropriately. Our major projects in those direction with unravel:

• Mechanisms of maturation of HCV particles by lipidation, towards the rational design of an HCV vaccine.
• Functions of Mucin/GP38, non-structural secreted proteins that favor CCHFV production and infectivity.

Harnessing host factors and pathways for cell entry.

Infection is initiated through virus binding to specific cellular receptors. We aim at clarifying mechanisms and cascades of interactions that determine receptor usage and entry pathways, including internalization and fusion of viral and host membranes that ultimately lead to release their genome into the cell cytoplasm. Key questions aim at unraveling:

• Receptor usage and novel CCHFV entry factors.
• HBV membrane fusion determinants and cellular co-factors.
• Mechanisms of HCV entry that involve delipidation of its viral particles by lipid receptors.
• Study role of secreted factors on SARS-CoV-2 entry and development of specific peptide inhibitors.

2 – Dynamics of infectious diseases: how can we anticipate and get prepared?

The study of virus-host associations becomes of great importance particularly in identifying specific factors involved in the emergence/re-emergence of infectious-diseases. CCHFV is an example of an emerging pathogen in Europe possibly due to increased vector bionomics and climate changes, for which counteracting measures are missing. Expansion of vectors and vectors-associated pathogens will affect the viral infections dynamics of the ecosystem possibly precipitating new viral disease emergence due in part to cross-species barriers transgression and virus adaptation to new hosts. To decrease our time response and develop precautionary measures to fight (re)-emerging infections, we aim to identify and characterize novel pathogens circulating in endemic areas, pathogenicity determinants as well as ecology and transmission parameters, which will get insights of their dynamics and in new targets for virus control.

Hunting for new pathogens.

The emergence of new viral diseases usually occurs when an established animal virus switches hosts into humans and is subsequently transmitted within human populations. Therefore, studying viral diversity and discovery of new pathogens and its relationship with environmental factors may facilitate our understanding of viral-host association, types of transmission and vectors (viral ecology), which in turn promotes the development of diagnostic tools, infectious disease surveillance and prompts the development of new therapeutics. Key questions include:

• Tracking novel Nairoviruses in bats and ticks to unravel ecology and transmission parameters.
• Identifying new helper viruses for HDV transmission in patient samples from endemic countries.

Coinfections and Pathogenesis.

Infectious diseases frequently lead to situations where two pathogens or more co-infect the host, as exemplified by co-infections with HDV and its helper virus, i.e., HBV or other HBV-unrelated viruses (HUV). Reciprocal interferences between either co-infecting virus could modulate their replication/propagation and/or associated pathogenesis. Therefore, beyond molecular and cellular assembly-compatibilities, it is essential explore in both in vitro and in vivo co-infection assays the determinants of synergy, or conversely, of antagonism between either virus as well as possible immunological mechanisms of interference. On the other hand, it is urgent to improve our knowledge of some zoonotic viruses in order to increase the overall level of preparation and to be able to respond to the emergence of new pathogens. Thus, using different ex vivo cellular assays but also immunocompetent and immunodeficient murine models as well as double-humanized HIS/HuHEP mice, we evaluate viral replication, co-infection interferences, and immunopathological parameters. Our specific projects aim at deciphering:

• Genetic and immune interferences between co-infecting viruses (HDV/HUV).
• Pathogenesis of novel nairoviruses with focus on vascular leakage induced by non-structural proteins.

3 – Technological developments towards biotherapies.

Translational medicine is a long-term goal of our team that aims at achieving efficient genetic modification of specific hematopoietic/immune cells of therapeutic relevance by direct in vivo vector inoculation. This would omit ex vivo handling of such target cells, which would technically and medically impact in many ways gene therapy and facilitate personalized therapies. Our long-term interest in deciphering processes and engineering of retroviral pseudotypes, i.e., the capacity of retroviruses to use heterologous envelope glycoproteins and hence, to modify ad libitum the surface of retrovirus-derived vectors, has put us on the forefront of VLP (virus-like particles) and viral vector-mediated gene delivery technological developments. Specifically, on a technological basis, we have pursued the invention of pseudotyped lentiviral vectors (LVs) that specifically transduce HSCs and immune effector cells such as B, T and NK cells and that offer several opportunities for both fundamental and translational projects. Overall, our general aims were to develop “stealth” vectors that do not modify cell physiology at the time of gene delivery. We have also established several mouse models with humanized blood (HIS) or liver (HuHEP) functions that are essential for evaluating the in vivo performance of our surface engineered LVs as well as for our studies on host pathogens interactions. Finally, we have developed new methods aiming to facilitate the adoptive transfer of mature immune cells (e.g., B cells), which is necessary to support our preclinical and translational studies in both humanized and immunocompetent mouse models.

Gene therapy.

Our long-term interest in genetic modifications of immune cells and HSCs lead to fascinating perspectives in gene therapy applications that we will evaluate in both preclinical and clinical settings through several applications in collaborations with other institutes and biotech companies. First, we will characterize our LVs pseudotyped with BaEV GPs for their capacity to functionally transduce therapeutic gene in several preclinical setting of inherited blood disorders. Second, we will move forward towards a clinical trial in beta-thalassemia and sickle cell disease via gene delivery in human HSCs.

Immunotherapy: reprogramming of immune effector cells.

For many pathologies, the continuous administration of drugs, such as e.g., antibodies, can induce significant deleterious effects. Our ambitions are to explore novel concepts in immunotherapy based on genetic reprogramming of immune effectors cells (T or B cells) by allowing spatio-temporally regulated expression of (bio)effectors, such as mAbs or cytokines. Such therapeutic molecules would also be delivered at the right place, because they would be secreted by the appropriate effector cells, and at the right time, i.e., only after sensing specific “danger” signals.