Biology of emerging viruses

Dengue and Zika virus entry into target cells

Over the recent years, our group has made key contributions in our understanding of the entry mechanisms used by arboviruses to infect their target cells. We focused our studies on dengue viruses (DENV) and ZIKA virus (ZIKV), two mosquito-borne flaviviruses that represent major global health problems during the last decades.

• We have identified the C-type lectin receptor DC-SIGN as a key entry factor for the four DENV serotypes and ZIKV into skin dendritic cells. (Navarro-Sanchez et al., Embo Reports, 2003; Lozach et al., JBC, 2005, Hamel et al. JVI 2005).

• We discovered that the TIM and TAM proteins, two receptor families that mediate the phosphatidylserine (PS)-dependent phagocytic removal of apoptotic cells, are DENV entry factors. TIM and TAM receptors mediate DENV infection by interacting with PS expressed on the surface of DENV particles (Amara et al. Nat Rev Microbiol 2015, Meertens et al., Cell Host & Microbes, 2012). These studies highlight for the first time that DENV mimics apoptotic debris and uses the apoptotic cell clearance pathway for its infectious entry.

• We showed that the PS receptor TIM-1 is an authentic DENV entry receptor (Dejarnac et al., Cell Reports, 2018). TIM-1 is constitutively ubiquitinated (Ub)at lysine residues K338 and K346 residues located in its cytoplasmic domain. Ub TIM-1 interacts with STAM-1, a component of the ESCRT-0 complex involved in intracellular trafficking of ubiquitinated cargos, to mediate DENV infection.

• ZIKV is an emerging flavivirus responsible for neurological complications, such as congenital microcephaly. We showed that ZIKV interacts with the AXL receptor to infect astrocytes and microglial cells in human fetal brain (Meertens et al., Cell Reports, 2017). ZIKV binding to AXL activates its receptor kinase activity, which initiates signal transduction leading to inhibition of the type I interferon response and therefore facilitates viral infection (Meertens et al., Cell Reports, 2017).

• We identified two AXL inhibitors (Axl decoy receptor MYD1 and the kinase inhibitor R428) that efficiently inhibit ZIKV infection (Meertens et al., Cell Reports, 2017, Espinosa et al. Front Immunol 2022).

Mechanisms of Dengue virus replication

DENV, like all flaviviruses, encodes seven non-structural (NS) proteins that co-assemble and recruit poorly characterized host factors to form the DENV replication complex (RC) essential for viral infection.  The assembly of DENV RC and its RNA genome generate specific organelle-like structures in the host endoplasmic reticulum that facilitate RNA amplification and protect the viral double-stranded RNA from immune responses.

• Using Flag-HA tagged DENV replicons, we have purified for the first time the DENV RC and provides a global proteomic analysis of its host factor composition (Hafirassou et al. Cell Reports, 2017).

• Functional studies highlight an important role of RACK1 and oligosaccharyltransferase (OST) complexes during DENV replication

• The OST complex mediates DENV NS1 and NS4B glycosylation, and pharmacological inhibition of its N-glycosylation activity strongly impairs DENV infection

• The scaffold protein RACK1, a core component of the 40S ribosomal subunit, recruits the RNA binding proteins Vigilin and SERBP1, which link the DENV RNA genome to the translation machinery for efficient infection (Brugier et al. J. Virol., 2022).

• Using a genome-wide CRISPR-Cas9 screen, we identified DPM1 and -3, two subunits of the DPMS complex, as important host factors for the replication of DENV as well as other related viruses such as ZIKV. We established that DPMS complex plays dual roles during viral infection, by regulating viral RNA replication and promoting viral structural glycoprotein folding/stability (Labeau et al. J. Virol. 2020)

Chikungunya virus replication and pathogenesis

 Our team has made major contribution in our understanding of the biology and pathogenesis of chikungunya virus (CHIKV), a re-emerging alphavirus that is transmitted to humans by mosquitoes and causes musculoskeletal and joint pain.

• We performed a genome-wide CRISPR-Cas9 screen to identify the host factors that account for CHIKV tropism for joint and muscles tissues.

• We identified the four-and-a-half lime domain protein 1 (FHL1), a cytoplasmic protein mainly expressed in muscles and fibroblasts, as a major host factor for CHIKV infection (Meertens et al., Nature, 2019).

• We found that dermal fibroblasts and muscle cells derived from patients with Emery–Dreifuss muscular dystrophy that lack functional FHL1 are resistant to CHIKV infection.

• Fhl1 knock out mice are resistant to CHIKV infection and do not develop disease.

• Mechanistically, FHL1 interacts with the viral protein nsP3 to mediate CHIKV replication

SARS-CoV-2 infection and COVID-19

Our group have participated to the effort against SARS-CoV-2 during the COVID-19 pandemic and provided the following key contributions:

• We have isolated primary SARS-CoV-2 viral strains from infected patients, and studied their interaction with human plasmacytoid pre-dendritic cells (pDC), a key player in antiviral immunity. We showed that human pDCs are activated by SARS-CoV-2 through IRAK4- and UNC93B1-regulated pathways and contribute to type I interferon-dependent immunity against SARS-CoV-2 (Onodi et al. J. Exp. Med., 2021).

• In parallel, we have collaborated with Pr Jean-Laurent Casanova’s team (Rockefeller University and Imagine Institute) to unravel the cellular mechanisms underlying severe COVID-19 in patients with mutations in genes involved in innate immunity. We showed that pDCs isolated from patients harboring IRF7 or TLR7 deficiency have a strong defect in their capacity to produce type I IFN in response to SARS-CoV-2 ( Zhang et al. Science 2020, Asano et al. Sci. Immunol. 2021).

• We undertook a comprehensive identification of RNA-binding protein by MS (ChIRP-MS) approach to establish a global map of the SARS-CoV-2 genome interactome. By combining these proteomics data with gene-silencing experiments, we identified a set of SARS-CoV-2 host dependency factors that affect infection and could be targetable for antiviral therapies (Labeau et al. Cell Reports 2022).