RNA-based immunity against flaviviruses in arthropods and mammalian cells – RIFLAVIRAM

Because they replicate inside cells and rely for the most part on the host molecular machineries for their replication, viruses have to deal with multiple defense mechanisms based on the recognition of their genome by the cell. This leads to a never-ending arms race in which the pathogen and its host have to co-evolve to respectively avoid and reinforce detection and clearance by the immune response. Nonetheless, this strict dependency on a host organism also makes them vulnerable, especially in the very early steps of the infection, since they have to unveil their genome in the cells they infect. For this reason, the sensing of foreign nucleic acids represents a common characteristic of the antiviral defense throughout evolution. Work over the past thirty years has revealed that viral nucleic acids, and in particular RNA, are important molecular patterns that can be sensed by cytosolic receptors. One of the key features representing a danger signal, is long double-stranded (ds) RNA, generated during RNA replication, or by convergent transcription. As a result, all eukaryotes have evolved an innate immune response based on dsRNA sensing receptors.
In this project, we propose to study cellular responses to viruses transmitted to humans by arthropods to identify and characterize complexes involved in the sensing of viral nucleic acids, focusing more specifically on dsRNA. We will study viruses from the Flaviviridae family that are transmitted by mosquitoes or ticks. More precisely, we will focus on Zika virus (ZIKV) and tick-borne encephalitis virus (TBEV). These viruses will be studied both in human cells and in arthropod systems such as mosquito and tick cells. We will also work at the level of the whole organism by using the genetically amenable Drosophila model, mosquitoes and ticks. Because arboviruses have to face different defense mechanisms depending on the host they infect at a given time, they offer a unique opportunity to unravel precisely the factors involved in dsRNA-based innate immunity at each end of the viral propagation cycle. The goal of this application is therefore to study viral infections in three organisms (human, mosquito, tick) to understand the antiviral innate immune system by (i) identifying the proteins involved in dsRNA recognition and sensing; (ii) determining which of these proteins have pro- or anti-viral activities and (iii) dissecting the molecular and cellular mode of action of the most promising factors. Our results will provide the community with a detailed picture of the mechanisms used by the human or arthropod cell to discriminate between self and non-self RNA and might pave the way toward designing novel therapeutic approaches.
The three laboratories with complementary skills ranging from virology, entomology, biochemistry, RNA biology proteomics and genetics will collaborate on this project. Since we have already generated a large amount of preliminary data, we can start to investigate the function of the proteins already identified in our different approaches. We have solid proof of principle that viral dsRNA is detected by specific proteins in host cells. The power of screening in cells will allow us to assess the importance of each candidates during viral infection. The genetics in drosophila can assess rapidly the function of these proteins at the level of an organism. This project will provide an integrated view of the recognition of viruses able to infect both arthropods and mammals. It will be of interest for a wide audience and will certainly prove useful to tackle viruses posing global health problems.