RNA regulation in viral infections

Project leader : Dr. Erika Girardi

Discrimination between “self” versus “non-self” is crucial in the immunity to nucleic acids. The innate immune system constitutes the first line of defence against invading microorganisms and it is triggered by the recognition of molecules expressed only by pathogens. One of these molecules is long double stranded RNA (dsRNA), which has long been considered a specific structural feature of viruses.

• Project 1 : Identification of the proteome associated with the viral RNA in alphavirus-infected human cells.

We recently developed an approach to identify new host factors involved in the recognition of viral double-stranded RNA in mammalian infected cells by isolating the viral dsRNA-protein interactome. This work allowed us to identify and characterize SFPQ and DDX5 as novel proviral proteins for Sindbis virus (SINV) (Girardi et al., Messmer et al) and gave a list of many other candidates which remain to be functionally characterized in the context of SINV infection. We also plan to characterize the proteome associated with viral dsRNAs in human cells infected with Chikungunya virus (CHIKV), a re-emerging alphavirus. Specifically, we will perform loss or gain of function CRISPR screens to measure the effect of selected candidate genes in alphavirus-infected cells by monitoring cell viability and fluorescence of GFP reporter viruses and in real-time.

• Project 2 : Impact of endogenous dsRNA accumulation on innate antiviral immunity

A growing number of reports emphasize that the innate immune system can be stimulated not only by exogenous nucleic acids but also by host-derived long dsRNAs under certain conditions. Since pattern recognition receptors (PRRs) can recognize the structure of dsRNAs larger than 40 bp rather than their sequence, the expression and accumulation of endogenous dsRNAs in the cytoplasm must be tightly regulated to prevent aberrant activation of inflammatory signalling. For instance, RNA editing by ADAR1 enzyme is a well-characterized way to avoid self-RNA immunogenicity. By taking advantage of the experience obtained studying the viral dsRNAome, we are currently undertaking the characterization of the endogenous dsRNA transcriptome and protein interactome in both uninfected and infected conditions, to understand the mechanisms fine-tuning the innate immunity upon viral infection and beyond.

CHIKV-infected HEK293 cells. Anti dsRNA staining (yellow), DAPI (blue)

Funding: project funded by ANR JCJC and IdEx Attractivité from University of Strasbourg.