Primary supervisor: Prof. E. Snijder, LUMC, Leiden, The Netherlands
Title: To define innate immune- and lipid metabolism changes associated with viral replication organelles
Collaborators: Prof. L. O’Neill, Trinity College Dublin, Ireland; Dr. N. Manel, Stimunity, Paris, France
Early Stage Researcher: Maria Soultsioti

Replication organelles (ROs) are elaborate membranous structures induced in the cytosol of cells during positive strand RNA virus infections. Our long-term studies have suggested that ROs act to provide a microenvironment for efficient viral RNA replication, while also shielding viral RNA replication products and intermediates from cytosolic innate immune sensors. Whereas their ultrastructure has been studied in detail, very little is known about how ROs influence innate immune sensing and signaling, and cellular (lipid) metabolism. Since all +RNA viruses, like SARS-CoV-2, induce such structures, such knowledge could provide important new clues for more general antiviral strategies.  In this project we will attempt to understand if and how the innate immune system is able to attack viral ROs induced by nidoviruses such as MERS-CoV, SARS-CoV-2 and equine arteritis virus (EAV). We recently published the first data indicating that ROs are indeed attacked by the type I IFN branch of the innate immune response. We will furthermore investigate the crosstalk between RO formation, innate immune responses and (lipid) metabolism during infection.  This ESR will use state-of-the-art molecular cloning techniques, and advanced electron microscopy methods, as well as CRISPr/Cas9 gene editing and RNA seq analyses in order to dissect innate immune- and metabolic factors involved in the hypothesized crosstalk. In collaboration with Prof. L. O’Neill  at Trinity College Dublin in Ireland the ESR will use Seahorse technology for analysis of metabolic changes in cells that form viral ROs. Also, the influence of viral RO formation on the STING-mediated pathways will be investigated in collaboration with Stimunity in France.