Evaluating viral RNA/DNA-bound proteins Across SpeciEs (ERASE)

Viruses are the most abundant infectious agents on Earth. In this proposal we aim at defining the repertoire of nucleic acid (NA) sensors that are operating against a wide spectrum of viruses and to employ this knowledge for rational design of generic vaccine strategies or antiviral treatments. In the recent years, mass spectrometry (MS) has evolved in a powerful tool to dissect the innate immune system. We have been using MS to identify proteins specifically binding to virus-like RNA successfully, e.g. IFIT1. However, low affinity interactions between viral NAs and cellular proteins may not allow for the identification of several functionally important interactions. Furthermore, MS analyses generate more data than can be functionally characterized. By combining unbiased investigations in multiple species (human, mouse, chicken, fly, worm, yeast) and advanced biological network-based bioinformatics we will increase our ability to identify new conserved viral sensors. Model organisms will further facilitate follow up in vivo functional tests on a larger scale. ERASE bioinformatics component will integrate experimental data with innate immunity-related information to provide a systems-level understanding of viral NA sensing. We will assemble a cross- species immune system knowledge base comprised of: (1) An integrated network of public protein- protein interactions and immune system pathways in each species; (2) The functional annotation of proteins/genes in this network with classical and immunity specific sources as well as data from genome- wide association studies and disease associations; (3) The global landscape of changes provided by the gene expression profiles. We will then identify proteins and biological pathways consistently involved in the association to viral nucleic acids. This will serve for selecting candidates for final functional validation in model systems and for intellectual design of vaccine regimes. The information provided by functional validation experiments will further enrich the knowledge base and thereby allow constructing an even more accurate map of the key proteins and pathways involved in the response to viral nucleic acids. Besides bioinformatics analyses we will use a knockout cell line collection to study the biological function of identified genes on a mechanistic basis.

The first line of immune defense against invading pathogens like bacteria are macrophages, immune cells that engulf every foreign object that crosses their way. After enclosing it in intracellular membrane vesicles, a process called phagocytosis, macrophages kill their prey with acid. However, it is not yet entirely understood how the acidification process is established. In their quest to systematically study proteins that transport chemicals across cellular membranes, researchers at CeMM, in the context of a FWF-funded project involving several european labs, characterized the critical role for transporter SLC4A7 in this process, providing valuable new insights for many pathologic conditions from inflammation to cancer. Their results were published in Cell Host & Microbe.