CRISPR screens for SARS-CoV-2 Host Factors

PROJECT SUMMARYIn collaboration with Dr. Wilen (Yale University) and Dr. Goujon (CNRS, France), we will establish cell linemodels and conduct genome-wide CRISPR screens to identify host genes that are necessary for SARS-CoV-2infection. We will first use Vero cells from the African Green Monkey, as they are a well-established model formany pathogens, and we had previously generated a genome-wide library for this species. Preliminary datasuggest that we have also generated human cell lines that can serve as effective model systems, and thesescreens will be conducted as soon as the models are sufficiently validated. Across these screens, we expect tofind host factors that are necessary for infection, such as the surface binding target for the virus, ACE2, andanticipate that the screens will identify additional genes that, when knocked out, prevent viral cytopathiceffects. Additionally, we can modulate the selective pressure to identify factors that, when lost, sensitize thecells to SARS-CoV-2, which will provide a complementary view into host cell biology. Likewise, we will alsoconduct CRISPR activation screens to identify host genes that, when overexpressed, provide protectionagainst infection, which may identify restriction factors that the virus must overcome. Primary screens will bevalidated with secondary pools, which will also allow for testing of genes across more conditions and cell types,establishing the generalizability of the results. Finally, combinatorial screens will be conducted to generateunbiased genetic interaction maps of hit genes, which can identify redundancies that are partially masked in aprimary screen, as well as unexpected synergies across pathways. Focused, mechanistic follow-up of genesidentified by these screens is outside the scope of this proposal, but is of immediate interest to the Wilen andGoujon groups.