Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses

Abstract

The Coronaviridae are a family of viruses that causes disease in humans ranging from mild respiratory infection to potentially lethal acute respiratory distress syndrome. Finding host factors that are common to multiple coronaviruses could facilitate the development of therapies to combat current and future coronavirus pandemics. Here, we conducted parallel genome-wide CRISPR screens in cells infected by SARS-CoV-2 as well as two seasonally circulating common cold coronaviruses, OC43 and 229E. This approach correctly identified the distinct viral entry factors ACE2 (for SARS-CoV-2), aminopeptidase N (for 229E) and glycosaminoglycans (for OC43). Additionally, we discovered phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis as critical host pathways supporting infection by all three coronaviruses. By contrast, the lysosomal protein TMEM106B appeared unique to SARS-CoV-2 infection. Pharmacological inhibition of phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis reduced replication of all three coronaviruses. These findings offer important insights for the understanding of the coronavirus life cycle as well as the potential development of host-directed therapies.

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions

“…The full screen dataset can be retrieved by clicking the download button (orange arrow). Linkouts to other resources are also provided (red arrow) recent preprint reports have described genome-wide CRISPR screens in the Vero-E6 African green monkey cell line 68 and the human HuH-7.5 liver cancer cell line 69 subjected to SARS-CoV-2 virus infection. As one of these screens was undertaken in the Vero-E6 cell line, new African green monkey gene annotation was loaded into BioGRID to allow screen curation.…”

“…CRISPR screens have identified known host cell genes required for viral entry such as ACE2 and heparan sulfate biosynthetic pathway genes, as well as novel host cell dependencies for viral replication including the SWI/SNF chromatin remodeling complex, the TGF-β signaling pathway, phosphatidylinositol metabolism and endosome maturation, among other processes. 68,69 . These host cell genetic requirements reveal candidate new drug targets for interdiction of the SARS-CoV-2 infection cycle.…”

SARS-CoV-2 infection remodels the host protein thermal stability landscape

“…Importantly, both UGDH and PAAF1 are required for SARS-CoV-2 infection 25 , and nsp6 was previously found to physically interact with UGDH, and the viral membrane glycoprotein M with UGDH and PAAF1 in BioID experiments 20 (Figure 4b). These data suggest that thermal destabilisation of UGDH and PAAF1 during SARS-CoV-2 infection capture functionally relevant changes in their biophysical state that impact SARS-CoV-2 proliferation.…”

“…Notably, the SAFB target gene product LARP1 was previously found to interact with the SARS-CoV-2 N protein, and the target gene neuroguidin (NGDN) with the SARS-CoV-1 protein nsp9 3,6 . Con rming the functional relevance for SARS-CoV-2, NGDN was recently shown to be required for SARS-CoV-2 proliferation 25 . These ndings allude to a potential temporal interplay between SARS-CoV-2 and SAFB, whereby phosphorylation of S604 on SAFB that induces the expression of proteins directly targeted by SARS-CoV-2 during infection.…”

“…SARS-CoV-2 hijacks host protein cell processes for its replication, packaging, and release, leading to alterations in cell signaling and protein expression [1][2][3][4] . Although genetic approaches are shedding light onto the functional relevance of such large-scale proteomic information [5][6][7] , complementary approaches are needed to expand our understanding of the biophysical changes that proteins can undergo within a live infection context.…”