Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of host factors influencing viral infection is critical to elucidate SARS-CoV-2–host interactions and the progression of Coronavirus disease 2019 (COVID-19). Here, we conducted genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2. We uncovered proviral and antiviral factors across highly interconnected host pathways, including clathrin transport, inflammatory signaling, cell-cycle regulation, and transcriptional and epigenetic regulation. We further identified mucins, a family of high molecular weight glycoproteins, as a prominent viral restriction network that inhibits SARS-CoV-2 infection in vitro and in murine models. These mucins also inhibit infection of diverse respiratory viruses. This functional landscape of SARS-CoV-2 host factors provides a physiologically relevant starting point for new host-directed therapeutics and highlights airway mucins as a host defense mechanism.

Kinase-independent activity of DYRK1A promotes viral entry of highly pathogenic human coronaviruses

“…During the COVID-19 pandemic, a number of genome-wide CRISPR/Cas9 screens have been performed to unveil host factors that regulate SARS-CoV-2 infection 22,23,[27][28][29][30][31][32][33]91,92 . We previously identified DYRK1A as a pro-viral gene for both SARS-CoVs and MERS-CoV in Vero-E6 cells and Calu-3 cells 22,23 .…”

“…During the COVID-19 pandemic, a number of genome-wide CRISPR/Cas9 screens have been performed to unveil host factors that regulate SARS-CoV-2 infection 22,23,[27][28][29][30][31][32][33]91,92 . We previously identified DYRK1A as a pro-viral gene for both SARS-CoVs and MERS-CoV in Vero-E6 cells and Calu-3 cells 22,23 . Additional recent independent screens in Vero-E6 and Calu-3 cells have confirmed our initial finding of DYRK1A as a host dependency factor for SARS-CoV-2 33,34 .…”

“…We performed a genome-wide CRISPR/Cas9-based inactivation screen in African green monkey kidney Vero-E6 cells and in human lung epithelial Calu-3 cells 22,23 . Both Vero-E6 and Calu-3 cells are permissive to SARS-CoV, SARS-CoV-2, and MERS-CoV and endogenously express the cognate receptors ACE2 and DPP4 [22][23][24][25][26] . Our screens revealed several pro-viral genes shared by SARS-CoV, SARS-CoV-2, and MERS-CoV in both Vero-E6 and Calu-3 cells 22,23 .…”

“…Both Vero-E6 and Calu-3 cells are permissive to SARS-CoV, SARS-CoV-2, and MERS-CoV and endogenously express the cognate receptors ACE2 and DPP4 [22][23][24][25][26] . Our screens revealed several pro-viral genes shared by SARS-CoV, SARS-CoV-2, and MERS-CoV in both Vero-E6 and Calu-3 cells 22,23 . Other genome-wide CRISPR/Cas9 screens for SARS-CoV-2 and other related coronaviruses have since identified additional host dependency factors including proteins involved in viral entry, endocytic trafficking and sorting, cholesterol homeostasis, and autophagy [27][28][29][30][31][32] .…”

“…While reproducibility between screens was excellent when performed on the same cell type, there was otherwise limited overlap across hits in these loss of function screens [27][28][29][30][31][32] . One notable exception was DYRK1A, which was a top enriched hit in both Vero-E6 and Calu-3 cells 22,23,33,34 . Interestingly, DYRK1A was not a hit in cell lines exogenously overexpressing ACE2, such as A549, Huh7.5, or HeLa cells [27][28][29][30][31][32] .…”