GSE175666
Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2,  MERS-CoV and seasonal HCoVs
Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor and didn't express TMPRSS2 protease, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity to pursue efforts to uncover the full landscape of SARS-CoV-2 regulators. We performed genome-wide, bidirectional CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. As well as identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Additionally, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins (MUC1, MUC4 and MUC21), IL6R and CD44 were identified . We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A virus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions. Overall design: 32 samples analyzed (24 generated by this study (raw+processed data) and 8 by the other studies mentioned (only processed data), Control named: initial population, Selected population named: resistant population, replicates are included and mentionned below We re-analyzed 8 genome-wide CRISPR screens using SARS-CoV-2 conducted by groups outside of ours for comparison purposes. 6 of these 8 screens are published, while the 2 screens from the Hsu lab have been released as a pre-print.  The authors of the corresponding manuscripts generously provided raw read count data for this meta-analysis, and we will refer to screens by the senior author of the manuscript. The same data processing pipeline was applied to each screen, which has been detailed in the "Data Processing" section below. For each screen, the control population refers to the uninfected population, while the experimental population refers to the samples infected with SARS-CoV-2. If there were multiple replicates of infected populations, they were averaged for the final processed z-score. Reanalyzed datasets: Wei et al., 2021: (Senior author: Wilen) ;  Title: Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection;  Cell line: Vero E6;  Screen type: Knockout (KO);  SARS-CoV-2 strain: USA-WA1/2020;  Library: C. sabeus;  CRISPR screen raw data location: available with paper Daniloski et al., 2021: (Senior author: Sanjana) ;  Title: Identification of Required Host Factors for SARSCoV-2 Infection in Human Cells;  Cell line: A549 (ACE2);  Screen type: Knockout (KO);  SARS-CoV-2 strain: USA-WA1/2020;  Library: GeCKOv2;  CRISPR screen raw data location: GEO (GSE158298) Zhu et al., 2021: (Senior author: Zhang) ;  Title: A genome-wide CRISPR screen identifies host factors that regulate SARS-CoV-2 entry;  Cell line: A549  (ACE2);  Screen type: Knockout (KO);  SARS-CoV-2 strain: nCoV-SH01;  Library: Brunello;  CRISPR screen raw data location: available with paper Wang et al., 2021: (Senior author: Puschnik)   Title: Genetic Screens Identify Host Factors for SARSCoV-2 and Common Cold Coronaviruses  Cell line: Huh-7.5.1-ACE2-TMPRSS2  Screen type: Knockout (KO)  SARS-CoV-2 strain: USA-WA1/2020  Library: GeCKOv2  CRISPR screen raw data location: EMBL-EBI ArrayExpress (E-MTAB-9638) Schneider et al., 2021: (Senior author: Poirier)   Title: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks  Cell line: Huh-7.5  Screen type: Knockout (KO)  SARS-CoV-2 strain: USA-WA1/2020  Library: Brunello  CRISPR screen raw data location: GEO (GSE162038) Baggen et al., 2021: (Senior author: Daelemans)   Title: Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2  Cell line: Huh-7  Screen type: Knockout (KO)  SARS-CoV-2 strain: Belgium/GHB-  03021/2020  Library: Brunello  CRISPR screen raw data location: SRA (SRR13255539, SRR13255540, SRR13255541, SRR13255542, SRR13255543, SRR13255544, SRR13255545, SRR13255546, SRR13255547) Biering et al., 2021: (Senior author: Hsu) ;  Title: Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection;  Cell line: Calu-3;  Screen type: Knockout (KO);  SARS-CoV-2 strain: USA-WA1/2020;  Library: Brunello;  CRISPR screen raw data location: not yet published Biering et al., 2021: (Senior author: Hsu) ;  Title: Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection;  Cell line: Calu-3;  Screen type: Activation;  SARS-CoV-2 strain: USA-WA1/2020;  Library: Calabrese Set A;  CRISPR screen raw data location: not yet published