Genome-wide CRISPR screen reveals novel host factors required for Staphylococcus aureus α-hemolysin-mediated toxicity

AbstractBackgroundRhinoviruses (RVs) cause more than half of common cold and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host factors, few of which has proven clinical relevance.ResultsHerein, we systematically compared genome-wide CRISPR screen and surface protein-focused CRISPR screen, referred to as surfaceome CRISPR screen, for their efficiencies in identifying RV host factors. It was found that surfaceome screen outperformed genome-wide screen in the success rate of hit identification. Importantly, using surfaceome screen we have identified olfactomedin like 3 (OLFML3) as a novel host factor of RV serotypes A and B including a clinical isolate. We found that OLFML3 was a RV-inducible suppressor of the innate immune response and that OLFML3 antagonized type I interferon (IFN) signaling in a SOCS3-dependent manner.ConclusionOur study has suggested that RV-induced OLFML3expression is an important mechanism for RV to hijack the immune system and underscored surfaceome CRISPR screen in identifying viral host factors.

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Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist

Genome Biology ◽

10.1186/s13059-021-02513-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Hong Mei ◽

Zhao Zha ◽

Wei Wang ◽

Yusang Xie ◽

Yuege Huang ◽

...

Keyword(s):

Type I Interferon ◽

Surface Protein ◽

Innate Immune ◽

Host Factors ◽

Type I ◽

Dependent Manner ◽

Genome Wide ◽

Crispr Screen ◽

Novel Host ◽

Hit Identification

Abstract Background Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host factors, few of which have proven clinical relevance. Results Herein, we systematically compare genome-wide CRISPR screen and surface protein-focused CRISPR screen, referred to as surfaceome CRISPR screen, for their efficiencies in identifying RV host factors. We find that surfaceome screen outperforms the genome-wide screen in the success rate of hit identification. Importantly, using the surfaceome screen, we identify olfactomedin-like 3 (OLFML3) as a novel host factor of RV serotypes A and B, including a clinical isolate. We find that OLFML3 is a RV-inducible suppressor of the innate immune response and that OLFML3 antagonizes type I interferon (IFN) signaling in a SOCS3-dependent manner. Conclusion Our study suggests that RV-induced OLFML3 expression is an important mechanism for RV to hijack the immune system and underscores surfaceome CRISPR screen in identifying viral host factors.

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A genome-wide CRISPR screen identifies UFMylation and TRAMP-like complexes as host factors required for hepatitis A virus infection

Cell Reports ◽

10.1016/j.celrep.2021.108859 ◽

2021 ◽

Vol 34 (11) ◽

pp. 108859

Author(s):

Jessie Kulsuptrakul ◽

Ruofan Wang ◽

Nathan L. Meyers ◽

Melanie Ott ◽

Andreas S. Puschnik

Keyword(s):

Virus Infection ◽

Hepatitis A ◽

Hepatitis A Virus ◽

Host Factors ◽

Genome Wide ◽

A Genome ◽

Crispr Screen

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A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets

PLoS Biology ◽

10.1371/journal.pbio.3001490 ◽

2021 ◽

Vol 19 (12) ◽

pp. e3001490

Author(s):

Annika Kratzel ◽

Jenna N. Kelly ◽

Philip V’kovski ◽

Jasmine Portmann ◽

Yannick Brüggemann ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Huh7 Cell ◽

Host Factors ◽

Genome Wide ◽

A Genome ◽

Dependent Inhibition ◽

Crispr Screen ◽

Human Coronaviruses ◽

Approved Drugs ◽

Huh7 Cell Line

Over the past 20 years, 3 highly pathogenic human coronaviruses (HCoVs) have emerged—Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and, most recently, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)—demonstrating that coronaviruses (CoVs) pose a serious threat to human health and highlighting the importance of developing effective therapies against them. Similar to other viruses, CoVs are dependent on host factors for their survival and replication. We hypothesized that evolutionarily distinct CoVs may exploit similar host factors and pathways to support their replication cycles. Herein, we conducted 2 independent genome-wide CRISPR/Cas-9 knockout (KO) screens to identify MERS-CoV and HCoV-229E host dependency factors (HDFs) required for HCoV replication in the human Huh7 cell line. Top scoring genes were further validated and assessed in the context of MERS-CoV and HCoV-229E infection as well as SARS-CoV and SARS-CoV-2 infection. Strikingly, we found that several autophagy-related genes, including TMEM41B, MINAR1, and the immunophilin FKBP8, were common host factors required for pan-CoV replication. Importantly, inhibition of the immunophilin protein family with the compounds cyclosporine A, and the nonimmunosuppressive derivative alisporivir, resulted in dose-dependent inhibition of CoV replication in primary human nasal epithelial cell cultures, which recapitulate the natural site of virus replication. Overall, we identified host factors that are crucial for CoV replication and demonstrated that these factors constitute potential targets for therapeutic intervention by clinically approved drugs.

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A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets

10.1101/2021.02.24.432634 ◽

2021 ◽

Author(s):

Annika Kratzel ◽

Jenna N. Kelly ◽

Yannick Brueggemann ◽

Jasmine Portmann ◽

Philip V’kovski ◽

...

Keyword(s):

Host Factors ◽

The Novel ◽

Genome Wide ◽

A Genome ◽

Dependent Inhibition ◽

Crispr Screen ◽

Dose Dependent Inhibition ◽

Autophagy Pathway ◽

Approved Drugs ◽

Dose Dependent

SummaryOver the past 20 years, the emergence of three highly pathogenic coronaviruses (CoV) – SARS-CoV, MERS-CoV, and most recently SARS-CoV-2 – has shown that CoVs pose a serious risk to human health and highlighted the importance of developing effective therapies against them. Similar to other viruses, CoVs are dependent on host factors for their survival and replication. We hypothesized that evolutionarily distinct CoVs may exploit similar host factors and pathways to support their replication cycle. Here, we conducted two independent genome-wide CRISPR/Cas9 knockout screens to identify pan-CoV host factors required for the replication of both endemic and emerging CoVs, including the novel CoV SARS-CoV-2. Strikingly, we found that several autophagy-related genes, including the immunophilin FKBP8, TMEM41B, and MINAR1, were common host factors required for CoV replication. Importantly, inhibition of the immunophilin family with the compounds Tacrolimus, Cyclosporin A, and the non-immunosuppressive derivative Alisporivir, resulted in dose-dependent inhibition of CoV replication in primary human nasal epithelial cell cultures that resemble the natural site of virus replication. Overall, we identified host factors that are crucial for CoV replication and demonstrate that these factors constitute potential targets for therapeutic intervention by clinically approved drugs.

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Genome-Wide CRISPR Screen Identifies Host Factors Required by Toxoplasma gondii Infection

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2019.00460 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 1

Author(s):

Shui-Zhen Wu ◽

Hai-Xia Wei ◽

Dan Jiang ◽

Sheng-Min Li ◽

Wei-Hao Zou ◽

...

Keyword(s):

Toxoplasma Gondii ◽

Host Factors ◽

Genome Wide ◽

Crispr Screen ◽

Toxoplasma Gondii Infection

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Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection

Nature Communications ◽

10.1038/s41467-019-13965-x ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 24

Author(s):

Bo Li ◽

Sara M. Clohisey ◽

Bing Shao Chia ◽

Bo Wang ◽

Ang Cui ◽

...

Keyword(s):

Virus Infection ◽

Influenza A Virus ◽

Influenza A ◽

Meta Analysis ◽

Host Factors ◽

Validation Data ◽

Genome Wide ◽

A Genome ◽

Crispr Screen ◽

Influenza A Virus Infection

AbstractHost dependency factors that are required for influenza A virus infection may serve as therapeutic targets as the virus is less likely to bypass them under drug-mediated selection pressure. Previous attempts to identify host factors have produced largely divergent results, with few overlapping hits across different studies. Here, we perform a genome-wide CRISPR/Cas9 screen and devise a new approach, meta-analysis by information content (MAIC) to systematically combine our results with prior evidence for influenza host factors. MAIC out-performs other meta-analysis methods when using our CRISPR screen as validation data. We validate the host factors, WDR7, CCDC115 and TMEM199, demonstrating that these genes are essential for viral entry and regulation of V-type ATPase assembly. We also find that CMTR1, a human mRNA cap methyltransferase, is required for efficient viral cap snatching and regulation of a cell autonomous immune response, and provides synergistic protection with the influenza endonuclease inhibitor Xofluza.

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A genome-wide CRISPR screen identifies ZCCHC14 as a host factor required for hepatitis B surface antigen production

10.1101/718940 ◽

2019 ◽

Author(s):

Anastasia Hyrina ◽

Christopher Jones ◽

Darlene Chen ◽

Scott Clarkson ◽

Nadire Cochran ◽

...

Keyword(s):

Hepatitis B ◽

Surface Antigen ◽

Hepatitis B Surface Antigen ◽

Genome Wide ◽

A Genome ◽

Chronic Hepatitis B Virus ◽

B Virus ◽

Crispr Screen ◽

Novel Host ◽

Circulating Levels

GRAPHICAL ABSTRACTSUMMARYA hallmark of chronic hepatitis B virus (CHB) infection is the presence of high circulating levels of non-infectious small lipid HBV surface antigen (HBsAg) vesicles. Although rare, sustained HBsAg loss is the idealized endpoint of any CHB therapy. A novel small molecule RG7834 has been previously reported to inhibit HBsAg expression by targeting terminal nucleotidyltransferase protein 4A and 4B (TENT4A and TENT4B). In this study, we describe a genome-wide CRISPR screen to identify other potential novel host factors required for HBsAg expression and to gain further insights into the mechanism of RG7834. We report more than 60 genes involved in regulating HBsAg and identified novel factors involved in RG7834 activity, including a zinc finger CCHC-type containing 14 (ZCCHC14) protein. We show that ZCCHC14, together with TENT4A/B, stabilizes HBsAg expression through HBV RNA tailing, providing a potential new therapeutic target to achieve functional cure in CHB patients.

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Genome-wide CRISPR activation screen identifies novel receptors for SARS-CoV-2 entry

10.1101/2021.04.08.438924 ◽

2021 ◽

Author(s):

Shiyou Zhu ◽

Ying Liu ◽

Zhuo Zhou ◽

Zhiying Zhang ◽

Xia Xiao ◽

...

Keyword(s):

Virus Entry ◽

Host Factors ◽

The Novel ◽

Host Proteins ◽

Alternative Pathways ◽

Genome Wide ◽

A Genome ◽

Novel Host ◽

Shed Light ◽

Crispr Activation

The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been endangering worldwide public health and economy. SARS-CoV-2 infects a variety of tissues where the known receptor ACE2 is low or almost absent, suggesting the existence of alternative pathways for virus entry. Here, we performed a genome-wide barcoded-CRISPRa screen to identify novel host factors that enable SARS-CoV-2 infection. In addition to known host proteins, i.e. ACE2, TMPRSS2, and NRP1, we identified multiple host components, among which LDLRAD3, TMEM30A, and CLEC4G were confirmed as functional receptors for SARS-CoV-2. All these membrane proteins bind directly to spike's N-terminal domain (NTD). Their essential and physiological roles have all been confirmed in either neuron or liver cells. In particular, LDLRAD3 and CLEC4G mediate SARS-CoV-2 entry and infection in a fashion independent of ACE2. The identification of the novel receptors and entry mechanisms could advance our understanding of the multiorgan tropism of SARS-CoV-2, and may shed light on the development of the therapeutic countermeasures against COVID-19.

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A genome-wide CRISPR screen identifies host factors that regulate SARS-CoV-2 entry

Nature Communications ◽

10.1038/s41467-021-21213-4 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 9

Author(s):

Yunkai Zhu ◽

Fei Feng ◽

Gaowei Hu ◽

Yuyan Wang ◽

Yin Yu ◽

...

Keyword(s):

Critical Role ◽

Surface Expression ◽

Host Factors ◽

Spike Protein ◽

Hamster Model ◽

Angiotensin Converting Enzyme 2 ◽

Genome Wide ◽

A Genome ◽

Public Health Challenges ◽

Crispr Screen

AbstractThe global spread of SARS-CoV-2 is posing major public health challenges. One feature of SARS-CoV-2 spike protein is the insertion of multi-basic residues at the S1/S2 subunit cleavage site. Here, we find that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site utilizes an endosomal entry pathway. Using Sdel as model, we perform a genome-wide CRISPR screen and identify several endosomal entry-specific regulators. Experimental validation of hits from the CRISPR screen shows that host factors regulating the surface expression of angiotensin-converting enzyme 2 (ACE2) affect entry of Sfull virus. Animal-to-animal transmission with the Sdel virus is reduced compared to Sfull in the hamster model. These findings highlight the critical role of the S1/S2 boundary of SARS-CoV-2 spike protein in modulating virus entry and transmission and provide insights into entry of coronaviruses.

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