Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection

Jin, Wei; Alfajaro, Mia Madel; DeWeirdt, Peter C; Hanna, Ruth E.; Lu-Culligan, William J.; Cai, Wesley L.; Strine, Madison S.; Zhang, Shang Min; Graziano, Vincent R.; Schmitz, Cameron O.; Chen, Jennifer; Mankowski, Madeleine C.; Filler, Renata; Ravindra, Neal G.; Gasque, Victor; Miguel, Fernando J. de; Patil, Ajinkya; Chen, Huacui; Oguntuyo, Kasopefoluwa Y.; Abriola, Laura; Surovtseva, Yulia V.; Orchard, Robert C.; Lee, Benhur; Lindenbach, Brett D.; Politi, Katerina; Dijk, David van; Kadoch, Cigall; Simon, Matthew D.; Yan, Qin; Doench, John G.; Wilen, Craig B.

doi:10.1016/j.cell.2020.10.028

Cited by 488 publications

(660 citation statements)

References 100 publications

(112 reference statements)

Supporting

Mentioning

604

Contrasting

Unclassified

Order By: Relevance

“…While the PPIA inhibitor cyclosporin A has immunosuppressive properties, the non-immunosuppressive cyclosporin A analogue alisporivir may offer greater translational potential 82 ; (2) a role for the RNA-binding metabolic enzyme ATP1A1 37 in coronavirus and respiratory syncytial virus infections has been reported previously 83,84 . ATP1A1 had a significant effect on virus-induced cell death in a SARS-CoV-2 CRISPR perturbation screen 67 . Hence, both genetic and pharmacological evidence point to ATP1A1 as an important SARS-CoV-2 host factor; (3) ARP2 is part of the actin-related protein 2/3 complex and contributes to regulating cell shape and motility, which can affect intracellular pathogens 82 .…”

Section: Discussionmentioning

confidence: 99%

“…To functionally stratify our direct RNA binders, we intersected the SARS-CoV-2 RNA interactome with a recent genome-wide CRISPR perturbation screen designed to identify host factors that affect cell survival after SARS-CoV-2 infection 67 . Out of 104 human proteins in our expanded RNA interactome, we obtained CRISPR z-scores for 94 proteins 67 ; depletion of 11 of these proteins had a statistically significant effect on SARS-CoV-2-induced cell death ( Fig. 4a).…”

Section: Genetic Screens Identify Functional Sars-cov-2 Rna Bindersmentioning

confidence: 99%

See 1 more Smart Citation

The SARS-CoV-2 RNA–protein interactome in infected human cells

et al. 2020

View full text Add to dashboard Cite

Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Genetic Screens Identify Functional Sars-cov-2 Rna Bindersmentioning

confidence: 99%

The SARS-CoV-2 RNA–protein interactome in infected human cells

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Alongside the first wave of clinical trials aimed at exploring off-the-shelf COVID-19 drugs, a parallel effort has searched for hits using phenotypic high throughput drug screens, in silico modeling of small molecule inhibitors with SARS-CoV-2 proteins and identification of host cell drug targets that are needed for viral proliferation (46,(57)(58)(59). These preclinical efforts have identified compounds that have low nanomolar IC 50 s against SARS-CoV-2 (57,60).…”

Section: Resultsmentioning

confidence: 99%

The Need for Antiviral Drugs for Pandemic Coronaviruses From a Global Health Perspective

et al. 2020

View full text Add to dashboard Cite

Respiratory failure due to SARS-CoV-2 has caused widespread mortality, creating an urgent need for effective treatments and a long-term need for antivirals for future emergent coronaviruses. Pharmacotherapy for respiratory viruses has largely been unsuccessful with the exception of early treatment of influenza viruses, which shortens symptom duration and prevents infection in close contacts. Under the rapidly evolving circumstances of the COVID-19 pandemic, most clinical trials of experimental treatments in the United States have focused on later stages of the disease process. Worldwide, the clinical studies of the most impactful drugs, remdesivir and dexamethasone in ACTT-1, RECOVERY, and Solidarity, have studied hospitalized patients. Less than half of clinical trials in the U.S. have investigated oral agents, and the majority have taken place in hospitals at a disease stage where the viral load is already decreasing. The limited success of treatments for respiratory viruses and the viral dynamics of COVID-19 suggest that an antiviral therapy with the greatest impact against pandemic coronaviruses would be orally administered, well-tolerated, target a highly conserved viral protein or host-coronavirus interaction and could be used effectively throughout the world, including resource-poor settings. We examine the treatment of respiratory viral infections and current clinical trials for COVID-19 to provide a framework for effective antiviral therapy and prevention of future emergent coronaviruses and call attention to the need for continued preclinical drug discovery.

show abstract

“…HMGB1 has long been the focus of studies of host inflammatory responses 80,81 , but its intranuclear role during infection is also intimately linked to viral infection 32 . Intriguingly, HMGB1 was recently found to be required for SARS-CoV-2 infection 82 . Although the mechanism is not known, preliminary evidence suggests that the interaction of HMGB1 with chromatin underlies this dependency, which hints that the novel vulnerability we expose in H1-HMGB1 antagonism may be exploited by a wide range of intracellular pathogens.…”

Section: Discussionmentioning

confidence: 99%

A viral histone-like protein exploits antagonism between linker histones and HMGB proteins to obstruct the cell cycle

Lynch

Bat-Erdene

Dillon

et al. 2020

Preprint

View full text Add to dashboard Cite

Virus infection necessarily requires redirecting cellular resources towards viral progeny production. Adenovirus encodes the histone-like protein VII that causes catastrophic global reorganization of host chromatin to promote virus infection. Protein VII recruits the family of high mobility group box (HMGB) proteins to chromatin along with the histone chaperone SET. As a consequence of this recruitment, we find that protein VII causes chromatin-depletion of several linker histone H1 isoforms. The relationship between linker histone H1 and the functionally opposite HMGB proteins is critical for higher order chromatin structure. However, the physiological consequences of perturbing this relationship are largely unknown. Here, we employ complementary systems in Saccharomyces cerevisiae and human cells to demonstrate that adenovirus protein VII disrupts the H1-HMGB balance to obstruct the cell cycle. We find that protein VII causes an accumulation of G2/M cells both in yeast and human systems, underscoring the high conservation of this chromatin vulnerability. In contrast, adenovirus E1A and E1B proteins are well-established to override cell cycle regulation and promote transformation of human cells. Strikingly, we find that protein VII obstructs the cell cycle even in the presence of E1A and E1B, suggesting that protein VII-directed cell cycle disruption ensures host resources are directed towards viral proliferation during infection. Together, our results demonstrate that protein VII targets H1-HMGB1 antagonism to obstruct cell cycle progression, revealing an unexpected chromatin vulnerability exploited for viral benefit.

show abstract

Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection

Cited by 488 publications

References 100 publications

The SARS-CoV-2 RNA–protein interactome in infected human cells

The SARS-CoV-2 RNA–protein interactome in infected human cells

The Need for Antiviral Drugs for Pandemic Coronaviruses From a Global Health Perspective

A viral histone-like protein exploits antagonism between linker histones and HMGB proteins to obstruct the cell cycle

Contact Info

Product

Resources

About