Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection

Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here we performed a genome-wide CRISPR screen with SARS-CoV-2 and identified known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex and key components of the TGF-β signaling pathway. Small molecule inhibitors of these pathways prevented SARS-CoV-2-induced cell death. We also revealed that the alarmin HMGB1 is critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.

[1]  J. Melnick,et al.  Defectiveness of Interferon Production and of Rubella Virus Interference in a Line of African Green Monkey Kidney Cells (Vero) , 1968, Journal of virology.

[2]  M J Morgan,et al.  Regulation of the interferon system: evidence that Vero cells have a genetic defect in interferon production. , 1979, The Journal of general virology.

[3]  R. Derynck,et al.  Receptor-associated Mad homologues synergize as effectors of the TGF-β response , 1996, Nature.

[4]  A. Hata,et al.  TGF-β signalling through the Smad pathway , 1997 .

[5]  Takeshi Imamura,et al.  TGF‐β receptor‐mediated signalling through Smad2, Smad3 and Smad4 , 1997 .

[6]  Sergey Brin,et al.  The Anatomy of a Large-Scale Hypertextual Web Search Engine , 1998, Comput. Networks.

[7]  Jia-Yun Chen,et al.  TGF-β induces apoptosis through Smad-mediated expression of DAP-kinase , 2002, Nature Cell Biology.

[8]  Jia-Yun Chen,et al.  TGF-beta induces apoptosis through Smad-mediated expression of DAP-kinase. , 2002, Nature cell biology.

[9]  X. L. Liu,et al.  Isolation and Characterization of Viruses Related to the SARS Coronavirus from Animals in Southern China , 2003, Science.

[10]  S. Diamond,et al.  Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  A. Kaneda,et al.  RUNX3 Suppresses Gastric Epithelial Cell Growth by Inducing p21WAF1/Cip1 Expression in Cooperation with Transforming Growth Factor β-Activated SMAD , 2005, Molecular and Cellular Biology.

[12]  M. Jinnin,et al.  Characterization of SIS3, a Novel Specific Inhibitor of Smad3, and Its Effect on Transforming Growth Factor-β1-Induced Extracellular Matrix Expression , 2006, Molecular Pharmacology.

[13]  J. Onderwater,et al.  Ultrastructure and Origin of Membrane Vesicles Associated with the Severe Acute Respiratory Syndrome Coronavirus Replication Complex , 2006, Journal of Virology.

[14]  Silke Stertz,et al.  The intracellular sites of early replication and budding of SARS-coronavirus , 2007, Virology.

[15]  D. Somer,et al.  Regulation of the Interferon System : Evidence that Vero Cells have a Genetic Defect in Interferon Production , 2007 .

[16]  J. Nicholls,et al.  Severe Acute Respiratory Syndrome-associated Coronavirus Nucleocapsid Protein Interacts with Smad3 and Modulates Transforming Growth Factor-β Signaling , 2008, Journal of Biological Chemistry.

[17]  Abraham J Koster,et al.  SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum , 2008, PLoS biology.

[18]  Martin Rosvall,et al.  Maps of random walks on complex networks reveal community structure , 2007, Proceedings of the National Academy of Sciences.

[19]  Ye Guang Chen,et al.  Severe acute respiratory syndrome-associated coronavirus nucleocapsid protein interacts with Smad3 and modulates transforming growth factor-beta signaling. , 2008, The Journal of biological chemistry.

[20]  J. Massagué,et al.  Genome-wide Impact of the BRG1 SWI/SNF Chromatin Remodeler on the Transforming Growth Factor β Transcriptional Program* , 2008, Journal of Biological Chemistry.

[21]  M. Mann,et al.  Jmjd6 Catalyses Lysyl-Hydroxylation of U2AF65, a Protein Associated with RNA Splicing , 2009, Science.

[22]  K. Mossman,et al.  Characterization of the interferon regulatory factor 3-mediated antiviral response in a cell line deficient for IFN production. , 2009, Molecular immunology.

[23]  K. Takeda,et al.  TGF-beta is necessary for induction of IL-23R and Th17 differentiation by IL-6 and IL-23. , 2009, Biochemical and biophysical research communications.

[24]  Sunil K. Lal,et al.  Molecular biology of the SARS-coronavirus , 2010 .

[25]  R. Marmorstein,et al.  Human CABIN1 Is a Functional Member of the Human HIRA/UBN1/ASF1a Histone H3.3 Chaperone Complex , 2011, Molecular and Cellular Biology.

[26]  Terry P Yamaguchi,et al.  Wnt5a Potentiates TGF-β Signaling to Promote Colonic Crypt Regeneration After Tissue Injury , 2012, Science.

[27]  A. Shilatifard,et al.  The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers , 2013, Molecular and Cellular Biology.

[28]  Yusuke Nakamura,et al.  Lysyl 5-Hydroxylation, a Novel Histone Modification, by Jumonji Domain Containing 6 (JMJD6)* , 2013, The Journal of Biological Chemistry.

[29]  G. Almouzni,et al.  Placing the HIRA histone chaperone complex in the chromatin landscape. , 2013, Cell reports.

[30]  J. Moffat,et al.  Measuring error rates in genomic perturbation screens: gold standards for human functional genomics , 2014, Molecular systems biology.

[31]  Avi Ma’ayan,et al.  Histone H3.3 and its proteolytically processed form drive a cellular senescence program , 2014, Nature Communications.

[32]  Meagan E. Sullender,et al.  Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation , 2014, Nature Biotechnology.

[33]  Neville E. Sanjana,et al.  Improved vectors and genome-wide libraries for CRISPR screening , 2014, Nature Methods.

[34]  J. Moffat,et al.  Measuring error rates in genomic perturbation screens: gold standards for human functional genomics , 2014, bioRxiv.

[35]  Christian Drosten,et al.  Evidence for camel-to-human transmission of MERS coronavirus. , 2014, The New England journal of medicine.

[36]  Thomas O. Metz,et al.  Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses , 2014, mBio.

[37]  D. Durocher,et al.  High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities , 2015, Cell.

[38]  S. Knapp,et al.  Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance , 2015, Science Advances.

[39]  Xiaoqin Xia,et al.  Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition , 2015, Scientific Reports.

[40]  Chiou-Hong Lin,et al.  Pathological Ace2-to-Ace enzyme switch in the stressed heart is transcriptionally controlled by the endothelial Brg1–FoxM1 complex , 2016, Proceedings of the National Academy of Sciences.

[41]  Stephanie L. Johnson,et al.  Mechanisms of ATP-Dependent Chromatin Remodeling Motors. , 2016, Annual review of biophysics.

[42]  Shondra M. Pruett-Miller,et al.  Discovery of a proteinaceous cellular receptor for a norovirus , 2016, Science.

[43]  M. Weitzman,et al.  A core viral protein binds host nucleosomes to sequester immune danger signals , 2016, Nature.

[44]  Meagan E. Sullender,et al.  Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 , 2015, Nature Biotechnology.

[45]  Fang Li,et al.  Structure, Function, and Evolution of Coronavirus Spike Proteins. , 2016, Annual review of virology.

[46]  Gorjan Alagic,et al.  #p , 2019, Quantum information & computation.

[47]  Rong Zhang,et al.  Deletion of SMARCA4 impairs alveolar epithelial type II cells proliferation and aggravates pulmonary fibrosis in mice , 2017, Genes & diseases.

[48]  Alexandra Schäfer,et al.  Epigenetic Landscape during Coronavirus Infection , 2017, Pathogens.

[49]  Janet Iwasa,et al.  Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes , 2017, Nature Reviews Molecular Cell Biology.

[50]  Huan Yang,et al.  High-mobility group box 1 protein (HMGB1) operates as an alarmin outside as well as inside cells. , 2018, Seminars in immunology.

[51]  T. Harford,et al.  Induction of High Mobility Group Box-1 in vitro and in vivo by Respiratory Syncytial Virus , 2018, Pediatric Research.

[52]  Lisa E. Gralinski,et al.  MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape , 2018, Proceedings of the National Academy of Sciences.

[53]  Zhènglì Shí,et al.  Origin and evolution of pathogenic coronaviruses , 2018, Nature Reviews Microbiology.

[54]  Yukari Sato,et al.  Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit , 2018, Nature Communications.

[55]  A. Nakashima,et al.  TGF-β1 promotes expression of fibrosis-related genes through the induction of histone variant H3.3 and histone chaperone HIRA , 2018, Scientific Reports.

[56]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[57]  H. Tsukahara,et al.  Combined effect of anti‐high‐mobility group box‐1 monoclonal antibody and peramivir against influenza A virus‐induced pneumonia in mice , 2018, Journal of medical virology.

[58]  Jacob D. Jaffe,et al.  Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate , 2019, Science.

[59]  Analysis of Resistance of Ebola Virus Glycoprotein-Driven Entry Against MDL28170, An Inhibitor of Cysteine Cathepsins , 2019, Pathogens.

[60]  Sergei L. Kosakovsky Pond,et al.  A structural basis for antibody-mediated neutralization of Nipah virus reveals a site of vulnerability at the fusion glycoprotein apex , 2019, Proceedings of the National Academy of Sciences.

[61]  Yan Zhao,et al.  Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. , 2020, JAMA.

[62]  Ruth R. Montgomery,et al.  Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium , 2020, bioRxiv.

[63]  SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology , 2020, The Journal of general virology.

[64]  Shinji Makino,et al.  An Infectious cDNA Clone of SARS-CoV-2 , 2020, Cell Host & Microbe.

[65]  Qiang Zhou,et al.  Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 , 2020, Science.

[66]  T. Geisbert,et al.  Establishment of an African green monkey model for COVID-19 , 2020, Nature Immunology.

[67]  Jason M. Sheltzer,et al.  Cigarette Smoke Exposure and Inflammatory Signaling Increase the Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract , 2020, bioRxiv.

[68]  Fumihiro Kato,et al.  Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells , 2020, Proceedings of the National Academy of Sciences.

[69]  Harry B. Greenberg,et al.  TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes , 2020, Science Immunology.

[70]  P. Spagnolo,et al.  Pulmonary fibrosis secondary to COVID-19: a call to arms? , 2020, The Lancet Respiratory Medicine.

[71]  Peter G. Schultz,et al.  A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals , 2020, bioRxiv.

[72]  Natacha S. Ogando,et al.  SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology , 2020, bioRxiv.

[73]  A. Walls,et al.  Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein , 2020, Cell.

[74]  Hugh Chen,et al.  From local explanations to global understanding with explainable AI for trees , 2020, Nature Machine Intelligence.

[75]  Fang Li,et al.  Cell entry mechanisms of SARS-CoV-2 , 2020, Proceedings of the National Academy of Sciences.

[76]  M. Hoffmann,et al.  A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells , 2020, Molecular Cell.

[77]  Andrea Marzi,et al.  Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses , 2020, Nature Microbiology.

[78]  M. Bertrand,et al.  RSV Infection Promotes Necroptosis and HMGB1 Release by Airway Epithelial Cells. , 2020, American journal of respiratory and critical care medicine.

[79]  Benjamin J. Polacco,et al.  A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing , 2020, Nature.

[80]  G. Herrler,et al.  SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor , 2020, Cell.

[81]  Yan Liu,et al.  Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV , 2020, Nature Communications.

[82]  E. Dong,et al.  An interactive web-based dashboard to track COVID-19 in real time , 2020, The Lancet Infectious Diseases.

[83]  K. Tracey,et al.  Extracellular HMGB1: a therapeutic target in severe pulmonary inflammation including COVID-19? , 2020, Molecular Medicine.

[84]  G. Gao,et al.  A Novel Coronavirus from Patients with Pneumonia in China, 2019 , 2020, The New England journal of medicine.

[85]  P. Alam.  ‘W’ , 2021, Composites Engineering.

[86]  P. Alam.  ‘T’ , 2021, Composites Engineering: An A–Z Guide.

[87]  P. Alam.  ‘L’ , 2021, Composites Engineering: An A–Z Guide.