1
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Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nat Commun 2023; 14:6245. [PMID: 37803001 PMCID: PMC10558542 DOI: 10.1038/s41467-023-41788-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023] Open
Abstract
Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.
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Affiliation(s)
- Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California, Berkeley-UCSF Joint Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oren S Rosenberg
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| | - Marco Y Hein
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Center for Medical Biochemistry, Vienna, Austria.
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2
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Samelson AJ, Tran QD, Robinot R, Carrau L, Rezelj VV, Kain AM, Chen M, Ramadoss GN, Guo X, Lim SA, Lui I, Nuñez JK, Rockwood SJ, Wang J, Liu N, Carlson-Stevermer J, Oki J, Maures T, Holden K, Weissman JS, Wells JA, Conklin BR, TenOever BR, Chakrabarti LA, Vignuzzi M, Tian R, Kampmann M. BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2. Nat Cell Biol 2022; 24:24-34. [PMID: 35027731 PMCID: PMC8820466 DOI: 10.1038/s41556-021-00821-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 11/24/2021] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 infection of human cells is initiated by the binding of the viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen to uncover druggable pathways controlling Spike protein binding to human cells. Here we show that the protein BRD2 is required for ACE2 transcription in human lung epithelial cells and cardiomyocytes, and BRD2 inhibitors currently evaluated in clinical trials potently block endogenous ACE2 expression and SARS-CoV-2 infection of human cells, including those of human nasal epithelia. Moreover, pharmacological BRD2 inhibition with the drug ABBV-744 inhibited SARS-CoV-2 replication in Syrian hamsters. We also found that BRD2 controls transcription of several other genes induced upon SARS-CoV-2 infection, including the interferon response, which in turn regulates the antiviral response. Together, our results pinpoint BRD2 as a potent and essential regulator of the host response to SARS-CoV-2 infection and highlight the potential of BRD2 as a therapeutic target for COVID-19.
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Affiliation(s)
- Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- École Doctorale BioSPC, Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Rémy Robinot
- Institut Pasteur, CIVIC Group, Virus and Immunity Unit, Université de Paris, Paris, France
| | - Lucia Carrau
- Microbiology Department, NYU-Langone, New York, NY, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- École Doctorale BioSPC, Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Merissa Chen
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Gokul N Ramadoss
- Gladstone Institutes, San Francisco, CA, USA
- Biomedical Sciences PhD Program, University of California San Francisco, San Francisco, CA, USA
| | - Xiaoyan Guo
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Shion A Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Antibody Engineering, Genentech Inc., San Francisco, CA, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | | | - Jianhui Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Na Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | | | | | | | | | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
| | - James A Wells
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Lisa A Chakrabarti
- Institut Pasteur, CIVIC Group, Virus and Immunity Unit, Université de Paris, Paris, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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3
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Affiliation(s)
- Megan L Hochstrasser
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - James K Nuñez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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4
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Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell 2021; 184:2503-2519.e17. [PMID: 33838111 PMCID: PMC8376083 DOI: 10.1016/j.cell.2021.03.025] [Citation(s) in RCA: 242] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 12/23/2022]
Abstract
A general approach for heritably altering gene expression has the potential to enable many discovery and therapeutic efforts. Here, we present CRISPRoff-a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks establishes rules for heritable gene silencing. We identify single guide RNAs (sgRNAs) capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. The broad ability of CRISPRoff to initiate heritable gene silencing even outside of CGIs expands the canonical model of methylation-based silencing and enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.
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Affiliation(s)
- James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Greg C Pommier
- Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - Carmen Adriaens
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Gokul N Ramadoss
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158
| | - Angela N Pogson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - James Y S Kim
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Amanda Chung
- Department of Urology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | | | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Volker Hovestadt
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA.
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5
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Chen J, Brunner AD, Cogan JZ, Nuñez JK, Fields AP, Adamson B, Itzhak DN, Li JY, Mann M, Leonetti MD, Weissman JS. Pervasive functional translation of noncanonical human open reading frames. Science 2020; 367:1140-1146. [PMID: 32139545 DOI: 10.1126/science.aay0262] [Citation(s) in RCA: 303] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 11/22/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022]
Abstract
Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). In this work, we exploit a systematic CRISPR-based screening strategy to identify hundreds of noncanonical CDSs that are essential for cellular growth and whose disruption elicits specific, robust transcriptomic and phenotypic changes in human cells. Functional characterization of the encoded microproteins reveals distinct cellular localizations, specific protein binding partners, and hundreds of microproteins that are presented by the human leukocyte antigen system. We find multiple microproteins encoded in upstream open reading frames, which form stable complexes with the main, canonical protein encoded on the same messenger RNA, thereby revealing the use of functional bicistronic operons in mammals. Together, our results point to a family of functional human microproteins that play critical and diverse cellular roles.
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Affiliation(s)
- Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Andreas-David Brunner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Alexander P Fields
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Britt Adamson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel N Itzhak
- Cell Atlas Initiative, Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jason Y Li
- Cell Atlas Initiative, Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.,Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Manuel D Leonetti
- Cell Atlas Initiative, Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA. .,Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
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6
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Tak YE, Kleinstiver BP, Nuñez JK, Hsu JY, Horng JE, Gong J, Weissman JS, Joung JK. Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors. Nat Methods 2017; 14:1163-1166. [PMID: 29083402 PMCID: PMC5909187 DOI: 10.1038/nmeth.4483] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/24/2017] [Indexed: 12/18/2022]
Abstract
Targeted and inducible regulation of mammalian gene expression is a broadly important capability. We engineered drug-inducible catalytically inactive Cpf1 fused to transcriptional activation domains to tune the expression of endogenous genes in human cells. Leveraging the multiplex capability of the Cpf1 platform, we demonstrate both synergistic and combinatorial gene expression in human cells. Our work should enable the development of multiplex gene perturbation library screens for understanding complex cellular phenotypes.
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Affiliation(s)
- Y Esther Tak
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin P Kleinstiver
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - James K Nuñez
- Department of Cellular & Molecular Pharmacology University of California, San Francisco, San Francisco, California, USA
| | - Jonathan Y Hsu
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Joy E Horng
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Jingyi Gong
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Jonathan S Weissman
- Department of Cellular & Molecular Pharmacology University of California, San Francisco, San Francisco, California, USA.,Howard Hughes Medical Institute, San Francisco, California, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
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7
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Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell 2016; 167:1867-1882.e21. [PMID: 27984733 PMCID: PMC5315571 DOI: 10.1016/j.cell.2016.11.048] [Citation(s) in RCA: 618] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/14/2016] [Accepted: 11/19/2016] [Indexed: 12/20/2022]
Abstract
Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis. Subjecting ∼100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses decoupled the three UPR branches, revealed bifurcated UPR branch activation among cells subject to the same perturbation, and uncovered differential activation of the branches across hits, including an isolated feedback loop between the translocon and IRE1α. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses.
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Affiliation(s)
- Britt Adamson
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Thomas M Norman
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Jost
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Min Y Cho
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James K Nuñez
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuwen Chen
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacqueline E Villalta
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Luke A Gilbert
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Max A Horlbeck
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Y Hein
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ryan A Pak
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew N Gray
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Atray Dixit
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02142, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Oren Parnas
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Jonathan S Weissman
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
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Wright AV, Nuñez JK, Doudna JA. Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering. Cell 2016; 164:29-44. [PMID: 26771484 DOI: 10.1016/j.cell.2015.12.035] [Citation(s) in RCA: 671] [Impact Index Per Article: 83.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Indexed: 12/26/2022]
Abstract
Bacteria and archaea possess a range of defense mechanisms to combat plasmids and viral infections. Unique among these are the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems, which provide adaptive immunity against foreign nucleic acids. CRISPR systems function by acquiring genetic records of invaders to facilitate robust interference upon reinfection. In this Review, we discuss recent advances in understanding the diverse mechanisms by which Cas proteins respond to foreign nucleic acids and how these systems have been harnessed for precision genome manipulation in a wide array of organisms.
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Affiliation(s)
- Addison V Wright
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James K Nuñez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute HHMI, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, Berkeley, CA 94720, USA.
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Abstract
The application of the CRISPR-Cas9 system for genome engineering has revolutionized the ability to interrogate genomes of mammalian cells. Programming the Cas9 endonuclease to induce DNA breaks at specified sites is achieved by simply modifying the sequence of its cognate guide RNA. Although Cas9-mediated genome editing has been shown to be highly specific, cleavage events at off-target sites have also been reported. Minimizing, and eventually abolishing, unwanted off-target cleavage remains a major goal of the CRISPR-Cas9 technology before its implementation for therapeutic use. Recent efforts have turned to chemical biology and biophysical approaches to engineer inducible genome editing systems for controlling Cas9 activity at the transcriptional and protein levels. Here, we review recent advancements to modulate Cas9-mediated genome editing by engineering split-Cas9 constructs, inteins, small molecules, protein-based dimerizing domains, and light-inducible systems.
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Affiliation(s)
- James K. Nuñez
- Department
of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Lucas B. Harrington
- Department
of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jennifer A. Doudna
- Department
of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Chemistry, Howard Hughes Medical Institute, Innovative Genomics
Institute, Center for RNA Systems Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA. Foreign DNA capture during CRISPR-Cas adaptive immunity. Nature 2015; 527:535-8. [PMID: 26503043 PMCID: PMC4662619 DOI: 10.1038/nature15760] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/06/2015] [Indexed: 12/21/2022]
Abstract
Bacteria and archaea generate adaptive immunity against phages and plasmids by integrating foreign DNA of specific 30-40-base-pair lengths into clustered regularly interspaced short palindromic repeat (CRISPR) loci as spacer segments. The universally conserved Cas1-Cas2 integrase complex catalyses spacer acquisition using a direct nucleophilic integration mechanism similar to retroviral integrases and transposases. How the Cas1-Cas2 complex selects foreign DNA substrates for integration remains unknown. Here we present X-ray crystal structures of the Escherichia coli Cas1-Cas2 complex bound to cognate 33-nucleotide protospacer DNA substrates. The protein complex creates a curved binding surface spanning the length of the DNA and splays the ends of the protospacer to allow each terminal nucleophilic 3'-OH to enter a channel leading into the Cas1 active sites. Phosphodiester backbone interactions between the protospacer and the proteins explain the sequence-nonspecific substrate selection observed in vivo. Our results uncover the structural basis for foreign DNA capture and the mechanism by which Cas1-Cas2 functions as a molecular ruler to dictate the sequence architecture of CRISPR loci.
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Affiliation(s)
- James K Nuñez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Philip J Kranzusch
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California 94720, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California 94720, USA.,Center for RNA Systems Biology, University of California, Berkeley, Berkeley, California 94720, USA
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Sullivan JT, Spence JV, Nuñez JK. Killing of Schistosoma mansoni sporocysts in Biomphalaria glabrata implanted with amoebocyte-producing organ allografts from resistant snails. J Parasitol 1995; 81:829-33. [PMID: 7472893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Schistosome-susceptible National Institutes of Health (NIH) albino Biomphalaria glabrata were implanted with the amoebocyte-producing organ (APO) from 4 types of donors: (1) exposed-resistant (eR), i.e., schistosome-resistant 13-16-R1 snails that had been exposed to miracidia of Schistosoma mansoni 30 or more days previously in order to verify their resistance, (2) exposed-susceptible (eS), i.e., NIH albino snails that had been similarly exposed to miracidia, (3) unexposed-resistant (uR), and (4) unexposed-susceptible (uS). Allograft recipients, along with unimplanted NIH albino and 13-16-R1 controls (cS and cR, respectively), were then challenged with 100 miracidia each of Schistosoma mansoni at 14-15 days postimplantation. Histological sections of tentacles fixed at 3 days postchallenge (PC) showed significantly fewer normal sporocysts and more numerous developmentally retarded sporocysts in cR snails than in the other 5 treatment groups, and significantly more killed sporocysts in both cR snails and recipients of eR APOs than in the other 4 groups. In addition, the histological condition of eR allografts in both unchallenged (at 1, 3, 7, 10, and 14 days postimplantation) and schistosome-challenged (at 3 days PC) NIH albino recipients was examined. Viable hematopoietic cells were found in 96% of implants, and in 86% of implants low numbers of mitotic figures were found among these cells, although no increased mitotic activity occurred in challenged recipients. These data suggest that lowered susceptibility to infection with S. mansoni in recipients of APO allografts results primarily from hemocyte-mediated resistance.
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Affiliation(s)
- J T Sullivan
- Department of Biology, Lamar University, Beaumont, Texas 77710, USA
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