51
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Rauch S, Jones KA, Dickinson BC. Small Molecule-Inducible RNA-Targeting Systems for Temporal Control of RNA Regulation. ACS CENTRAL SCIENCE 2020; 6:1987-1996. [PMID: 33274276 PMCID: PMC7706094 DOI: 10.1021/acscentsci.0c00537] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Indexed: 06/12/2023]
Abstract
All aspects of mRNA lifetime and function, including its stability, translation into protein, and trafficking through the cell, are tightly regulated through coordinated post-transcriptional modifications and interactions with a multitude of RNA effector proteins. Despite the increasing recognition of RNA regulation as a critical layer of mammalian gene expression control and its increasing excitement as a therapeutic target, tools to study and control RNA regulatory mechanisms with temporal precision in their endogenous environment are lacking. Here, we present small molecule-inducible RNA-targeting effectors based on our previously developed CRISPR/Cas-inspired RNA targeting system (CIRTS). The CIRTS biosensor platform is based on guide RNA (gRNA)-dependent RNA binding domains that interact with a target transcript using Watson-Crick-Franklin base pair interactions. Addition of a small molecule recruits an RNA effector to the target transcript, thereby eliciting a local effect on the transcript. In this work, we showcase that these CIRTS biosensors can trigger inducible RNA editing, degradation, or translation on target transcripts in a small molecule-dependent manner. We further go on to show that the CIRTS RNA base editor biosensor can induce RNA base editing in a small molecule-controllable manner in vivo. Collectively this work provides a new set of tools to probe the dynamics of RNA regulatory systems and control gene expression at the RNA level.
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Affiliation(s)
- Simone Rauch
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Krysten A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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52
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Ahmadi F, Quach ABV, Shih SCC. Is microfluidics the "assembly line" for CRISPR-Cas9 gene-editing? BIOMICROFLUIDICS 2020; 14:061301. [PMID: 33262863 PMCID: PMC7688342 DOI: 10.1063/5.0029846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Acclaimed as one of the biggest scientific breakthroughs, the technology of CRISPR has brought significant improvement in the biotechnological spectrum-from editing genetic defects in diseases for gene therapy to modifying organisms for the production of biofuels. Since its inception, the CRISPR-Cas9 system has become easier and more versatile to use. Many variants have been found, giving the CRISPR toolkit a great range that includes the activation and repression of genes aside from the previously known knockout and knockin of genes. Here, in this Perspective, we describe efforts on automating the gene-editing workflow, with particular emphasis given on the use of microfluidic technology. We discuss how automation can address the limitations of gene-editing and how the marriage between microfluidics and gene-editing will expand the application space of CRISPR.
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Affiliation(s)
| | | | - Steve C. C. Shih
- Author to whom correspondence should be addressed:. Tel.: +1-(514) 848-2424 x7579
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53
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Carlson-Stevermer J, Kelso R, Kadina A, Joshi S, Rossi N, Walker J, Stoner R, Maures T. CRISPRoff enables spatio-temporal control of CRISPR editing. Nat Commun 2020; 11:5041. [PMID: 33028827 PMCID: PMC7542431 DOI: 10.1038/s41467-020-18853-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/16/2020] [Indexed: 12/12/2022] Open
Abstract
Following introduction of CRISPR-Cas9 components into a cell, genome editing occurs unabated until degradation of its component nucleic acids and proteins by cellular processes. This uncontrolled reaction can lead to unintended consequences including off-target editing and chromosomal translocations. To address this, we develop a method for light-induced degradation of sgRNA termed CRISPRoff. Here we show that light-induced inactivation of ribonucleoprotein attenuates genome editing within cells and allows for titratable levels of editing efficiency and spatial patterning via selective illumination.
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Affiliation(s)
| | - Reed Kelso
- Synthego Corporation, 3565 Haven Avenue, Menlo Park, CA, 94025, USA
- Freenome, 259 East Grand Ave, South San Francisco, CA, 94080, USA
| | - Anastasia Kadina
- Synthego Corporation, 3565 Haven Avenue, Menlo Park, CA, 94025, USA
| | - Sahil Joshi
- Synthego Corporation, 3565 Haven Avenue, Menlo Park, CA, 94025, USA
| | - Nicholas Rossi
- Synthego Corporation, 3565 Haven Avenue, Menlo Park, CA, 94025, USA
| | - John Walker
- Synthego Corporation, 3565 Haven Avenue, Menlo Park, CA, 94025, USA
| | - Rich Stoner
- Synthego Corporation, 3565 Haven Avenue, Menlo Park, CA, 94025, USA
| | - Travis Maures
- Synthego Corporation, 3565 Haven Avenue, Menlo Park, CA, 94025, USA
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54
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Abstract
Over a thousand diseases are caused by mutations that alter gene expression levels. The potential of nuclease-deficient zinc fingers, TALEs or CRISPR fusion systems to treat these diseases by modulating gene expression has recently emerged. These systems can be applied to modify the activity of gene-regulatory elements - promoters, enhancers, silencers and insulators, subsequently changing their target gene expression levels to achieve therapeutic benefits - an approach termed cis-regulation therapy (CRT). Here, we review emerging CRT technologies and assess their therapeutic potential for treating a wide range of diseases caused by abnormal gene dosage. The challenges facing the translation of CRT into the clinic are discussed.
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55
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Azangou-Khyavy M, Ghasemi M, Khanali J, Boroomand-Saboor M, Jamalkhah M, Soleimani M, Kiani J. CRISPR/Cas: From Tumor Gene Editing to T Cell-Based Immunotherapy of Cancer. Front Immunol 2020; 11:2062. [PMID: 33117331 PMCID: PMC7553049 DOI: 10.3389/fimmu.2020.02062] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats system has demonstrated considerable advantages over other nuclease-based genome editing tools due to its high accuracy, efficiency, and strong specificity. Given that cancer is caused by an excessive accumulation of mutations that lead to the activation of oncogenes and inactivation of tumor suppressor genes, the CRISPR/Cas9 system is a therapy of choice for tumor genome editing and treatment. In defining its superior use, we have reviewed the novel applications of the CRISPR genome editing tool in discovering, sorting, and prioritizing targets for subsequent interventions, and passing different hurdles of cancer treatment such as epigenetic alterations and drug resistance. Moreover, we have reviewed the breakthroughs precipitated by the CRISPR system in the field of cancer immunotherapy, such as identification of immune system-tumor interplay, production of universal Chimeric Antigen Receptor T cells, inhibition of immune checkpoint inhibitors, and Oncolytic Virotherapy. The existing challenges and limitations, as well as the prospects of CRISPR based systems, are also discussed.
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Affiliation(s)
| | - Mobina Ghasemi
- Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Khanali
- Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Monire Jamalkhah
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Masoud Soleimani
- Hematology Department, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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56
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Zhang Y, Ling X, Su X, Zhang S, Wang J, Zhang P, Feng W, Zhu YY, Liu T, Tang X. Optical Control of a CRISPR/Cas9 System for Gene Editing by Using Photolabile crRNA. Angew Chem Int Ed Engl 2020; 59:20895-20899. [DOI: 10.1002/anie.202009890] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xiaoxuan Su
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Shilin Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Pingjing Zhang
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - Wenjian Feng
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - York Yuanyuan Zhu
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
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57
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Zhang Y, Ling X, Su X, Zhang S, Wang J, Zhang P, Feng W, Zhu YY, Liu T, Tang X. Optical Control of a CRISPR/Cas9 System for Gene Editing by Using Photolabile crRNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xiaoxuan Su
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Shilin Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Pingjing Zhang
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - Wenjian Feng
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - York Yuanyuan Zhu
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
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58
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Directed Evolution of CRISPR/Cas Systems for Precise Gene Editing. Trends Biotechnol 2020; 39:262-273. [PMID: 32828556 DOI: 10.1016/j.tibtech.2020.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022]
Abstract
CRISPR technology is a universal tool for genome engineering that has revolutionized biotechnology. Recently identified unique CRISPR/Cas systems, as well as re-engineered Cas proteins, have rapidly expanded the functions and applications of CRISPR/Cas systems. The structures of Cas proteins are complex, containing multiple functional domains. These protein domains are evolutionarily conserved polypeptide units that generally show independent structural or functional properties. In this review, we propose using protein domains as a new way to classify protein engineering strategies for these proteins and discuss common ways to engineer key domains to modify the functions of CRISPR/Cas systems.
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59
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Lim D, Sreekanth V, Cox KJ, Law BK, Wagner BK, Karp JM, Choudhary A. Engineering designer beta cells with a CRISPR-Cas9 conjugation platform. Nat Commun 2020; 11:4043. [PMID: 32792475 PMCID: PMC7426819 DOI: 10.1038/s41467-020-17725-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 07/10/2020] [Indexed: 12/23/2022] Open
Abstract
Genetically fusing protein domains to Cas9 has yielded several transformative technologies; however, the genetic modifications are limited to natural polypeptide chains at the Cas9 termini, which excludes a diverse array of molecules useful for gene editing. Here, we report chemical modifications that allow site-specific and multiple-site conjugation of a wide assortment of molecules on both the termini and internal sites of Cas9, creating a platform for endowing Cas9 with diverse functions. Using this platform, Cas9 can be modified to more precisely incorporate exogenously supplied single-stranded oligonucleotide donor (ssODN) at the DNA break site. We demonstrate that the multiple-site conjugation of ssODN to Cas9 significantly increases the efficiency of precision genome editing, and such a platform is compatible with ssODNs of diverse lengths. By leveraging the conjugation platform, we successfully engineer INS-1E, a β-cell line, to repurpose the insulin secretion machinery, which enables the glucose-dependent secretion of protective immunomodulatory factor interleukin-10. Cas9 fusions partners are often limited to natural polypeptide chains at the Cas9 termni. Here the authors present a platform for site-specific and multiple-site conjugation to both termini and internal sites of Cas9, and they apply this platform to efficiently engineer insulin-producing β cells.
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Affiliation(s)
- Donghyun Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Vedagopuram Sreekanth
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Kurt J Cox
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Benjamin K Law
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.,Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jeffrey M Karp
- Engineering in Medicine, Department of Medicine, Center for Regenerative Therapeutics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA, 02139, USA.,Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA. .,Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA.
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60
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Medhi D, Jasin M. CRISPR at lightning speeds. Science 2020; 368:1180-1181. [PMID: 32527814 DOI: 10.1126/science.abc3997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Darpan Medhi
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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61
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Zhou W, Brown W, Bardhan A, Delaney M, Ilk AS, Rauen RR, Kahn SI, Tsang M, Deiters A. Spatiotemporal Control of CRISPR/Cas9 Function in Cells and Zebrafish using Light-Activated Guide RNA. Angew Chem Int Ed Engl 2020; 59:8998-9003. [PMID: 32160370 PMCID: PMC7250724 DOI: 10.1002/anie.201914575] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/14/2020] [Indexed: 12/27/2022]
Abstract
We developed a new method for the conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos using photochemically activated, caged guide RNAs (gRNAs). Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5'-protospacer region with caged nucleobases during synthesis. Caging confers complete suppression of gRNA:dsDNA-target hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation. This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off-to-on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes. Caged gRNAs are novel tools for the conditional control of gene editing, thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
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Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Michael Delaney
- Horizon Discovery, 2650 Crescent Drive, Lafayette, CO, 80026, USA
| | - Amber S Ilk
- Horizon Discovery, 2650 Crescent Drive, Lafayette, CO, 80026, USA
| | - Randy R Rauen
- Horizon Discovery, 2650 Crescent Drive, Lafayette, CO, 80026, USA
| | - Shoeb I Kahn
- Horizon Discovery, 2650 Crescent Drive, Lafayette, CO, 80026, USA
| | - Michael Tsang
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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62
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Zuo Z, Liu J. Allosteric regulation of CRISPR-Cas9 for DNA-targeting and cleavage. Curr Opin Struct Biol 2020; 62:166-174. [PMID: 32070859 PMCID: PMC7308215 DOI: 10.1016/j.sbi.2020.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/29/2022]
Abstract
The CRISPR-Cas9 system from Streptococcus pyogenes has been exploited as a programmable RNA-guided DNA-targeting and DNA-editing platform. This evolutionary tool enables diverse genetic manipulations with unprecedented precision and ease. Cas9 is an allosteric enzyme, which is allosterically regulated in conformational activation, target recognition, and DNA cleavage. Here, we outline the underlying allosteric control over the Cas9 complex assembly and targeting specificity. We further review the strategies for mitigating intrinsic Cas9 off-target effects through allosteric modulations and the advances in engineering controllable Cas9 systems that are responsive to external allosteric signals. Future development of highly specific, tunable CRISPR-Cas9 systems through allosteric modulations would greatly benefit applications that require both conditional control and high precision.
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Affiliation(s)
- Zhicheng Zuo
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
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63
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Zhou W, Brown W, Bardhan A, Delaney M, Ilk AS, Rauen RR, Kahn SI, Tsang M, Deiters A. Spatiotemporal Control of CRISPR/Cas9 Function in Cells and Zebrafish using Light‐Activated Guide RNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914575] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Wes Brown
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Anirban Bardhan
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Michael Delaney
- Horizon Discovery 2650 Crescent Drive Lafayette CO 80026 USA
| | - Amber S. Ilk
- Horizon Discovery 2650 Crescent Drive Lafayette CO 80026 USA
| | - Randy R. Rauen
- Horizon Discovery 2650 Crescent Drive Lafayette CO 80026 USA
| | - Shoeb I. Kahn
- Horizon Discovery 2650 Crescent Drive Lafayette CO 80026 USA
| | - Michael Tsang
- Department of Developmental Biology School of Medicine University of Pittsburgh Pittsburgh PA 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
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64
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Hulton CH, Costa EA, Shah NS, Quintanal-Villalonga A, Heller G, de Stanchina E, Rudin CM, Poirier JT. Direct genome editing of patient-derived xenografts using CRISPR-Cas9 enables rapid in vivo functional genomics. ACTA ACUST UNITED AC 2020; 1:359-369. [PMID: 33345196 DOI: 10.1038/s43018-020-0040-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Patient-derived xenografts are high fidelity in vivo tumor models that accurately reflect many key aspects of human cancer. In contrast to either cancer cell lines or genetically engineered mouse models, the utility of PDXs has been limited by the inability to perform targeted genome editing of these tumors. To address this limitation, we have developed methods for CRISPR-Cas9 editing of PDXs using a tightly regulated, inducible Cas9 vector that does not require in vitro culture for selection of transduced cells. We demonstrate the utility of this platform in PDXs (1) to analyze genetic dependencies by targeted gene disruption and (2) to analyze mechanisms of acquired drug resistance by site-specific gene editing using templated homology-directed repair. This flexible system has broad application to other explant models and substantially augments the utility of PDXs as genetically programmable models of human cancer.
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Affiliation(s)
- Christopher H Hulton
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily A Costa
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Nisargbhai S Shah
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alvaro Quintanal-Villalonga
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Glenn Heller
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John T Poirier
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
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65
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Near-infrared optogenetic engineering of photothermal nanoCRISPR for programmable genome editing. Proc Natl Acad Sci U S A 2020; 117:2395-2405. [PMID: 31941712 DOI: 10.1073/pnas.1912220117] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We herein report an optogenetically activatable CRISPR-Cas9 nanosystem for programmable genome editing in the second near-infrared (NIR-II) optical window. The nanosystem, termed nanoCRISPR, is composed of a cationic polymer-coated Au nanorod (APC) and Cas9 plasmid driven by a heat-inducible promoter. The APC not only serves as a carrier for intracellular plasmid delivery but also can harvest external NIR-II photonic energy and convert it into local heat to induce the gene expression of the Cas9 endonuclease. Due to high transfection activity, the APC shows strong ability to induce a significant level of disruption in different genomic loci upon optogenetic activation. Moreover, the precise control of genome-editing activity can be simply programmed by finely tuning exposure time and irradiation time in vitro and in vivo and also enables editing at multiple time points, thus proving the sensitivity and inducibility of such an editing modality. The NIR-II optical feature of nanoCRISPR enables therapeutic genome editing at deep tissue, by which treatment of deep tumor and rescue of fulminant hepatic failure are demonstrated as proof-of-concept therapeutic examples. Importantly, this modality of optogenetic genome editing can significantly minimize the off-target effect of CRISPR-Cas9 in most potential off-target sites. The optogenetically activatable CRISPR-Cas9 nanosystem we have developed offers a useful tool to expand the current applications of CRISPR-Cas9, and also defines a programmable genome-editing strategy toward high precision and spatial specificity.
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66
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Sahoo N, Cuello V, Udawant S, Litif C, Mustard JA, Keniry M. CRISPR-Cas9 Genome Editing in Human Cell Lines with Donor Vector Made by Gibson Assembly. Methods Mol Biol 2020; 2115:365-383. [PMID: 32006411 PMCID: PMC7391466 DOI: 10.1007/978-1-0716-0290-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
CRISPR Cas9 genome editing allows researchers to modify genes in a multitude of ways including to obtain deletions, epitope-tagged loci, and knock-in mutations. Within 6 years of its initial application, CRISPR-Cas9 genome editing has been widely employed, but disadvantages to this method, such as low modification efficiencies and off-target effects, need careful consideration. Obtaining custom donor vectors can also be expensive and time-consuming. This chapter details strategies to overcome barriers to CRISPR-Cas9 genome editing as well as recent developments in employing this technique.
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Affiliation(s)
- Nirakar Sahoo
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Victoria Cuello
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Shreya Udawant
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Carl Litif
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Julie A Mustard
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Megan Keniry
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA.
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Engineering nucleic acid chemistry for precise and controllable CRISPR/Cas9 genome editing. Sci Bull (Beijing) 2019; 64:1841-1849. [PMID: 36659580 DOI: 10.1016/j.scib.2019.07.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 01/21/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) genome editing technology is revolutionizing our approach and capability to precisely manipulate the genetic flow of mammalians. The facile programmability of Cas9 protein and guide RNA (gRNA) sequence has recently expanded biomedical application of CRISPR/Cas9 technology from editing mammalian genome to various genetic manipulations. The therapeutic and clinical translation potential of CRISPR/Cas9 genome editing, however, are challenged by its off-target effect and low genome editing efficiency. In this regard, developing new Cas9 variants and conditional control of Cas9/gRNA activity are of great potential for improving genome editing accuracy and on-target efficiency. In this review, we summarize chemical strategies that have been developed recently to engineer the nucleic acid chemistry of gRNA to enhance CRISPR/Cas9 genome editing efficacy, specificity and controllability. This review aims to highlight the endeavor that has been made to solve bottleneck problems in the field of CRISPR/Cas9 and inspire innovative researches to fulfill the gap between bench and bed.
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Richardson NH, Luttrell JB, Bryant JS, Chamberlain D, Khawaja S, Neeli I, Radic M. Tuning the performance of CAR T cell immunotherapies. BMC Biotechnol 2019; 19:84. [PMID: 31783836 PMCID: PMC6884819 DOI: 10.1186/s12896-019-0576-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/08/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Simultaneous advances in gene editing, T cell engineering and biotechnology currently provide an opportunity for rapid progress in medicine. The approval of chimeric antigen receptor (CAR) T cell therapies by the US Food and Drug Administration (FDA) and the European Commission have generated substantial momentum for these first-in-class therapies to be used in patients with B cell malignancies. MAIN BODY Considerable efforts focus on improved outcomes and reduced side effects of the newly approved therapies. Using innovative strategies, researchers aim to extend CAR T cell use to tackle difficulties inherent in solid tumors. Efforts are underway to broaden the applications of CAR T cells, and the strategy has been successful in chronic viral infections and preclinical models of autoimmunity. Research is in progress to generate "off-the-shelf" CAR T cells, an advance, which would greatly increase patient availability and reduce treatment cost. CONCLUSIONS In this thematic review, we highlight advances that may help develop genetically engineered cells into a new category of medical therapies.
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Affiliation(s)
- Noah H Richardson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38163, USA
| | - Jordan B Luttrell
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38163, USA
| | - Jonathan S Bryant
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38163, USA
| | - Damian Chamberlain
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38163, USA
| | - Saleem Khawaja
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38163, USA
| | - Indira Neeli
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38163, USA
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38163, USA.
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Geller SH, Antwi EB, Di Ventura B, McClean MN. Optogenetic Repressors of Gene Expression in Yeasts Using Light-Controlled Nuclear Localization. Cell Mol Bioeng 2019; 12:511-528. [PMID: 31719930 PMCID: PMC6816687 DOI: 10.1007/s12195-019-00598-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 09/03/2019] [Indexed: 01/30/2023] Open
Abstract
INTRODUCTION Controlling gene expression is a fundamental goal of basic and synthetic biology because it allows insight into cellular function and control of cellular activity. We explored the possibility of generating an optogenetic repressor of gene expression in the model organism Saccharomyces cerevisiae by using light to control the nuclear localization of nuclease-dead Cas9, dCas9. METHODS The dCas9 protein acts as a repressor for a gene of interest when localized to the nucleus in the presence of an appropriate guide RNA (sgRNA). We engineered dCas9, the mammalian transcriptional repressor Mxi1, and an optogenetic tool to control nuclear localization (LINuS) as parts in an existing yeast optogenetic toolkit. This allowed expression cassettes containing novel dCas9 repressor configurations and guide RNAs to be rapidly constructed and integrated into yeast. RESULTS Our library of repressors displays a range of basal repression without the need for inducers or promoter modification. Populations of cells containing these repressors can be combined to generate a heterogeneous population of yeast with a 100-fold expression range. We find that repression can be dialed modestly in a light dose- and intensity-dependent manner. We used this library to repress expression of the lanosterol 14-alpha-demethylase Erg11, generating yeast with a range of sensitivity to the important antifungal drug fluconazole. CONCLUSIONS This toolkit will be useful for spatiotemporal perturbation of gene expression in Saccharomyces cerevisiae. Additionally, we believe that the simplicity of our scheme will allow these repressors to be easily modified to control gene expression in medically relevant fungi, such as pathogenic yeasts.
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Affiliation(s)
- Stephanie H. Geller
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1550 Engineering Drive, Madison, WI 53706 USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, 1525 Linden Dr., Madison, WI 53706 USA
| | - Enoch B. Antwi
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), 69120 Heidelberg, Germany
| | - Barbara Di Ventura
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1550 Engineering Drive, Madison, WI 53706 USA
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70
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Mills EM, Barlow VL, Luk LYP, Tsai YH. Applying switchable Cas9 variants to in vivo gene editing for therapeutic applications. Cell Biol Toxicol 2019; 36:17-29. [PMID: 31418127 PMCID: PMC7051928 DOI: 10.1007/s10565-019-09488-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Progress in targeted gene editing by programmable endonucleases has paved the way for their use in gene therapy. Particularly, Cas9 is an endonuclease with high activity and flexibility, rendering it an attractive option for therapeutic applications in clinical settings. Many disease-causing mutations could potentially be corrected by this versatile new technology. In addition, recently developed switchable Cas9 variants, whose activity can be controlled by an external stimulus, provide an extra level of spatiotemporal control on gene editing and are particularly desirable for certain applications. Here, we discuss the considerations and difficulties for implementing Cas9 to in vivo gene therapy. We put particular emphasis on how switchable Cas9 variants may resolve some of these barriers and advance gene therapy in the clinical setting.
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Affiliation(s)
- Emily M Mills
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | | | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
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71
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Cunningham-Bryant D, Sun J, Fernandez B, Zalatan JG. CRISPR-Cas-Mediated Chemical Control of Transcriptional Dynamics in Yeast. Chembiochem 2019; 20:1519-1523. [PMID: 30710419 PMCID: PMC6570556 DOI: 10.1002/cbic.201800823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Indexed: 11/07/2022]
Abstract
Synthetic CRISPR-Cas transcription factors enable the construction of complex gene-expression programs, and chemically inducible systems allow precise control over the expression dynamics. To provide additional modes of regulatory control, we have constructed a chemically inducible CRISPR activation (CRISPRa) system in yeast that is mediated by recruitment to MS2-functionalized guide RNAs. We use reporter gene assays to systematically map the dose dependence, time dependence, and reversibility of the system. Because the recruitment function is encoded at the level of the guide RNA, it is straightforward to target multiple genes and independently regulate expression dynamics at individual targets. This approach provides a new method to engineer sophisticated, multigene programs with precise control over the dynamics of gene expression.
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Affiliation(s)
| | - Jingwen Sun
- Department of Chemistry, University of Washington, 36 Bagley Hall, Seattle, WA, 98195, USA
| | - Brianna Fernandez
- Department of Chemistry, University of Washington, 36 Bagley Hall, Seattle, WA, 98195, USA
| | - Jesse G Zalatan
- Department of Chemistry, University of Washington, 36 Bagley Hall, Seattle, WA, 98195, USA
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72
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Manna D, Maji B, Gangopadhyay SA, Cox KJ, Zhou Q, Law BK, Mazitschek R, Choudhary A. A Singular System with Precise Dosing and Spatiotemporal Control of CRISPR‐Cas9. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Debasish Manna
- Chemical Biology and Therapeutics Science Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Divisions of Renal Medicine and Engineering Brigham and Women's Hospital Boston MA 02115 USA
| | - Basudeb Maji
- Chemical Biology and Therapeutics Science Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Divisions of Renal Medicine and Engineering Brigham and Women's Hospital Boston MA 02115 USA
| | - Soumyashree A. Gangopadhyay
- Chemical Biology and Therapeutics Science Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Divisions of Renal Medicine and Engineering Brigham and Women's Hospital Boston MA 02115 USA
| | - Kurt J. Cox
- Chemical Biology and Therapeutics Science Broad Institute of MIT and Harvard Cambridge MA 02142 USA
| | - Qingxuan Zhou
- Chemical Biology and Therapeutics Science Broad Institute of MIT and Harvard Cambridge MA 02142 USA
| | - Benjamin K. Law
- Chemical Biology and Therapeutics Science Broad Institute of MIT and Harvard Cambridge MA 02142 USA
| | - Ralph Mazitschek
- Chemical Biology and Therapeutics Science Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Harvard T. H. Chan School of Public Health Boston MA 02115 USA
- Center for Systems Biology Massachusetts General Hospital Boston MA 02114 USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Divisions of Renal Medicine and Engineering Brigham and Women's Hospital Boston MA 02115 USA
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73
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Manna D, Maji B, Gangopadhyay SA, Cox KJ, Zhou Q, Law BK, Mazitschek R, Choudhary A. A Singular System with Precise Dosing and Spatiotemporal Control of CRISPR-Cas9. Angew Chem Int Ed Engl 2019; 58:6285-6289. [PMID: 30834641 PMCID: PMC7067309 DOI: 10.1002/anie.201900788] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/24/2019] [Indexed: 12/29/2022]
Abstract
Several genome engineering applications of CRISPR-Cas9, an RNA-guided DNA endonuclease, require precision control of Cas9 activity over dosage, timing, and targeted site in an organism. While some control of Cas9 activity over dose and time have been achieved using small molecules, and spatial control using light, no singular system with control over all the three attributes exists. Furthermore, the reported small-molecule systems lack wide dynamic range, have background activity in the absence of the small-molecule controller, and are not biologically inert, while the optogenetic systems require prolonged exposure to high-intensity light. We previously reported a small-molecule-controlled Cas9 system with some dosage and temporal control. By photocaging this Cas9 activator to render it biologically inert and photoactivatable, and employing next-generation protein engineering approaches, we have built a system with a wide dynamic range, low background, and fast photoactivation using a low-intensity light while rendering the small-molecule activator biologically inert. We anticipate these precision controls will propel the development of practical applications of Cas9.
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Affiliation(s)
- Debasish Manna
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Basudeb Maji
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Soumyashree A Gangopadhyay
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Kurt J Cox
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Qingxuan Zhou
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Benjamin K Law
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ralph Mazitschek
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA
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74
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Maji B, Gangopadhyay SA, Lee M, Shi M, Wu P, Heler R, Mok B, Lim D, Siriwardena SU, Paul B, Dančík V, Vetere A, Mesleh MF, Marraffini LA, Liu DR, Clemons PA, Wagner BK, Choudhary A. A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9. Cell 2019; 177:1067-1079.e19. [PMID: 31051099 PMCID: PMC7182439 DOI: 10.1016/j.cell.2019.04.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 09/17/2018] [Accepted: 04/03/2019] [Indexed: 12/26/2022]
Abstract
The precise control of CRISPR-Cas9 activity is required for a number of genome engineering technologies. Here, we report a generalizable platform that provided the first synthetic small-molecule inhibitors of Streptococcus pyogenes Cas9 (SpCas9) that weigh <500 Da and are cell permeable, reversible, and stable under physiological conditions. We developed a suite of high-throughput assays for SpCas9 functions, including a primary screening assay for SpCas9 binding to the protospacer adjacent motif, and used these assays to screen a structurally diverse collection of natural-product-like small molecules to ultimately identify compounds that disrupt the SpCas9-DNA interaction. Using these synthetic anti-CRISPR small molecules, we demonstrated dose and temporal control of SpCas9 and catalytically impaired SpCas9 technologies, including transcription activation, and identified a pharmacophore for SpCas9 inhibition using structure-activity relationships. These studies establish a platform for rapidly identifying synthetic, miniature, cell-permeable, and reversible inhibitors against both SpCas9 and next-generation CRISPR-associated nucleases.
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Affiliation(s)
- Basudeb Maji
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Soumyashree A Gangopadhyay
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Miseon Lee
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mengchao Shi
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Peng Wu
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Beverly Mok
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Donghyun Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sachini U Siriwardena
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bishwajit Paul
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vlado Dančík
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amedeo Vetere
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael F Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 11231, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA.
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