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Zhan H, Xiao L, Li A, Yao L, Cai Z, Liu Y. Engineering Cellular Signal Sensors based on CRISPR-sgRNA Reconstruction Approaches. Int J Biol Sci 2020; 16:1441-1449. [PMID: 32210731 PMCID: PMC7085220 DOI: 10.7150/ijbs.42299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/24/2020] [Indexed: 11/05/2022] Open
Abstract
The discovery of the CRISPR systems has enriched the application of gene therapy and biotechnology. As a type of robust and simple toolbox, the CRISPR system has greatly promoted the development of cellular signal sensors at the genomic level. Although CRISPR systems have demonstrated that they can be used in eukaryotic and even mammalian cells after extraction from prokaryotic cells, controlling their gene-editing activity remains a challenge. Here we summarize the advantages and disadvantages of building a CRIRPR-based signal sensor through sgRNA reconstruction, as well as possible ways to reprogram the signal network of cells. We also propose how to further improve the design of the current signal sensors based on sgRNA-riboswitch. We believe that the development of these technologies and the construction of platforms can further promote the development of environment detection, disease diagnosis, and gene therapy by means of synthetic biology.
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Affiliation(s)
- Hengji Zhan
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Lulu Xiao
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Aolin Li
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Zhiming Cai
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518035, China
- Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518035, China
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52
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Amirkhanov RN, Stepanov GA. Systems of Delivery of CRISPR/Cas9 Ribonucleoprotein Complexes for Genome Editing. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Abstract
The simple applicability and facile target programming of the CRISPR/Cas9-system abolish the major boundaries of previous genome editing tools, making it the tool of choice for generating site-specific genome alterations. Its versatility and efficacy have been demonstrated in various organisms; however, accurately predicting guide RNA efficiencies remains an organism-independent challenge. Thus, designing optimal guide RNAs is essential to maximize the experimental outcome. Here, we summarize the current knowledge for guide RNA design and highlight discrepancies between different experimental systems.
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Affiliation(s)
- Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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Moon SB, Kim DY, Ko JH, Kim YS. Recent advances in the CRISPR genome editing tool set. Exp Mol Med 2019; 51:1-11. [PMID: 31685795 PMCID: PMC6828703 DOI: 10.1038/s12276-019-0339-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/08/2019] [Accepted: 09/11/2019] [Indexed: 12/26/2022] Open
Abstract
Genome editing took a dramatic turn with the development of the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) system. The CRISPR-Cas system is functionally divided into classes 1 and 2 according to the composition of the effector genes. Class 2 consists of a single effector nuclease, and routine practice of genome editing has been achieved by the development of the Class 2 CRISPR-Cas system, which includes the type II, V, and VI CRISPR-Cas systems. Types II and V can be used for DNA editing, while type VI is employed for RNA editing. CRISPR techniques induce both qualitative and quantitative alterations in gene expression via the double-stranded breakage (DSB) repair pathway, base editing, transposase-dependent DNA integration, and gene regulation using the CRISPR-dCas or type VI CRISPR system. Despite significant technical improvements, technical challenges should be further addressed, including insufficient indel and HDR efficiency, off-target activity, the large size of Cas, PAM restrictions, and immune responses. If sophisticatedly refined, CRISPR technology will harness the process of DNA rewriting, which has potential applications in therapeutics, diagnostics, and biotechnology.
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Affiliation(s)
- Su Bin Moon
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Do Yon Kim
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jeong-Heon Ko
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea.
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea.
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55
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Ghogare R, Williamson-Benavides B, Ramírez-Torres F, Dhingra A. CRISPR-associated nucleases: the Dawn of a new age of efficient crop improvement. Transgenic Res 2019; 29:1-35. [PMID: 31677059 DOI: 10.1007/s11248-019-00181-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/23/2019] [Indexed: 12/26/2022]
Abstract
The world stands at a new threshold today. As a planet, we face various challenges, and the key one is how to continue to produce enough food, feed, fiber, and fuel to support the burgeoning population. In the past, plant breeding and the ability to genetically engineer crops contributed to increasing food production. However, both approaches rely on random mixing or integration of genes, and the process can be unpredictable and time-consuming. Given the challenge of limited availability of natural resources and changing environmental conditions, the need to rapidly and precisely improve crops has become urgent. The discovery of CRISPR-associated endonucleases offers a precise yet versatile platform for rapid crop improvement. This review summarizes a brief history of the discovery of CRISPR-associated nucleases and their application in genome editing of various plant species. Also provided is an overview of several new endonucleases reported recently, which can be utilized for editing of specific genes in plants through various forms of DNA sequence alteration. Genome editing, with its ever-expanding toolset, increased efficiency, and its potential integration with the emerging synthetic biology approaches hold promise for efficient crop improvement to meet the challenge of supporting the needs of future generations.
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Josipović G, Tadić V, Klasić M, Zanki V, Bečeheli I, Chung F, Ghantous A, Keser T, Madunić J, Bošković M, Lauc G, Herceg Z, Vojta A, Zoldoš V. Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system. Nucleic Acids Res 2019; 47:9637-9657. [PMID: 31410472 PMCID: PMC6765142 DOI: 10.1093/nar/gkz709] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/15/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022] Open
Abstract
Establishing causal relationship between epigenetic marks and gene transcription requires molecular tools, which can precisely modify specific genomic regions. Here, we present a modular and extensible CRISPR/dCas9-based toolbox for epigenetic editing and direct gene regulation. It features a system for expression of orthogonal dCas9 proteins fused to various effector domains and includes a multi-gRNA system for simultaneous targeting dCas9 orthologs to up to six loci. The C- and N-terminal dCas9 fusions with DNMT3A and TET1 catalytic domains were thoroughly characterized. We demonstrated simultaneous use of the DNMT3A-dSpCas9 and TET1-dSaCas9 fusions within the same cells and showed that imposed cytosine hyper- and hypo-methylation altered level of gene transcription if targeted CpG sites were functionally relevant. Dual epigenetic manipulation of the HNF1A and MGAT3 genes, involved in protein N-glycosylation, resulted in change of the glycan phenotype in BG1 cells. Furthermore, simultaneous targeting of the TET1-dSaCas9 and VPR-dSpCas9 fusions to the HNF1A regulatory region revealed strong and persistent synergistic effect on gene transcription, up to 30 days following cell transfection, suggesting involvement of epigenetic mechanisms in maintenance of the reactivated state. Also, modulation of dCas9 expression effectively reduced off-target effects while maintaining the desired effects on target regions.
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Affiliation(s)
- Goran Josipović
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Vanja Tadić
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Marija Klasić
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Vladimir Zanki
- Department of Chemistry, Division of Biochemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ivona Bečeheli
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Felicia Chung
- Epigenetics group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Akram Ghantous
- Epigenetics group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10000 Zagreb, Croatia
| | - Josip Madunić
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Maria Bošković
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Gordan Lauc
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10000 Zagreb, Croatia
- Genos Glycoscience Research Laboratory, Borogajska cesta 83 h, 10000 Zagreb, Croatia
| | - Zdenko Herceg
- Epigenetics group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Aleksandar Vojta
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Vlatka Zoldoš
- Department of Biology, Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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57
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Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing. Proc Natl Acad Sci U S A 2019; 116:20959-20968. [PMID: 31570623 DOI: 10.1073/pnas.1818461116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off-targeting at multiple loci across the genome. Here we report that Francisella novicida Cas9 (FnCas9) shows a very high specificity of binding to its intended targets and negligible binding to off-target loci. The specificity is determined by its minimal binding affinity with DNA when mismatches to the target single-guide RNA (sgRNA) are present in the sgRNA:DNA heteroduplex. FnCas9 produces staggered cleavage, higher homology-directed repair rates, and very low nonspecific genome editing compared to SpCas9. We demonstrate FnCas9-mediated correction of the sickle cell mutation in patient-derived induced pluripotent stem cells and propose that it can be used for precise therapeutic genome editing for a wide variety of genetic disorders.
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58
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Abstract
The emergence of the CRISPR-Cas9 gene editing system has brought much hope and excitement to the field of gene therapy and the larger scientific community. However, in order for CRISPR-based therapies to be translated to the clinical setting, there is an urgent need to develop optimized vectors for their delivery. The delivery vector is a crucial determinant of the therapeutic efficacy of gene editing and should be designed to accommodate various factors including the form of the payload, the physiological environment, and the potential immune responses. Recently, biomaterials have become an attractive option for the delivery of Cas9 due to their tunability, biocompatibility and increasing efficacy at drug delivery. Biomaterials offer a unique solution for creating tailored vectors to meet the demands of various applications that cannot be easily met by other delivery methods. In this review, we will discuss the various biomaterial systems that have been used to deliver Cas9 in its plasmid, mRNA and protein forms. In addition, the functions of these materials will be reviewed to understand their roles in Cas9 delivery. Finally, the immune challenges associated with Cas9 and the delivery materials will be discussed as an understanding of the immune responses along with the functions of biomaterials will ultimately guide the field in designing new delivery systems for the clinical applications of CRISPR-Cas9.
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Affiliation(s)
- Joon Eoh
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, USA.
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59
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Campenhout CV, Cabochette P, Veillard AC, Laczik M, Zelisko-Schmidt A, Sabatel C, Dhainaut M, Vanhollebeke B, Gueydan C, Kruys V. Guidelines for optimized gene knockout using CRISPR/Cas9. Biotechniques 2019; 66:295-302. [PMID: 31039627 DOI: 10.2144/btn-2018-0187] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
CRISPR/Cas9 technology has evolved as the most powerful approach to generate genetic models both for fundamental and preclinical research. Despite its apparent simplicity, the outcome of a genome-editing experiment can be substantially impacted by technical parameters and biological considerations. Here, we present guidelines and tools to optimize CRISPR/Cas9 genome-targeting efficiency and specificity. The nature of the target locus, the design of the single guide RNA and the choice of the delivery method should all be carefully considered prior to a genome-editing experiment. Different methods can also be used to detect off-target cleavages and decrease the risk of unwanted mutations. Together, these optimized tools and proper controls are essential to the assessment of CRISPR/Cas9 genome-editing experiments.
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Affiliation(s)
| | - Pauline Cabochette
- Laboratoire de Signalisation Neurovasculaire, Faculté des Sciences, Université libre de Bruxelles (ULB), 12 rue des Profs. Jeener et Brachet, 6041 Gosselies, Belgium
| | | | - Miklos Laczik
- Diagenode, SA, Liège Science Park, 4102 Seraing, Belgium
| | | | - Céline Sabatel
- Diagenode, SA, Liège Science Park, 4102 Seraing, Belgium
| | - Maxime Dhainaut
- Precision Immunology Institute, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benoit Vanhollebeke
- Laboratoire de Signalisation Neurovasculaire, Faculté des Sciences, Université libre de Bruxelles (ULB), 12 rue des Profs. Jeener et Brachet, 6041 Gosselies, Belgium
- Walloon Excellence in Life Sciences & Biotechnology (WELBIO), Belgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du Gène, Faculté des Sciences, Université libre de Bruxelles (ULB), 12 rue des Profs. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du Gène, Faculté des Sciences, Université libre de Bruxelles (ULB), 12 rue des Profs. Jeener et Brachet, 6041 Gosselies, Belgium
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60
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Cota-Coronado A, Díaz-Martínez NF, Padilla-Camberos E, Díaz-Martínez NE. Editing the Central Nervous System Through CRISPR/Cas9 Systems. Front Mol Neurosci 2019; 12:110. [PMID: 31191241 PMCID: PMC6546027 DOI: 10.3389/fnmol.2019.00110] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/15/2019] [Indexed: 12/26/2022] Open
Abstract
The translational gap to treatments based on gene therapy has been reduced in recent years because of improvements in gene editing tools, such as the CRISPR/Cas9 system and its variations. This has allowed the development of more precise therapies for neurodegenerative diseases, where access is privileged. As a result, engineering of complexes that can access the central nervous system (CNS) with the least potential inconvenience is fundamental. In this review article, we describe current alternatives to generate systems based on CRISPR/Cas9 that can cross the blood-brain barrier (BBB) and may be used further clinically to improve treatment for neurodegeneration in Parkinson's and Alzheimer's disease (AD).
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Affiliation(s)
- Agustin Cota-Coronado
- Biotecnología Médica y Farmacéutica CONACYT, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
| | | | - Eduardo Padilla-Camberos
- Biotecnología Médica y Farmacéutica CONACYT, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
| | - N Emmanuel Díaz-Martínez
- Biotecnología Médica y Farmacéutica CONACYT, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
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61
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Bisht DS, Bhatia V, Bhattacharya R. Improving plant-resistance to insect-pests and pathogens: The new opportunities through targeted genome editing. Semin Cell Dev Biol 2019; 96:65-76. [PMID: 31039395 DOI: 10.1016/j.semcdb.2019.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/09/2019] [Accepted: 04/12/2019] [Indexed: 12/26/2022]
Abstract
The advantages of high input agriculture are fading away due to degenerating soil health and adverse effects of climate change. Safeguarding crop yields in the changing environment and dynamics of pest and pathogens, has posed new challenges to global agriculture. Thus, integration of new technologies in crop improvement has been imperative for achieving the breeding objectives in faster ways. Recently, enormous potential of genome editing through engineered nucleases has been demonstrated in plants. Continuous refinements of the genome editing tools have increased depth and breadth of their applications. So far, genome editing has been demonstrated in more than fifty plant species. These include model species like Arabidopsis, as well as important crops like rice, wheat, maize etc. Particularly, CRISPR/Cas9 based two component genome editing system has been facile with wider applicability. Potential of genome editing has unfurled enormous possibilities for engineering diverse agronomic traits including durable resistance against insect-pests and pathogens. Novel propositions of developing insect and pathogen resistant crops by genome editing include altering the effector-target interaction, knocking out of host-susceptibility genes, engineering synthetic immune receptor eliciting broad spectrum resistance, uncoupling of antagonistic action of defense hormones etc. Alternatively, modification of insect genomes has been used either to create gene drive or to counteract resistance to various insecticides. The distinct advantage of genome editing system is that it can knock out specific target region in the genome without leaving the unwanted vector backbone. In this article, we have reviewed the novel opportunities offered by the genome editing technologies for developing insect and pathogen resistant crop-types, their future prospects and anticipated challenges.
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Affiliation(s)
- Deepak Singh Bisht
- ICAR-National Institute for Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, India
| | - Varnika Bhatia
- Deen Dayal Upadhyaya College, University of Delhi, Delhi, India
| | - Ramcharan Bhattacharya
- ICAR-National Institute for Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, India.
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62
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63
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Fu BXH, Smith JD, Fuchs RT, Mabuchi M, Curcuru J, Robb GB, Fire AZ. Target-dependent nickase activities of the CRISPR-Cas nucleases Cpf1 and Cas9. Nat Microbiol 2019; 4:888-897. [PMID: 30833733 PMCID: PMC6512873 DOI: 10.1038/s41564-019-0382-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/21/2019] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) machineries are prokaryotic immune systems that have been adapted as versatile gene editing and manipulation tools. We found that CRISPR nucleases from two families, Cpf1 (also known as Cas12a) and Cas9, exhibit differential guide RNA (gRNA) sequence requirements for cleavage of the two strands of target DNA in vitro. As a consequence of the differential gRNA requirements, both Cas9 and Cpf1 enzymes can exhibit potent nickase activities on an extensive class of mismatched double-stranded DNA (dsDNA) targets. These properties allow the production of efficient nickases for a chosen dsDNA target sequence, without modification of the nuclease protein, using gRNAs with a variety of patterns of mismatch to the intended DNA target. In parallel to the nicking activities observed with purified Cas9 in vitro, we observed sequence-dependent nicking for both perfectly matched and partially mismatched target sequences in a Saccharomyces cerevisiae system. Our findings have implications for CRISPR spacer acquisition, off-target potential of CRISPR gene editing/manipulation, and tool development using homology-directed nicking.
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Affiliation(s)
- Becky Xu Hua Fu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Justin D Smith
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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64
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Chen K, Wang Y, Zhang R, Zhang H, Gao C. CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:667-697. [PMID: 30835493 DOI: 10.1146/annurev-arplant-050718-100049] [Citation(s) in RCA: 619] [Impact Index Per Article: 123.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enhanced agricultural production through innovative breeding technology is urgently needed to increase access to nutritious foods worldwide. Recent advances in CRISPR/Cas genome editing enable efficient targeted modification in most crops, thus promising to accelerate crop improvement. Here, we review advances in CRISPR/Cas9 and its variants and examine their applications in plant genome editing and related manipulations. We highlight base-editing tools that enable targeted nucleotide substitutions and describe the various delivery systems, particularly DNA-free methods, that have linked genome editing with crop breeding. We summarize the applications of genome editing for trait improvement, development of techniques for fine-tuning gene regulation, strategies for breeding virus resistance, and the use of high-throughput mutant libraries. We outline future perspectives for genome editing in plant synthetic biology and domestication, advances in delivery systems, editing specificity, homology-directed repair, and gene drives. Finally, we discuss the challenges and opportunities for precision plant breeding and its bright future in agriculture.
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Affiliation(s)
- Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
- University of Chinese Academy of Sciences, Beijing, China 100864
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65
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Safe CRISPR: Challenges and Possible Solutions. Trends Biotechnol 2019; 37:389-401. [DOI: 10.1016/j.tibtech.2018.09.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 12/26/2022]
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66
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Galizi R, Jaramillo A. Engineering CRISPR guide RNA riboswitches for in vivo applications. Curr Opin Biotechnol 2019; 55:103-113. [PMID: 30265865 DOI: 10.1016/j.copbio.2018.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 02/07/2023]
Abstract
CRISPR-based genome editing provides a simple and scalable toolbox for a variety of therapeutic and biotechnology applications. Whilst the fundamental properties of CRISPR proved easily transferable from the native prokaryotic hosts to eukaryotic and multicellular organisms, the tight control of the CRISPR-editing activity remains a major challenge. Here we summarise recent developments of CRISPR and riboswitch technologies and recommend novel functionalised synthetic-gRNA (sgRNA) designs to achieve inducible and spatiotemporal regulation of CRISPR-based genetic editors in response to cellular or extracellular stimuli. We believe that future advances of these tools will have major implications for both basic and applied research, spanning from fundamental genetic studies and synthetic biology to genetic editing and gene therapy.
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Affiliation(s)
- Roberto Galizi
- Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom; ISSB, CNRS, Univ Evry, CEA, Université Paris-Saclay, 91025 Evry, France; Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, 46980 Paterna, Spain.
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67
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Abstract
Vector control programs based on population reduction by matings with mass-released sterile insects require the release of only male mosquitoes, as the release of females, even if sterile, would increase the number of biting and potentially disease-transmitting individuals. While small-scale releases demonstrated the applicability of sterile males releases to control the yellow fever mosquito Aedes aegypti, large-scale programs for mosquitoes are currently prevented by the lack of efficient sexing systems in any of the vector species.Different approaches of sexing are pursued, including classical genetic and mechanical methods of sex separation. Another strategy is the development of transgenic sexing systems. Such systems already exist in other insect pests. Genome modification tools could be used to apply similar strategies to mosquitoes. Three major tools to modify mosquito genomes are currently used: transposable elements, site-specific recombination systems, and genome editing via TALEN or CRISPR/Cas. All three can serve the purpose of developing sexing systems and vector control strains in mosquitoes in two ways: first, via their use in basic research. A better understanding of mosquito biology, including the sex-determining pathways and the involved genes can greatly facilitate the development of sexing strains. Moreover, basic research can help to identify other regulatory elements and genes potentially useful for the construction of transgenic sexing systems. Second, these genome modification tools can be used to apply the gained knowledge to build and test mosquito sexing strains for vector control.
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Affiliation(s)
- Irina Häcker
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Marc F Schetelig
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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68
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Russo MT, Aiese Cigliano R, Sanseverino W, Ferrante MI. Assessment of genomic changes in a CRISPR/Cas9 Phaeodactylum tricornutum mutant through whole genome resequencing. PeerJ 2018; 6:e5507. [PMID: 30310734 PMCID: PMC6174884 DOI: 10.7717/peerj.5507] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 07/30/2018] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, co-opted from a bacterial defense natural mechanism, is the cutting edge technology to carry out genome editing in a revolutionary fashion. It has been shown to work in many different model organisms, from human to microbes, including two diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana. Transforming P. tricornutum by bacterial conjugation, we have performed CRISPR/Cas9-based mutagenesis delivering the nuclease as an episome; this allowed for avoiding unwanted perturbations due to random integration in the genome and for excluding the Cas9 activity when it was no longer required, reducing the probability of obtaining off-target mutations, a major drawback of the technology. Since there are no reports on off-target occurrence at the genome level in microalgae, we performed whole-genome Illumina sequencing and found a number of different unspecific changes in both the wild type and mutant strains, while we did not observe any preferential mutation in the genomic regions in which off-targets were predicted. Our results confirm that the CRISPR/Cas9 technology can be efficiently applied to diatoms, showing that the choice of the conjugation method is advantageous for minimizing unwanted changes in the genome of P. tricornutum.
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Affiliation(s)
- Monia Teresa Russo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
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69
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Mendoza BJ, Trinh CT. In Silico Processing of the Complete CRISPR-Cas Spacer Space for Identification of PAM Sequences. Biotechnol J 2018; 13:e1700595. [PMID: 30076736 DOI: 10.1002/biot.201700595] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/23/2018] [Indexed: 12/16/2022]
Abstract
Despite extensive exploration of the diversity of CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR associated) systems, biological applications have been mostly confined to Class 2 systems, specifically the Cas9 and Cas12 (formerly Cpf1) single effector proteins. A key limitation of exploring and utilizing other CRISPR-Cas systems with unique functionalities, particularly Class I types and their multi-protein effector complex, is the knowledge of the system's protospacer adjacent motif (PAM) sequence identity. In this work, the authors developed a systematic pipeline, named CASPERpam, that enables a comprehensive assessment of the PAM sequences of all the available CRISPR-Cas systems in the NCBI database of bacterial genomes. The CASPERpam analysis reveals that within the 30 389 assemblies previously screened for CRISPR arrays, there exists 26 364 spacers that match somewhere in the viral, bacterial, and plasmid databases of NCBI, using the constraints of 95% sequence identity and 95% sequence coverage for blast hits. When grouping these results by species, the authors identified putative PAM sequences for 1049 among 1493 unique species. The remaining species either have insufficient data or an undetermined result from the analysis. Finally, the authors assigned a confidence score to each species' PAM prediction and generate categories that largely cover the revealed diversity of PAM motifs, providing a baseline for further experimental studies including PAM assays. The authors envision CASPERpam is a useful bioinformatic tool for understanding and harnessing the diversity of CRISPR-Cas systems.
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Affiliation(s)
- Brian J Mendoza
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA
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70
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Wilson LOW, O’Brien AR, Bauer DC. The Current State and Future of CRISPR-Cas9 gRNA Design Tools. Front Pharmacol 2018; 9:749. [PMID: 30050439 PMCID: PMC6052051 DOI: 10.3389/fphar.2018.00749] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/20/2018] [Indexed: 12/20/2022] Open
Abstract
Recent years have seen the development of computational tools to assist researchers in performing CRISPR-Cas9 experiment optimally. More specifically, these tools aim to maximize on-target activity (guide efficiency) while also minimizing potential off-target effects (guide specificity) by analyzing the features of the target site. Nonetheless, currently available tools cannot robustly predict experimental success as prediction accuracy depends on the approximations of the underlying model and how closely the experimental setup matches the data the model was trained on. Here, we present an overview of the available computational tools, their current limitations and future considerations. We discuss new trends around personalized health by taking genomic variants into account when predicting target sites as well as discussing other governing factors that can improve prediction accuracy.
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Affiliation(s)
- Laurence O. W. Wilson
- Commonwealth Scientific and Industrial Research Organisation, Sydney, NSW, Australia
| | - Aidan R. O’Brien
- Commonwealth Scientific and Industrial Research Organisation, Sydney, NSW, Australia
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Acton, ACT, Australia
| | - Denis C. Bauer
- Commonwealth Scientific and Industrial Research Organisation, Sydney, NSW, Australia
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71
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Burnight ER, Giacalone JC, Cooke JA, Thompson JR, Bohrer LR, Chirco KR, Drack AV, Fingert JH, Worthington KS, Wiley LA, Mullins RF, Stone EM, Tucker BA. CRISPR-Cas9 genome engineering: Treating inherited retinal degeneration. Prog Retin Eye Res 2018; 65:28-49. [PMID: 29578069 PMCID: PMC8210531 DOI: 10.1016/j.preteyeres.2018.03.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 12/18/2022]
Abstract
Gene correction is a valuable strategy for treating inherited retinal degenerative diseases, a major cause of irreversible blindness worldwide. Single gene defects cause the majority of these retinal dystrophies. Gene augmentation holds great promise if delivered early in the course of the disease, however, many patients carry mutations in genes too large to be packaged into adeno-associated viral vectors and some, when overexpressed via heterologous promoters, induce retinal toxicity. In addition to the aforementioned challenges, some patients have sustained significant photoreceptor cell loss at the time of diagnosis, rendering gene replacement therapy insufficient to treat the disease. These patients will require cell replacement to restore useful vision. Fortunately, the advent of induced pluripotent stem cell and CRISPR-Cas9 gene editing technologies affords researchers and clinicians a powerful means by which to develop strategies to treat patients with inherited retinal dystrophies. In this review we will discuss the current developments in CRISPR-Cas9 gene editing in vivo in animal models and in vitro in patient-derived cells to study and treat inherited retinal degenerative diseases.
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Affiliation(s)
- Erin R Burnight
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Joseph C Giacalone
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Jessica A Cooke
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Jessica R Thompson
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Laura R Bohrer
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Kathleen R Chirco
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Arlene V Drack
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - John H Fingert
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Kristan S Worthington
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States; Department of Biochemical Engineering, University of Iowa, Iowa City, IA, United States
| | - Luke A Wiley
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Robert F Mullins
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Edwin M Stone
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Budd A Tucker
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States.
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72
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Abstract
Genome editing technologies have been revolutionized by the discovery of prokaryotic RNA-guided defense system called CRISPR-Cas. Cas9, a single effector protein found in type II CRISPR systems, has been at the heart of this genome editing revolution. Nearly half of the Cas9s discovered so far belong to the type II-C subtype but have not been explored extensively. Type II-C CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins. Cas9s are central players in type II-C systems since they function in multiple steps of the CRISPR pathway, including adaptation and interference. Type II-C CRISPR systems are found in bacteria and archaea from very diverse environments, resulting in Cas9s with unique and potentially useful properties. Certain type II-C Cas9s possess unusually long PAMs, function in unique conditions (e.g., elevated temperature), and tend to be smaller in size. Here, we review the biology, mechanism, and applications of the type II-C CRISPR systems with particular emphasis on their Cas9s.
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Affiliation(s)
- Aamir Mir
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
| | - Alireza Edraki
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
| | - Jooyoung Lee
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
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73
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Chen P, You L, Lu Y. Applications of CRISPR-Cas9 Technology in Translational Research on Solid-Tumor Cancers. CRISPR J 2018; 1:47-54. [PMID: 31021191 DOI: 10.1089/crispr.2017.0001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Since its introduction to genome editing, CRISPR-Cas9 has been used to generate cell and animal models of disease, investigate relations between genomes and phenotypes, and interfere with disease development. Although most of its applications have been in basic research, efforts are underway to move CRISPR-Cas9 from bench to bedside. This review summarizes current and prospective applications of the CRISPR-Cas9 system in biomedical and translational research on solid tumors, as well as the challenges of expanding this technology into clinical use.
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Affiliation(s)
- Patricia Chen
- 1 Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China .,2 Drexel University College of Medicine , Philadelphia, Pennsylvania
| | - Liting You
- 1 Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - You Lu
- 1 Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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74
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Moreb EA, Hoover B, Yaseen A, Valyasevi N, Roecker Z, Menacho-Melgar R, Lynch MD. Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity. ACS Synth Biol 2017; 6:2209-2218. [PMID: 28915012 DOI: 10.1021/acssynbio.7b00174] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes, and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well as mutation rates through induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants. We report an approach to inhibiting the SOS response and RecA activity through the expression of a mutant dominant negative form of RecA, which incorporates into wild type RecA filaments and inhibits activity. Using a plasmid-based system in which Cas9 and recA mutants are coexpressed, we can achieve increased efficiency and consistency of CRISPR-Cas9-mediated selection and recombineering in E. coli, while reducing the induction of the SOS response. To date, this approach has been shown to be independent of recA genotype and host strain lineage. Using this system, we demonstrate increased CRISPR-Cas selection efficacy with over 10 000 guides covering the E. coli chromosome. The use of dominant negative RecA or homologues may be of broad use in bacterial CRISPR-Cas-based genome editing where the SOS pathways are present.
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Affiliation(s)
- Eirik Adim Moreb
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Benjamin Hoover
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Adam Yaseen
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Nisakorn Valyasevi
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Zoe Roecker
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Romel Menacho-Melgar
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Michael D. Lynch
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
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75
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Korona D, Koestler SA, Russell S. Engineering the Drosophila Genome for Developmental Biology. J Dev Biol 2017; 5:jdb5040016. [PMID: 29615571 PMCID: PMC5831791 DOI: 10.3390/jdb5040016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 02/07/2023] Open
Abstract
The recent development of transposon and CRISPR-Cas9-based tools for manipulating the fly genome in vivo promises tremendous progress in our ability to study developmental processes. Tools for introducing tags into genes at their endogenous genomic loci facilitate imaging or biochemistry approaches at the cellular or subcellular levels. Similarly, the ability to make specific alterations to the genome sequence allows much more precise genetic control to address questions of gene function.
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Affiliation(s)
- Dagmara Korona
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Stefan A Koestler
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
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76
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Killian T, Dickopf S, Haas AK, Kirstenpfad C, Mayer K, Brinkmann U. Disruption of diphthamide synthesis genes and resulting toxin resistance as a robust technology for quantifying and optimizing CRISPR/Cas9-mediated gene editing. Sci Rep 2017; 7:15480. [PMID: 29133816 PMCID: PMC5684134 DOI: 10.1038/s41598-017-15206-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 10/24/2017] [Indexed: 12/26/2022] Open
Abstract
We have devised an effective and robust method for the characterization of gene-editing events. The efficacy of editing-mediated mono- and bi-allelic gene inactivation and integration events is quantified based on colony counts. The combination of diphtheria toxin (DT) and puromycin (PM) selection enables analyses of 10,000-100,000 individual cells, assessing hundreds of clones with inactivated genes per experiment. Mono- and bi-allelic gene inactivation is differentiated by DT resistance, which occurs only upon bi-allelic inactivation. PM resistance indicates integration. The robustness and generalizability of the method were demonstrated by quantifying the frequency of gene inactivation and cassette integration under different editing approaches: CRISPR/Cas9-mediated complete inactivation was ~30-50-fold more frequent than cassette integration. Mono-allelic inactivation without integration occurred >100-fold more frequently than integration. Assessment of gRNA length confirmed 20mers to be most effective length for inactivation, while 16-18mers provided the highest overall integration efficacy. The overall efficacy was ~2-fold higher for CRISPR/Cas9 than for zinc-finger nuclease and was significantly increased upon modulation of non-homologous end joining or homology-directed repair. The frequencies and ratios of editing events were similar for two different DPH genes (independent of the target sequence or chromosomal location), which indicates that the optimization parameters identified with this method can be generalized.
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Affiliation(s)
- Tobias Killian
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Steffen Dickopf
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Alexander K Haas
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Claudia Kirstenpfad
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany.
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