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Zhang D, Pries V, Boch J. Targeted C•G-to-T•A base editing with TALE-cytosine deaminases in plants. BMC Biol 2024; 22:99. [PMID: 38679734 PMCID: PMC11057107 DOI: 10.1186/s12915-024-01895-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND TALE-derived DddA-based cytosine base editors (TALE-DdCBEs) can perform efficient base editing of mitochondria and chloroplast genomes. They use transcription activator-like effector (TALE) arrays as programmable DNA-binding domains and a split version of the double-strand DNA cytidine deaminase (DddA) to catalyze C•G-to-T•A editing. This technology has not been optimized for use in plant cells. RESULTS To systematically investigate TALE-DdCBE architectures and editing rules, we established a β-glucuronidase reporter for transient assays in Nicotiana benthamiana. We show that TALE-DdCBEs function with distinct spacer lengths between the DNA-binding sites of their two TALE parts. Compared to canonical DddA, TALE-DdCBEs containing evolved DddA variants (DddA6 or DddA11) showed a significant improvement in editing efficiency in Nicotiana benthamiana and rice. Moreover, TALE-DdCBEs containing DddA11 have broader sequence compatibility for non-TC target editing. We have successfully regenerated rice with C•G-to-T•A conversions in their chloroplast genome, as well as N. benthamiana with C•G-to-T•A editing in the nuclear genome using TALE-DdCBE. We also found that the spontaneous assembly of split DddA halves can cause undesired editing by TALE-DdCBEs in plants. CONCLUSIONS Altogether, our results refined the targeting scope of TALE-DdCBEs and successfully applied them to target the chloroplast and nuclear genomes. Our study expands the base editing toolbox in plants and further defines parameters to optimize TALE-DdCBEs for high-fidelity crop improvement.
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Affiliation(s)
- Dingbo Zhang
- Leibniz University Hannover, Institute of Plant Genetics, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Vanessa Pries
- Leibniz University Hannover, Institute of Plant Genetics, Herrenhäuser Str. 2, Hannover, 30419, Germany
| | - Jens Boch
- Leibniz University Hannover, Institute of Plant Genetics, Herrenhäuser Str. 2, Hannover, 30419, Germany.
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Zhang C, Xu J, Wu Y, Xu C, Xu P. Base Editors-Mediated Gene Therapy in Hematopoietic Stem Cells for Hematologic Diseases. Stem Cell Rev Rep 2024:10.1007/s12015-024-10715-5. [PMID: 38644403 DOI: 10.1007/s12015-024-10715-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2024] [Indexed: 04/23/2024]
Abstract
Base editors, developed from the CRISPR/Cas system, consist of components such as deaminase and Cas variants. Since their emergence in 2016, the precision, efficiency, and safety of base editors have been gradually optimized. The feasibility of using base editors in gene therapy has been demonstrated in several disease models. Compared with the CRISPR/Cas system, base editors have shown great potential in hematopoietic stem cells (HSCs) and HSC-based gene therapy, because they do not generate double-stranded breaks (DSBs) while achieving the precise realization of single-base substitutions. This precise editing mechanism allows for the permanent correction of genetic defects directly at their source within HSCs, thus promising a lasting therapeutic effect. Recent advances in base editors are expected to significantly increase the number of clinical trials for HSC-based gene therapies. In this review, we summarize the development and recent progress of DNA base editors, discuss their applications in HSC gene therapy, and highlight the prospects and challenges of future clinical stem cell therapies.
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Affiliation(s)
- Chengpeng Zhang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Jinchao Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Yikang Wu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Can Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Peng Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China.
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Lv P, Su F, Chen F, Yan C, Xia D, Sun H, Li S, Duan Z, Ma C, Zhang H, Wang M, Niu X, Zhu J, Zhang J. Genome editing in rice using CRISPR/Cas12i3. Plant Biotechnol J 2024; 22:379-385. [PMID: 37822083 PMCID: PMC10826996 DOI: 10.1111/pbi.14192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/17/2023] [Accepted: 09/23/2023] [Indexed: 10/13/2023]
Abstract
The CRISPR/Cas type V-I is a family of programmable nuclease systems that prefers a T-rich protospacer adjacent motif (PAM) and is guided by a short crRNA. In this study, the genome-editing application of Cas12i3, a type V-I family endonuclease, was characterized in rice. We developed a CRIPSR/Cas12i3-based Multiplex direct repeats (DR)-spacer Array Genome Editing (iMAGE) system that was efficient in editing various genes in rice. Interestingly, iMAGE produced chromosomal structural variations with a higher frequency than CRISPR/Cas9. In addition, we developed base editors using deactivated Cas12i3 and generated herbicide-resistant rice plants using the base editors. These CRIPSR/Cas12i3-based genome editing systems will facilitate precision molecular breeding in plants.
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Affiliation(s)
- Ping Lv
- Bellagen Biotechnology Co. LtdJi'nanChina
- School of Life SciencesShandong Normal UniversityJi'nanChina
| | - Fei Su
- Bellagen Biotechnology Co. LtdJi'nanChina
- School of Life SciencesShandong Normal UniversityJi'nanChina
- Center for Advanced Bioindustry TechnologiesChinese Academy of Agricultural SciencesBeijingChina
| | - Fangyuan Chen
- Bellagen Biotechnology Co. LtdJi'nanChina
- School of Life SciencesShandong Normal UniversityJi'nanChina
| | - Chunxue Yan
- Bellagen Biotechnology Co. LtdJi'nanChina
- School of Life SciencesShandong Normal UniversityJi'nanChina
| | - Dandan Xia
- Bellagen Biotechnology Co. LtdJi'nanChina
- School of Life SciencesShandong Normal UniversityJi'nanChina
| | - Hui Sun
- Bellagen Biotechnology Co. LtdJi'nanChina
| | | | | | - Changle Ma
- School of Life SciencesShandong Normal UniversityJi'nanChina
| | - Hui Zhang
- College of Life ScienceShanghai Normal UniversityShanghaiChina
| | - Mugui Wang
- National Nanfan Research Institute (Sanya)Chinese Academy of Agricultural SciencesSanyaChina
| | - Xiaomu Niu
- Bellagen Biotechnology Co. LtdJi'nanChina
| | - Jian‐Kang Zhu
- Center for Advanced Bioindustry TechnologiesChinese Academy of Agricultural SciencesBeijingChina
- Institute of Advanced Biotechnology and School of Life SciencesSouthern University of Science and TechnologyShenzhenChina
| | - Jinshan Zhang
- Bellagen Biotechnology Co. LtdJi'nanChina
- School of Life SciencesShandong Normal UniversityJi'nanChina
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Wang Z, Yuan H, Yang L, Ma L, Zhang Y, Deng J, Li X, Xiao W, Li Z, Qiu J, Ouyang H, Pang D. Decreasing predictable DNA off-target effects and narrowing editing windows of adenine base editors by fusing human Rad18 protein variant. Int J Biol Macromol 2023; 253:127418. [PMID: 37848112 DOI: 10.1016/j.ijbiomac.2023.127418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Adenine base editors, enabling targeted A-to-G conversion in genomic DNA, have enormous potential in therapeutic applications. However, the currently used adenine base editors are limited by wide editing windows and off-target effects in genetic therapy. Here, we report human e18 protein, a RING type E3 ubiquitin ligase variant, fusing with adenine base editors can significantly improve the preciseness and narrow the editing windows compared with ABEmax and ABE8e by diminishing the abundance of base editor protein. As a proof of concept, ABEmax-e18 and ABE8e-e18 dramatically decrease Cas9-dependent and Cas9-independent off-target effects than traditional adenine base editors. Moreover, we utilized ABEmax-e18 to establish syndactyly mouse models and achieve accurate base conversion at human PCSK9 locus in HepG2 cells which exhibited its potential in genetic therapy. Furthermore, a truncated version of base editors-RING (ABEmax-RING or AncBE4max-RING), which fusing the 63 amino acids of e18 protein RING domain to the C terminal of ABEmax or AncBE4max, exhibited similar effect compared to ABEmax-e18 or AncBE4max-e18.In summary, the e18 or RING protein fused with base editors strengthens the precise toolbox in gene modification and maybe works well with various base editing tools with a more applicable to precise genetic therapies in the future.
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Affiliation(s)
- Ziru Wang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Hongming Yuan
- College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China; Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China.
| | - Lin Yang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Lerong Ma
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yuanzhu Zhang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jiacheng Deng
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Xueyuan Li
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Wenyu Xiao
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Zhanjun Li
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jiazhang Qiu
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hongsheng Ouyang
- College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China; Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China.
| | - Daxin Pang
- College of Animal Sciences, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China; Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China.
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Xiang J, Xu W, Wu J, Luo Y, Yang B, Chen J. Nucleoside deaminases: the key players in base editing toolkit. Biophys Rep 2023; 9:325-337. [PMID: 38524700 PMCID: PMC10960570 DOI: 10.52601/bpr.2023.230029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/28/2023] [Indexed: 03/26/2024] Open
Abstract
The development of nucleoside deaminase-containing base editors realized targeted single base change with high efficiency and precision. Such nucleoside deaminases include adenosine and cytidine deaminases, which can catalyze adenosine-to-inosine (A-to-I) and cytidine-to-uridine (C-to-U) conversion respectively. These nucleoside deaminases are under the spotlight because of their vast application potential in gene editing. Recent advances in the engineering of current nucleoside deaminases and the discovery of new nucleoside deaminases greatly broaden the application scope and improve the editing specificity of base editors. In this review, we cover current knowledge about the deaminases used in base editors, including their key structural features, working mechanisms, optimization, and evolution.
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Affiliation(s)
- Jiangchao Xiang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenchao Xu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Wu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yaxin Luo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Bei Yang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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Arimura SI, Nakazato I. Genome editing of plant mitochondrial and chloroplast genomes. Plant Cell Physiol 2023:pcad162. [PMID: 38113380 DOI: 10.1093/pcp/pcad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Plastids (including chloroplasts) and mitochondria are remnants of endosymbiotic bacteria yet maintain their own genomes, which encode vital components for photosynthesis and respiration, respectively. Organellar genomes have distinctive features, such as being present as multicopies, being mostly inherited maternally, having characteristic genomic structures, and undergoing frequent homologous recombination. To date, it has proven challenging to modify these genomes. For example, while CRISPR/Cas9 is a widely used system for editing nuclear genes, it has not yet been successfully applied to organellar genomes. Recently, however, precise gene editing technologies have been successfully applied to organellar genomes. Protein-based enzymes, especially TALENs and artificial enzymes utilizing TALEs, have been successfully used to modify these genomes by harnessing organellar targeting signals. This short review introduces and discusses the use of targeted nucleases and base editors on organellar genomes, their effects, and their potential applications in plant science and breeding.
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Affiliation(s)
- Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Issei Nakazato
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
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7
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Lakhina Y, Boulis NM, Donsante A. Current and emerging targeted therapies for spinal muscular atrophy. Expert Rev Neurother 2023; 23:1189-1199. [PMID: 37843301 DOI: 10.1080/14737175.2023.2268276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION Spinal muscular atrophy (SMA) is a progressive neurodegenerative disorder caused by insufficiency or total absence of the survival motor neuron protein due to a mutation in the SMN1 gene. The copy number of its paralog, SMN2, influences disease onset and phenotype severity. Current therapeutic approaches include viral and non-viral modalities affecting gene expression. Regulatory-approved drugs Spinraza (Nusinersen), Zolgensma (Onasemnogene abeparvovec), and Evrysdi (Risdiplam) are still being investigated during clinical trials and show benefits in the long-term for symptomatic and pre-symptomatic patients. However, some ongoing interventions require repeated drug administration. AREAS COVERED In this review, the authors describe the existing therapy based on point of application, focusing on recent clinical trials of antisense oligonucleotides, viral gene therapy, and splice modulators and thepotential routes for correcting the mutation to provide therapeutic levels of SMN protein. EXPERT OPINION In the opinion of the authors, multiple treatment options for patients with SMA shifted the treatment paradigm from palliative supportive care to improvedmotor function, increased survival, and greater quality of life for such patients. They further believe that the future in SMA treatment development lies incombining existing treatment options, targeting aspects of the disease refractory to these treatments, and using gene editing technologies.
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Affiliation(s)
- Yuliya Lakhina
- Department of Neurosurgery, Emory University, Atlanta, USA
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Park JC, Park MJ, Lee SY, Kim D, Kim KT, Jang HK, Cha HJ. Gene editing with 'pencil' rather than 'scissors' in human pluripotent stem cells. Stem Cell Res Ther 2023; 14:164. [PMID: 37340491 DOI: 10.1186/s13287-023-03394-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/02/2023] [Indexed: 06/22/2023] Open
Abstract
Owing to the advances in genome editing technologies, research on human pluripotent stem cells (hPSCs) have recently undergone breakthroughs that enable precise alteration of desired nucleotide bases in hPSCs for the creation of isogenic disease models or for autologous ex vivo cell therapy. As pathogenic variants largely consist of point mutations, precise substitution of mutated bases in hPSCs allows researchers study disease mechanisms with "disease-in-a-dish" and provide functionally repaired cells to patients for cell therapy. To this end, in addition to utilizing the conventional homologous directed repair system in the knock-in strategy based on endonuclease activity of Cas9 (i.e., 'scissors' like gene editing), diverse toolkits for editing the desirable bases (i.e., 'pencils' like gene editing) that avoid the accidental insertion and deletion (indel) mutations as well as large harmful deletions have been developed. In this review, we summarize the recent progress in genome editing methodologies and employment of hPSCs for future translational applications.
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Affiliation(s)
- Ju-Chan Park
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Mihn Jeong Park
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Seung-Yeon Lee
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Dayeon Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Keun-Tae Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Hyeon-Ki Jang
- Division of Chemical Engineering and Bioengineering, College of Art Culture and Engineering, Kangwon National University, Chuncheon, South Korea
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea.
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Park JC, Kim KT, Jang HK, Cha HJ. Transition Substitution of Desired Bases in Human Pluripotent Stem Cells with Base Editors: A Step-by-Step Guide. Int J Stem Cells 2023; 16:234-243. [PMID: 36823978 DOI: 10.15283/ijsc22171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 02/25/2023] Open
Abstract
The recent advances in human pluripotent stem cells (hPSCs) enable to precisely edit the desired bases in hPSCs to be used for the establishment of isogenic disease models and autologous ex vivo cell therapy. The knock-in approach based on the homologous directed repair with Cas9 endonuclease, causing DNA double-strand breaks (DSBs), produces not only insertion and deletion (indel) mutations but also deleterious large deletions. On the contrary, due to the lack of Cas9 endonuclease activity, base editors (BEs) such as adenine base editor (ABE) and cytosine base editor (CBE) allow precise base substitution by conjugated deaminase activity, free from DSB formation. Despite the limitation of BEs in transition substitution, precise base editing by BEs with no massive off-targets is suggested to be a prospective alternative in hPSCs for clinical applications. Considering the unique cellular characteristics of hPSCs, a few points should be considered. Herein, we describe an updated and optimized protocol for base editing in hPSCs. We also describe an improved methodology for CBE-based C to T substitutions, which are generally lower than A to G substitutions in hPSCs.
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Affiliation(s)
- Ju-Chan Park
- College of Pharmacy, Seoul National University, Seoul, Korea
| | - Keun-Tae Kim
- College of Pharmacy, Seoul National University, Seoul, Korea
| | - Hyeon-Ki Jang
- Division of Chemical Engineering and Bioengineering, College of Art Culture and Engineering, Kangwon National University, Chuncheon, Korea
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, Korea
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Kesavan G. Innovations in CRISPR-Based Therapies. Mol Biotechnol 2023; 65:138-145. [PMID: 34586618 DOI: 10.1007/s12033-021-00411-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/21/2021] [Indexed: 01/18/2023]
Abstract
Gene and cell therapies have shown tremendous advancement in the last 5 years. Prominent examples include the successful use of CRISPR-edited stem cells for treating blood disorders like sickle cell anemia and beta-thalassemia, and ongoing clinical trials for treating blindness. This mini-review assesses the status of CRISPR-based therapies, both in vivo and ex vivo, and the challenges associated with clinical translation. In vivo CRISPR therapies have been used to treat eye and liver diseases due to the practicality of delivering editing components to the target tissue. In contrast, even though ex vivo CRISPR therapy involves cell isolation, expansion, and infusion, its advantages include characterizing the gene edits before infusion and restricting off-target effects in other tissues. Further, the safety, affordability, and feasibility of CRISPR therapies, especially for treating large number of patients, are discussed.
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Affiliation(s)
- Gokul Kesavan
- Vowels Lifesciences Private Limited, 271, 5th Main Rd, 4th Block, Jayanagar, Bengaluru, Karnataka, 560011, India. .,Vowels Advanced School of Learning and Research, 271, 5th Main Rd, 4th Block, Jayanagar, Bengaluru, Karnataka, 560011, India.
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11
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Kim Y, Jeong J, Choi D. Ex Vivo Base Editing Therapy with Chemically Derived Hepatic Progenitors. Methods Mol Biol 2023; 2606:171-178. [PMID: 36592315 DOI: 10.1007/978-1-0716-2879-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ex vivo gene therapy through convergence study with progenitors and base/prime editors provides valuable approaches that can be utilized in the study and treatment of hereditary intractable diseases and models. Small molecule-mediated reprogramming of hepatocytes into bi-potent hepatic progenitors is a safe and efficient strategy for ex vivo gene therapy. Here, we described how to generate hepatic progenitors from terminally differentiated hepatocytes, deliver base/prime editors into the cells, select corrected hepatic progenitors, and transplant them into mice of inborn error of metabolism.
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Affiliation(s)
- Yohan Kim
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jaemin Jeong
- Department of Surgery, Hanyang University College of Medicine, Seoul, Republic of Korea.
- HY Indang Center of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul, Republic of Korea.
| | - Dongho Choi
- Department of Surgery, Hanyang University College of Medicine, Seoul, Republic of Korea.
- HY Indang Center of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul, Republic of Korea.
- Department of HY-KIST Bio-Convergence, Hanyang University, Seoul, Republic of Korea.
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Park JC, Jang HK, Kim J, Han JH, Jung Y, Kim K, Bae S, Cha HJ. High expression of uracil DNA glycosylase determines C to T substitution in human pluripotent stem cells. Mol Ther Nucleic Acids 2022; 27:175-183. [PMID: 34976436 PMCID: PMC8688811 DOI: 10.1016/j.omtn.2021.11.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/28/2021] [Indexed: 10/29/2022]
Abstract
Precise genome editing of human pluripotent stem cells (hPSCs) is crucial not only for basic science but also for biomedical applications such as ex vivo stem cell therapy and genetic disease modeling. However, hPSCs have unique cellular properties compared to somatic cells. For instance, hPSCs are extremely susceptible to DNA damage, and therefore Cas9-mediated DNA double-strand breaks (DSB) induce p53-dependent cell death, resulting in low Cas9 editing efficiency. Unlike Cas9 nucleases, base editors including cytosine base editor (CBE) and adenine base editor (ABE) can efficiently substitute single nucleotides without generating DSBs at target sites. Here, we found that the editing efficiency of CBE was significantly lower than that of ABE in human embryonic stem cells (hESCs), which are associated with high expression of DNA glycosylases, the key component of the base excision repair pathway. Sequential depletion of DNA glycosylases revealed that high expression of uracil DNA glycosylase (UNG) not only resulted in low editing efficiency but also affected CBE product purity (i.e., C to T) in hESCs. Therefore, additional suppression of UNG via transient knockdown would also improve C to T base substitutions in hESCs. These data suggest that the unique cellular characteristics of hPSCs could determine the efficiency of precise genome editing.
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Affiliation(s)
- Ju-Chan Park
- College of Pharmacy, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hyeon-Ki Jang
- Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jumee Kim
- College of Pharmacy, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jun Hee Han
- Department of Chemistry, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Youngri Jung
- Department of Chemistry, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Keuntae Kim
- College of Pharmacy, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sangsu Bae
- Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea
- Department of Chemistry, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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Abstract
CRISPR/Cas9-based technology has revolutionized biomedical research by providing a high-fidelity gene-editing method, foreshadowing a significant impact on the therapeutics of many human genetic disorders previously considered untreatable. However, off-target events represent a critical hurdle before genome editing can be fully established in clinical practice. This mini-review recapitulates some recent advances for detecting and overcoming off-target effects mediated by the CRISPR/Cas9 system that could increase the likelihood of clinical success of the CRISPR-based approaches.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico; Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, Mexico.
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14
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Abstract
The discovery of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system, and its development into a set of powerful tools for manipulating the genome, has revolutionized genome editing. Precise, targeted CRISPR/Cas-based genome editing has become the most widely used platform in organisms ranging from plants to animals. The CRISPR/Cas system has been extensively modified to increase its efficiency and fidelity. In addition, the fusion of various protein motifs to Cas effector proteins has facilitated diverse set of genetic manipulations, such as base editing, transposition, recombination, and epigenetic regulation. The CRISPR/Cas system is undergoing continuous development to overcome current limitations, including off-target effects, narrow targeting scope, and issues associated with the delivery of CRISPR components for genome engineering and therapeutic approaches. Here, we review recent progress in a diverse array of CRISPR/Cas-based tools. We also describe limitations and concerns related to the use of CRISPR/Cas technologies.
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15
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Song B, Kang CY, Han JH, Kano M, Konnerth A, Bae S. In vivo genome editing in single mammalian brain neurons through CRISPR-Cas9 and cytosine base editors. Comput Struct Biotechnol J 2021; 19:2477-2485. [PMID: 34025938 PMCID: PMC8113754 DOI: 10.1016/j.csbj.2021.04.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 10/31/2022] Open
Abstract
Gene manipulation is a useful approach for understanding functions of genes and is important for investigating basic mechanisms of brain function on the level of single neurons and circuits. Despite the development and the wide range of applications of CRISPR-Cas9 and base editors (BEs), their implementation for an analysis of individual neurons in vivo remained limited. In fact, conventional gene manipulations are generally achieved only on the population level. Here, we combined either CRISPR-Cas9 or BEs with the targeted single-cell electroporation technique as a proof-of-concept test for gene manipulation in single neurons in vivo. Our assay consisted of CRISPR-Cas9- or BEs-induced gene knockout in single Purkinje cells in the cerebellum. Our results demonstrate the feasibility of both gene editing and base editing in single cells in the intact brain, providing a tool through which molecular perturbations of individual neurons can be used for analysis of circuits and, ultimately, behaviors.
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Affiliation(s)
- Beomjong Song
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chan Young Kang
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, South Korea
| | - Jun Hee Han
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, South Korea
| | - Masanobu Kano
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Arthur Konnerth
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Institute of Neuroscience, Technical University of Munich, 80802 Munich, Germany.,Munich Cluster for Systems Neurology, Technical University of Munich, 80802 Munich, Germany
| | - Sangsu Bae
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, South Korea
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16
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Yarra R, Sahoo L. Base editing in rice: current progress, advances, limitations, and future perspectives. Plant Cell Rep 2021; 40:595-604. [PMID: 33423074 DOI: 10.1007/s00299-020-02656-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/27/2020] [Indexed: 05/27/2023]
Abstract
Base editing is one of the promising genome editing tools for generating single-nucleotide changes in rice genome. Rice (Oryza sativa L.) is an important staple food crop, feeding half of the population around the globe. Developing new rice varieties with desirable agronomic traits is necessary for sustaining global food security. The use of genome editing technologies for developing rice varieties is pre-requisite in the present scenario. Among the genome editing technologies developed for rice crop improvement, base editing technology has emerged as an efficient and reliable tool for precise genome editing in rice plants. Base editing technology utilizes either adenosine or cytidine base editor for precise editing at the target region. A base editor (adenosine or cytidine) is a fusion of catalytically inactive CRISPR/Cas9 domain and adenosine or cytidine deaminase domain. In this review, authors have discussed the different adenine and cytosine base editors developed so far for precise genome editing of rice via base editing technology. We address the current progress, advances, limitations, as well as future perspectives of the base editing technology for rice crop improvement.
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Affiliation(s)
- Rajesh Yarra
- Department of Agronomy, IFAS, University of Florida, Gainesville, FL, USA
| | - Lingaraj Sahoo
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India.
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17
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Yang L, Tang J, Ma X, Lin Y, Ma G, Shan M, Wang L, Yang Y. Progression and application of CRISPR-Cas genomic editors. Methods 2021; 194:65-74. [PMID: 33774156 DOI: 10.1016/j.ymeth.2021.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/18/2021] [Accepted: 03/21/2021] [Indexed: 12/27/2022] Open
Abstract
Base editing technology is an efficient tool for genome editing, particularly in the correction of base mutations. Diverse base editing systems were developed according to the dCas9 or nCas9 linked with different deaminase or reverse transcriptase in the editors, including ABEs, CBEs, PEs and dual-functional of base editor (such as CGBE1, A&C-BEmax, ACBE, etc.). Currently, Base editing technology has been widely applied to various fields such as microorganisms, plants, animals and medicine for basic research and therapeutics. Here, we reviewed the advancement of base editing technology. We also discussed the application of base editors in different areas in the future.
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Affiliation(s)
- Li Yang
- Basic Medical School, Ningxia Medical University, Yinchuan, People's Republic of China
| | - Jing Tang
- Basic Medical School, Ningxia Medical University, Yinchuan, People's Republic of China
| | - Xuelei Ma
- Basic Medical School, Ningxia Medical University, Yinchuan, People's Republic of China
| | - Yuan Lin
- Basic Medical School, Ningxia Medical University, Yinchuan, People's Republic of China
| | - Guorong Ma
- Basic Medical School, Ningxia Medical University, Yinchuan, People's Republic of China
| | - Minghai Shan
- General Hospital of Ningxia Medical University, Yinchuan, People's Republic of China
| | - Libin Wang
- General Hospital of Ningxia Medical University, Yinchuan, People's Republic of China.
| | - Yanhui Yang
- Basic Medical School, Ningxia Medical University, Yinchuan, People's Republic of China.
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18
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Kuang J, Lyu Q, Wang J, Cui Y, Zhao J. Advances in base editing with an emphasis on an AAV-based strategy. Methods 2021; 194:56-64. [PMID: 33774157 DOI: 10.1016/j.ymeth.2021.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/07/2021] [Accepted: 03/21/2021] [Indexed: 01/01/2023] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based base editors have been developed for precisely installing point mutations in genomes with high efficiency. Two editing systems of cytosine base editors (CBEs) and adenine base editors (ABEs) have been developed for conversion of C.G-to-T.A and A.T-to-G.C, respectively, showing the prominence in genomic DNA correction and mutation. Here, we summarize recent optimized approaches in improving base editors, including the evolution of Cas proteins, the choice of deamination enzymes, modification on linker length, base-editor expression, and addition of functional domains. Specifically, in this paper we highlight a strategy of split-intein mediated base-editor reconstitution for its adeno-associated virus (AAV) delivery. The purpose of this article is to offer readers with a better understanding of AAV-mediated base editors, and facilitate them to use this tool in in vivo experiments and potential clinical applications.
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Affiliation(s)
- Jiajie Kuang
- Shenzhen Eye Institute, Shenzhen Eye Hospital, Jinan University, Shenzhen 518000, China; Department of Ophthalmology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Qinghua Lyu
- School of Ophthalmology & Optometry, Shenzhen Eye Hospital, Shenzhen University, Shenzhen 518000, China; Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jiao Wang
- School of Ophthalmology & Optometry, Shenzhen Eye Hospital, Shenzhen University, Shenzhen 518000, China
| | - Yubo Cui
- Department of Ophthalmology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Jun Zhao
- Shenzhen Eye Institute, Shenzhen Eye Hospital, Jinan University, Shenzhen 518000, China; Department of Ophthalmology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China.
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19
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Abstract
CRISPR/Cas9 system has emerged as a powerful genome engineering tool to study gene function and improve plant traits. Genome editing is achieved at a specific genome sequence by Cas9 endonuclease to generate double standard breaks (DSBs) directed by short guide RNAs (sgRNAs). The DSB is repaired by error-prone nonhomologous end joining (NHEJ) or error-free homology-directed repair (HDR) pathways, resulting in gene mutation or sequence replacement, respectively. These cellular DSB repair pathways can be exploited to knock out or replace genes. Also, cytidine or adenine base editors (CBEs or ABEs) fused to catalytically dead Cas9 (dCas9) or nickase Cas9 (nCas9) are used to perform precise base editing without generating DSBs. In this chapter, we describe a detailed procedure to carry out single/multiple gene mutations and precise base editing in the Arabidopsis genome by using CRISPR/Cas9-based system. Specifically, the steps of target gene selection, sgRNA design, vector construction, transformation, and analysis of transgenic lines are described. The protocol is potentially adaptable to perform genome editing in other plant species such as rice.
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Affiliation(s)
- Daisuke Miki
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Gaurav Zinta
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenxin Zhang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fangnan Peng
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Feng
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
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20
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Kondrateva E, Demchenko A, Lavrov A, Smirnikhina S. An overview of currently available molecular Cas-tools for precise genome modification. Gene 2020; 769:145225. [PMID: 33059029 DOI: 10.1016/j.gene.2020.145225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/17/2022]
Abstract
CRISPR-Cas system was first mentioned in 1987, and over the years have been studied so active that now it becomes the state-of-the-art tool for genome editing. Its working principle is based on Cas nuclease ability to bind short RNA, which targets it to complementary DNA or RNA sequence for highly precise cleavage. This alone or together with donor DNA allows to modify targeted sequence in different ways. Considering the many limitations of using native CRISPR-Cas systems, scientists around the world are working on creating modified variants to improve their specificity and efficiency in different objects. In addition, the use of the Cas effectors' targeting function in complex systems with other proteins is a promising work direction, as a result of which new tools are created with features such as single base editing, editing DNA without break and donor DNA, activation and repression of transcription, epigenetic regulation, modifying of different repair pathways involvement etc. In this review, we decided to consider in detail exactly this issue of variants of Cas effectors, their modifications and fusion molecules, which improve DNA-targeting and expand the scope of Cas effectors.
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Affiliation(s)
- Ekaterina Kondrateva
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia.
| | - Anna Demchenko
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia
| | - Alexander Lavrov
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia
| | - Svetlana Smirnikhina
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia
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21
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Yarra R, Cao H, Jin L, Mengdi Y, Zhou L. CRISPR/Cas mediated base editing: a practical approach for genome editing in oil palm. 3 Biotech 2020; 10:306. [PMID: 32566443 DOI: 10.1007/s13205-020-02302-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/11/2020] [Indexed: 10/24/2022] Open
Abstract
The improvement of the yield and quality of oil palm via precise genome editing has been indispensable goal for oil palm breeders. Genome editing via the CRISPR/Cas9 (CRISPR-associated protein 9) system, ZFN (zinc finger nucleases) and TALEN (transcription activator-like effector nucleases) has flourished as an efficient technology for precise target modifications in the genomes of various crops. Among the genome editing technologies, base editing approach has emerged as novel technology that could generate single base changes i.e. irreversible conversion of one target base in to other in a programmable manner. A base editor (adenine or cytosine) is a fusion of catalytically inactive CRISPR-Cas9 domain (Cas9 variants) and cytosine or adenosine deaminase domain that introduces desired point mutations. However, till date no such genetic modifications have ever been developed in oil palm via base editing technology. Precise genome editing via base editing approach can be a challenging task in oil palm due to its complex genome as well as difficulties in tissue culture and genetic transformation methods. However, availability of whole genome sequencing data in oil palm provides a platform for developing the base editing technology. Here, we briefly review the potential application and future implications of base editing technology for the genetic improvement of oil palm.
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22
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Li J, Hong S, Chen W, Zuo E, Yang H. Advances in detecting and reducing off-target effects generated by CRISPR-mediated genome editing. J Genet Genomics 2019; 46:513-521. [PMID: 31911131 DOI: 10.1016/j.jgg.2019.11.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors. Currently, poor efficiency and off-target problems have impeded the application of CRISPR systems. The on-target efficiency has been improved in several advanced versions of CRISPR systems, whereas the off-target detection still remains a key challenge. Here, we outline the different versions of CRISPR systems and off-target detection strategies, discuss the merits and limitations of off-target detection methods, and provide potential implications for further gene editing research.
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Affiliation(s)
- Jinjing Li
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Shunyan Hong
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China.
| | - Erwei Zuo
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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23
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Liu Z, Chen M, Shan H, Chen S, Xu Y, Song Y, Zhang Q, Yuan H, Ouyang H, Li Z, Lai L. Expanded targeting scope and enhanced base editing efficiency in rabbit using optimized xCas9(3.7). Cell Mol Life Sci 2019; 76:4155-4164. [PMID: 31030226 DOI: 10.1007/s00018-019-03110-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/26/2019] [Accepted: 04/16/2019] [Indexed: 12/27/2022]
Abstract
Evolved xCas9(3.7) variant with broad PAM compatibility has been reported in cell lines, while its editing efficiency was site-specific. Here, we show that xCas9(3.7) can recognize a broad PAMs including NGG, NGA, and NGT, in both embryos and Founder (F0) rabbits. Furthermore, the codon-optimized xCas9-derived base editors, exBE4 and exABE, can dramatically improve the base editing efficiencies in rabbit embryos. Our results demonstrated that the optimized xCas9 with expanded PAM compatibility and enhanced base editing efficiency could be used for precise gene modifications in organisms.
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Affiliation(s)
- Zhiquan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Mao Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Huanhuan Shan
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Siyu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yuxin Xu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yuning Song
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Quanjun Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Hongming Yuan
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Hongsheng Ouyang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Zhanjun Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China.
| | - Liangxue Lai
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Animal Science, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou, 510005, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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