351
|
Cao X, Guo J, Huang S, Yu W, Li G, An L, Li X, Tao W, Liu Q, Huang X, Jin X, Ma X. Engineering of near-PAMless adenine base editor with enhanced editing activity and reduced off-target. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:732-742. [PMID: 35664696 PMCID: PMC9126838 DOI: 10.1016/j.omtn.2022.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 04/29/2022] [Indexed: 11/22/2022]
Abstract
About 47% of pathogenic point mutations could be corrected by ABE-induced A·T-to-G·C conversions. However, the applications of ABEs are still hindered by undesired editing efficiency, limited editing scopes, and off-targeting effects. Here, we develop a new adenine base editor, by embedding TadA-8e monomer into SpRY-nCas9, named as CE-8e-SpRY, which exhibits higher activity at NRN than NYN PAMs favored by SpRY nuclease. CE-8e-SpRY could target nearly all genomic sites in principle and induces the highest targeting efficiency among tested SpRY-based ABEs. In addition, CE-8e-SpRY also shows reduced RNA and DNA off-targeting activities. With optimized sgRNAs, CE-8e-SpRY induces efficient or desired target editing at some disease-relevant loci where conventional ABEs were unable to induce precise and satisfied editing. Taken together, our CE-8e-SpRY could broaden the applicability of ABEs in correcting or introducing pathogenic point mutations.
Collapse
Affiliation(s)
- Xiaofang Cao
- National Research Institute for Family Planning, Beijing 100081, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
- National Human Genetic Resources Center, Beijing 102206, China
| | - Junfan Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxia Yu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lisha An
- National Research Institute for Family Planning, Beijing 100081, China
- National Human Genetic Resources Center, Beijing 102206, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanyu Tao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Liu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaohua Jin
- National Research Institute for Family Planning, Beijing 100081, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
- National Human Genetic Resources Center, Beijing 102206, China
- Corresponding author Xiaohua Jin, National Research Institute for Family Planning, Beijing 100081, China.
| | - Xu Ma
- National Research Institute for Family Planning, Beijing 100081, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
- National Human Genetic Resources Center, Beijing 102206, China
- Corresponding author Xu Ma, National Research Institute for Family Planning, Beijing 100081, China.
| |
Collapse
|
352
|
Yuan Q, Gao X. Multiplex base- and prime-editing with drive-and-process CRISPR arrays. Nat Commun 2022; 13:2771. [PMID: 35589728 PMCID: PMC9120480 DOI: 10.1038/s41467-022-30514-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 05/04/2022] [Indexed: 12/17/2022] Open
Abstract
Current base- and prime-editing technologies lack efficient strategies to edit multiple genomic loci simultaneously, limiting their applications in complex genomics and polygenic diseases. Here, we describe drive-and-process (DAP) CRISPR array architectures for multiplex base-editing (MBE) and multiplex prime-editing (MPE) in human cells. We leverage tRNA as the RNA polymerase III promoter to drive the expression of tandemly assembled tRNA-guide RNA (gRNA) arrays, of which the individual gRNAs are released by the cellular endogenous tRNA processing machinery. We engineer a 75-nt human cysteine tRNA (hCtRNA) for the DAP array, achieving up to 31-loci MBE and up to 3-loci MPE. By applying MBE or MPE elements for deliveries via adeno-associated virus (AAV) and lentivirus, we demonstrate simultaneous editing of multiple disease-relevant genomic loci. Our work streamlines the expression and processing of gRNAs on a single array and establishes efficient MBE and MPE strategies for biomedical research and therapeutic applications.
Collapse
Affiliation(s)
- Qichen Yuan
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
- Department of Chemistry, Rice University, Houston, TX, USA.
| |
Collapse
|
353
|
Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, Hurtado J, Zhang Q, Donato García-García J, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Ángel Fernández L, Shoulders MD, Liu CC. In vivo hypermutation and continuous evolution. NATURE REVIEWS. METHODS PRIMERS 2022; 2:37. [PMID: 37073402 PMCID: PMC10108624 DOI: 10.1038/s43586-022-00130-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rosana S. Molina
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
| | - Gordon Rix
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Amanuella A. Mengiste
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Beatriz Alvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Daeje Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Haiqi Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juan Hurtado
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Qiong Zhang
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jorge Donato García-García
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona 2514, Nuevo Mexico, C.P. 45138, Zapopan, Jalisco, Mexico
| | - Zachary J. Heins
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Patrick J. Almhjell
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Frances H. Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ahmad S. Khalil
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David V. Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92617, USA
| |
Collapse
|
354
|
Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases. Cell 2022; 185:1764-1776.e12. [PMID: 35472302 DOI: 10.1016/j.cell.2022.03.039] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/18/2022] [Accepted: 03/24/2022] [Indexed: 02/02/2023]
Abstract
Mitochondrial DNA (mtDNA) editing paves the way for disease modeling of mitochondrial genetic disorders in cell lines and animals and also for the treatment of these diseases in the future. Bacterial cytidine deaminase DddA-derived cytosine base editors (DdCBEs) enabling mtDNA editing, however, are largely limited to C-to-T conversions in the 5'-TC context (e.g., TC-to-TT conversions), suitable for generating merely 1/8 of all possible transition (purine-to-purine and pyrimidine-to-pyrimidine) mutations. Here, we present transcription-activator-like effector (TALE)-linked deaminases (TALEDs), composed of custom-designed TALE DNA-binding arrays, a catalytically impaired, full-length DddA variant or split DddA originated from Burkholderia cenocepacia, and an engineered deoxyadenosine deaminase derived from the E. coli TadA protein, which induce targeted A-to-G editing in human mitochondria. Custom-designed TALEDs were highly efficient in human cells, catalyzing A-to-G conversions at a total of 17 target sites in various mitochondrial genes with editing frequencies of up to 49%.
Collapse
|
355
|
Liang Y, Xie J, Zhang Q, Wang X, Gou S, Lin L, Chen T, Ge W, Zhuang Z, Lian M, Chen F, Li N, Ouyang Z, Lai C, Liu X, Li L, Ye Y, Wu H, Wang K, Lai L. AGBE: a dual deaminase-mediated base editor by fusing CGBE with ABE for creating a saturated mutant population with multiple editing patterns. Nucleic Acids Res 2022; 50:5384-5399. [PMID: 35544322 PMCID: PMC9122597 DOI: 10.1093/nar/gkac353] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 12/26/2022] Open
Abstract
Establishing saturated mutagenesis in a specific gene through gene editing is an efficient approach for identifying the relationships between mutations and the corresponding phenotypes. CRISPR/Cas9-based sgRNA library screening often creates indel mutations with multiple nucleotides. Single base editors and dual deaminase-mediated base editors can achieve only one and two types of base substitutions, respectively. A new glycosylase base editor (CGBE) system, in which the uracil glycosylase inhibitor (UGI) is replaced with uracil-DNA glycosylase (UNG), was recently reported to efficiently induce multiple base conversions, including C-to-G, C-to-T and C-to-A. In this study, we fused a CGBE with ABE to develop a new type of dual deaminase-mediated base editing system, the AGBE system, that can simultaneously introduce 4 types of base conversions (C-to-G, C-to-T, C-to-A and A-to-G) as well as indels with a single sgRNA in mammalian cells. AGBEs can be used to establish saturated mutant populations for verification of the functions and consequences of multiple gene mutation patterns, including single-nucleotide variants (SNVs) and indels, through high-throughput screening.
Collapse
Affiliation(s)
- Yanhui Liang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingke Xie
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Quanjun Zhang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Xiaomin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shixue Gou
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Lihui Lin
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Tao Chen
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Weikai Ge
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Zhenpeng Zhuang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Lian
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Fangbing Chen
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Nan Li
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Zhen Ouyang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.,Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Chengdan Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.,Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Xiaoyi Liu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinghua Ye
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Han Wu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Kepin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.,Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Liangxue Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China.,Sanya institute of Swine resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.,Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| |
Collapse
|
356
|
Bellingrath JS, McClements ME, Shanks M, Clouston P, Fischer MD, MacLaren RE. Envisioning the development of a CRISPR-Cas mediated base editing strategy for a patient with a novel pathogenic CRB1 single nucleotide variant. Ophthalmic Genet 2022; 43:661-670. [PMID: 35538629 DOI: 10.1080/13816810.2022.2073599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Inherited retinal degeneration (IRD) associated with mutations in the Crumbs homolog 1 (CRB1) gene is associated with a severe, early-onset retinal degeneration for which no therapy currently exists. Base editing, with its capability to precisely catalyse permanent nucleobase conversion in a programmable manner, represents a novel therapeutic approach to targeting this autosomal recessive IRD, for which a gene supplementation is challenging due to the need to target three different retinal CRB1 isoforms. PURPOSE To report and classify a novel CRB1 variant and envision a possible therapeutic approach in form of base editing. METHODS Case report. RESULTS A 16-year-old male patient with a clinical diagnosis of early-onset retinitis pigmentosa (RP) and characteristic clinical findings of retinal thickening and coarse lamination was seen at the Oxford Eye Hospital. He was found to be compound heterozygous for two CRB1 variants: a novel pathogenic nonsense variant in exon 9, c.2885T>A (p.Leu962Ter), and a likely pathogenic missense change in exon 6, c.2056C>T (p.Arg686Cys). While a base editing strategy for c.2885T>A would encompass a CRISPR-pass mediated "read-through" of the premature stop codon, the resulting missense changes were predicted to be "possibly damaging" in in-silico analysis. On the other hand, the transversion missense change, c.2056C>T, is amenable to transition editing with an adenine base editor (ABE) fused to a SaCas9-KKH with a negligible chance of bystander edits due to an absence of additional Adenines (As) in the editing window. CONCLUSIONS This case report records a novel pathogenic nonsense variant in CRB1 and gives an example of thinking about a base editing strategy for a patient compound heterozygous for CRB1 variants.
Collapse
Affiliation(s)
- J-S Bellingrath
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - M E McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - M Shanks
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - P Clouston
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - M D Fischer
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - R E MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| |
Collapse
|
357
|
Abstract
Inherited retinal dystrophies (IRDs) are a heterogeneous group of diseases that affect more than 2 million people worldwide. Gene therapy (GT) has emerged as an exciting treatment modality with the potential to provide long-term benefit to patients. Today, gene addition is the most straightforward GT for autosomal recessive IRDs. However, there are three scenarios where this approach falls short. First, in autosomal dominant diseases caused by gain-of-function or dominant-negative mutations, the toxic mutated protein needs to be silenced. Second, a number of IRD genes exceed the limited carrying capacity of adeno-associated virus vectors. Third, there are still about 30% of patients with unknown mutations. In the first two contexts, precise editing tools, such as CRISPR-Cas9, base editors, or prime editors, are emerging as potential GT solutions for the treatment of IRDs. Here, we review gene editing tools based on CRISPR-Cas9 technology that have been used in vivo and the recent first-in-human application of CRISPR-Cas9 in an IRD.
Collapse
Affiliation(s)
- Juliette Pulman
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France.,Fondation Ophtalmologique Rothschild, Paris, France
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| |
Collapse
|
358
|
Barrera-Paez JD, Moraes CT. Mitochondrial genome engineering coming-of-age. Trends Genet 2022; 38:869-880. [PMID: 35599021 PMCID: PMC9283244 DOI: 10.1016/j.tig.2022.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/11/2022] [Accepted: 04/27/2022] [Indexed: 12/16/2022]
Abstract
The mitochondrial genome has been difficult to manipulate because it is shielded by the organelle double membranes, preventing efficient nucleic acid entry. Moreover, mitochondrial DNA (mtDNA) recombination is not a robust system in most species. This limitation has forced investigators to rely on naturally occurring alterations to study both mitochondrial function and pathobiology. Because most pathogenic mtDNA mutations are heteroplasmic, the development of specific nucleases has allowed us to selectively eliminate mutant species. Several 'protein only' gene-editing platforms have been successfully used for this purpose. More recently, a DNA double-strand cytidine deaminase has been identified and adapted to edit mtDNA. This enzyme was also used as a component to adapt a DNA single-strand deoxyadenosine deaminase to mtDNA editing. These are major advances in our ability to precisely alter the mtDNA in animal cells.
Collapse
|
359
|
Abstract
Over the past decade, CRISPR has become as much a verb as it is an acronym, transforming biomedical research and providing entirely new approaches for dissecting all facets of cell biology. In cancer research, CRISPR and related tools have offered a window into previously intractable problems in our understanding of cancer genetics, the noncoding genome and tumour heterogeneity, and provided new insights into therapeutic vulnerabilities. Here, we review the progress made in the development of CRISPR systems as a tool to study cancer, and the emerging adaptation of these technologies to improve diagnosis and treatment.
Collapse
Affiliation(s)
- Alyna Katti
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Bianca J Diaz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Christina M Caragine
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- Department of Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | - Lukas E Dow
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
360
|
Tan J, Zeng D, Zhao Y, Wang Y, Liu T, Li S, Xue Y, Luo Y, Xie X, Chen L, Liu Y, Zhu Q. PhieABEs: a PAM-less/free high-efficiency adenine base editor toolbox with wide target scope in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:934-943. [PMID: 34984801 PMCID: PMC9055815 DOI: 10.1111/pbi.13774] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Adenine base editors (ABEs), which are generally engineered adenosine deaminases and Cas variants, introduce site-specific A-to-G mutations for agronomic trait improvement. However, notably varying editing efficiencies, restrictive requirements for protospacer-adjacent motifs (PAMs) and a narrow editing window greatly limit their application. Here, we developed a robust high-efficiency ABE (PhieABE) toolbox for plants by fusing an evolved, highly active form of the adenosine deaminase TadA8e and a single-stranded DNA-binding domain (DBD), based on PAM-less/free Streptococcus pyogenes Cas9 (SpCas9) nickase variants that recognize the PAM NGN (for SpCas9n-NG and SpGn) or NNN (for SpRYn). By targeting 29 representative targets in rice and assessing the results, we demonstrate that PhieABEs have significantly improved base-editing activity, expanded target range and broader editing windows compared to the ABE7.10 and general ABE8e systems. Among these PhieABEs, hyper ABE8e-DBD-SpRYn (hyABE8e-SpRY) showed nearly 100% editing efficiency at some tested sites, with a high proportion of homozygous base substitutions in the editing windows and no single guide RNA (sgRNA)-dependent off-target changes. The original sgRNA was more compatible with PhieABEs than the evolved sgRNA. In conclusion, the DBD fusion effectively promotes base-editing efficiency, and this novel PhieABE toolbox should have wide applications in plant functional genomics and crop improvement.
Collapse
Affiliation(s)
- Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Dongchang Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yanchang Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yaxi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Taoli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Shuangchun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yang Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yuyu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yao‐Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| |
Collapse
|
361
|
Pan C, Li G, Malzahn AA, Cheng Y, Leyson B, Sretenovic S, Gurel F, Coleman GD, Qi Y. Boosting plant genome editing with a versatile CRISPR-Combo system. NATURE PLANTS 2022; 8:513-525. [PMID: 35596077 DOI: 10.1038/s41477-022-01151-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/11/2022] [Indexed: 05/06/2023]
Abstract
CRISPR-Cas9, its derived base editors and CRISPR activation systems have greatly aided genome engineering in plants. However, these systems are mostly used separately, leaving their combinational potential largely untapped. Here we develop a versatile CRISPR-Combo platform, based on a single Cas9 protein, for simultaneous genome editing (targeted mutagenesis or base editing) and gene activation in plants. We showcase the powerful applications of CRISPR-Combo for boosting plant genome editing. First, CRISPR-Combo is used to shorten the plant life cycle and reduce the efforts in screening transgene-free genome-edited plants by activation of a florigen gene in Arabidopsis. Next, we demonstrate accelerated regeneration and propagation of genome-edited plants by activation of morphogenic genes in poplar. Furthermore, we apply CRISPR-Combo to achieve rice regeneration without exogenous plant hormones, which is established as a new method to predominately enrich heritable targeted mutations. In conclusion, CRISPR-Combo is a versatile genome engineering tool with promising applications in crop breeding.
Collapse
Affiliation(s)
- Changtian Pan
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Gen Li
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yanhao Cheng
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Benjamin Leyson
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Filiz Gurel
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Gary D Coleman
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
| |
Collapse
|
362
|
Wei C, Liu H, Wang W, Luo P, Chen Q, Li R, Wang C, Botella JR, Zhang H. Expanding the Editing Window of Cytidine Base Editors With the Rad51 DNA-Binding Domain in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:865848. [PMID: 35548314 PMCID: PMC9083192 DOI: 10.3389/fpls.2022.865848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/18/2022] [Indexed: 06/15/2023]
Abstract
Recently developed base editors provide a powerful tool for plant research and crop improvement. Although a number of different deaminases and Cas proteins have been used to improve base editors the editing efficiency, and editing window are still not optimal. Fusion of a non-sequence-specific single-stranded DNA-binding domain (DBD) from the human Rad51 protein between Cas9 nickase and the deaminase has been reported to dramatically increase the editing efficiency and expand the editing window of base editors in the mammalian cell lines and mouse embryos. We report the use of this strategy in rice, by fusing a rice codon-optimized human Rad51 DBD to the cytidine base editors AncBE4max, AncBE4max-NG, and evoFERNY. Our results show that the addition of Rad51 DBD did not increase editing efficiency in the major editing window but the editing range was expanded in all the three systems. Replacing the human Rad51 DBD with the rice Rad51 DBD homolog also expanded the editing window effectively.
Collapse
Affiliation(s)
- Chunjie Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hao Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenwen Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Pengyu Luo
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qiuling Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Rou Li
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Chong Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - José Ramón Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Hui Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| |
Collapse
|
363
|
Thean DGL, Chu HY, Fong JHC, Chan BKC, Zhou P, Kwok CCS, Chan YM, Mak SYL, Choi GCG, Ho JWK, Zheng Z, Wong ASL. Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities. Nat Commun 2022; 13:2219. [PMID: 35468907 PMCID: PMC9039034 DOI: 10.1038/s41467-022-29874-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/04/2022] [Indexed: 12/12/2022] Open
Abstract
The genome-editing Cas9 protein uses multiple amino-acid residues to bind the target DNA. Considering only the residues in proximity to the target DNA as potential sites to optimise Cas9’s activity, the number of combinatorial variants to screen through is too massive for a wet-lab experiment. Here we generate and cross-validate ten in silico and experimental datasets of multi-domain combinatorial mutagenesis libraries for Cas9 engineering, and demonstrate that a machine learning-coupled engineering approach reduces the experimental screening burden by as high as 95% while enriching top-performing variants by ∼7.5-fold in comparison to the null model. Using this approach and followed by structure-guided engineering, we identify the N888R/A889Q variant conferring increased editing activity on the protospacer adjacent motif-relaxed KKH variant of Cas9 nuclease from Staphylococcus aureus (KKH-SaCas9) and its derived base editor in human cells. Our work validates a readily applicable workflow to enable resource-efficient high-throughput engineering of genome editor’s activity. Screening combinatorial mutants is too massive for wet-lab experiment alone. Here the authors present a machine learning-coupled combinatorial mutagenesis approach to vastly reduce experimental burden for engineering Cas9 genome editing enzymes.
Collapse
Affiliation(s)
- Dawn G L Thean
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Hoi Yee Chu
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Oncology and Immunology Limited, Hong Kong Science Park, Hong Kong, SAR, China
| | - John H C Fong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Becky K C Chan
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Oncology and Immunology Limited, Hong Kong Science Park, Hong Kong, SAR, China
| | - Peng Zhou
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, SAR, China
| | - Cynthia C S Kwok
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Yee Man Chan
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, SAR, China
| | - Silvia Y L Mak
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, SAR, China
| | - Gigi C G Choi
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Oncology and Immunology Limited, Hong Kong Science Park, Hong Kong, SAR, China
| | - Joshua W K Ho
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong, SAR, China
| | - Zongli Zheng
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, SAR, China.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, SAR, China.,Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Alan S L Wong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China. .,Centre for Oncology and Immunology Limited, Hong Kong Science Park, Hong Kong, SAR, China. .,Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, SAR, China.
| |
Collapse
|
364
|
Das D, Singha DL, Paswan RR, Chowdhury N, Sharma M, Reddy PS, Chikkaputtaiah C. Recent advancements in CRISPR/Cas technology for accelerated crop improvement. PLANTA 2022; 255:109. [PMID: 35460444 DOI: 10.1007/s00425-022-03894-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Precise genome engineering approaches could be perceived as a second paradigm for targeted trait improvement in crop plants, with the potential to overcome the constraints imposed by conventional CRISPR/Cas technology. The likelihood of reduced agricultural production due to highly turbulent climatic conditions increases as the global population expands. The second paradigm of stress-resilient crops with enhanced tolerance and increased productivity against various stresses is paramount to support global production and consumption equilibrium. Although traditional breeding approaches have substantially increased crop production and yield, effective strategies are anticipated to restore crop productivity even further in meeting the world's increasing food demands. CRISPR/Cas, which originated in prokaryotes, has surfaced as a coveted genome editing tool in recent decades, reshaping plant molecular biology in unprecedented ways and paving the way for engineering stress-tolerant crops. CRISPR/Cas is distinguished by its efficiency, high target specificity, and modularity, enables precise genetic modification of crop plants, allowing for the creation of allelic variations in the germplasm and the development of novel and more productive agricultural practices. Additionally, a slew of advanced biotechnologies premised on the CRISPR/Cas methodologies have augmented fundamental research and plant synthetic biology toolkits. Here, we describe gene editing tools, including CRISPR/Cas and its imitative tools, such as base and prime editing, multiplex genome editing, chromosome engineering followed by their implications in crop genetic improvement. Further, we comprehensively discuss the latest developments of CRISPR/Cas technology including CRISPR-mediated gene drive, tissue-specific genome editing, dCas9 mediated epigenetic modification and programmed self-elimination of transgenes in plants. Finally, we highlight the applicability and scope of advanced CRISPR-based techniques in crop genetic improvement.
Collapse
Affiliation(s)
- Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Dhanawantari L Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Ricky Raj Paswan
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Monica Sharma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Palakolanu Sudhakar Reddy
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
| |
Collapse
|
365
|
Muhtaseb AW, Duan J. Modeling common and rare genetic risk factors of neuropsychiatric disorders in human induced pluripotent stem cells. Schizophr Res 2022:S0920-9964(22)00156-6. [PMID: 35459617 PMCID: PMC9735430 DOI: 10.1016/j.schres.2022.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Recent genome-wide association studies (GWAS) and whole-exome sequencing of neuropsychiatric disorders, especially schizophrenia, have identified a plethora of common and rare disease risk variants/genes. Translating the mounting human genetic discoveries into novel disease biology and more tailored clinical treatments is tied to our ability to causally connect genetic risk variants to molecular and cellular phenotypes. When combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) nuclease-mediated genome editing system, human induced pluripotent stem cell (hiPSC)-derived neural cultures (both 2D and 3D organoids) provide a promising tractable cellular model for bridging the gap between genetic findings and disease biology. In this review, we first conceptualize the advances in understanding the disease polygenicity and convergence from the past decade of iPSC modeling of different types of genetic risk factors of neuropsychiatric disorders. We then discuss the major cell types and cellular phenotypes that are most relevant to neuropsychiatric disorders in iPSC modeling. Finally, we critically review the limitations of iPSC modeling of neuropsychiatric disorders and outline the need for implementing and developing novel methods to scale up the number of iPSC lines and disease risk variants in a systematic manner. Sufficiently scaled-up iPSC modeling and a better functional interpretation of genetic risk variants, in combination with cutting-edge CRISPR/Cas9 gene editing and single-cell multi-omics methods, will enable the field to identify the specific and convergent molecular and cellular phenotypes in precision for neuropsychiatric disorders.
Collapse
Affiliation(s)
- Abdurrahman W Muhtaseb
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, United States of America; Department of Human Genetics, The University of Chicago, Chicago, IL 60637, United States of America
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, United States of America; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, United States of America.
| |
Collapse
|
366
|
Abdullah, Wang P, Han T, Liu W, Ren W, Wu Y, Xiao Y. Adenine Base Editing System for Pseudomonas and Prediction Workflow for Protein Dysfunction via ABE. ACS Synth Biol 2022; 11:1650-1657. [PMID: 35389616 DOI: 10.1021/acssynbio.2c00066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pseudomonas is a large genus that inhabits diverse environments due to its distinct metabolic versatility. Its applications range from environmental to industrial biotechnology. Molecular tools that allow precise and efficient genetic manipulation are required to understand and harness its full potential. Here, we report the development of a highly efficient adenine base editing system, i.e., dxABE-PS, for Pseudomonas species. The system allows A:T → G:C transition with up to 100% efficiency along a broad target spectrum because we use xCas9 3.7, which recognizes NG PAM. To enhance the dxABE-PS utility, we develop a prediction workflow for protein dysfunction using ABE, namely, DABE-CSP (dysfunction via ABE through CRISPOR-SIFT prediction). We applied DABE-CSP to inactivate several genes in Pseudomonas putida KT2440 to accumulate a nylon precursor, i.e., muconic acid from catechol with 100% yield. Moreover, we expanded the ABE to non-model Pseudomonas species by developing an nxABE system for P. chengduensisDY56-96, isolated from sediment samples from the seamount area in the West Pacific Ocean. Taken together, the establishment of the ABE systems along with DABE-CSP will fast-track research on Pseudomonas species.
Collapse
Affiliation(s)
- Abdullah
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
| | - Pujie Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
| | - Tongren Han
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
| | - Wei Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
| | - Wenting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Yuehong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, 800 Dongchuan RD. Minhang District, Shanghai 200240, China
| |
Collapse
|
367
|
Xiong X, Li Z, Liang J, Liu K, Li C, Li JF. A cytosine base editor toolkit with varying activity windows and target scopes for versatile gene manipulation in plants. Nucleic Acids Res 2022; 50:3565-3580. [PMID: 35286371 PMCID: PMC8989527 DOI: 10.1093/nar/gkac166] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas-derived base editing tools empower efficient alteration of genomic cytosines or adenines associated with essential genetic traits in plants and animals. Diversified target sequences and customized editing products call for base editors with distinct features regarding the editing window and target scope. Here we developed a toolkit of plant base editors containing AID10, an engineered human AID cytosine deaminase. When fused to the N-terminus or C-terminus of the conventional Cas9 nickase (nSpCas9), AID10 exhibited a broad or narrow activity window at the protospacer adjacent motif (PAM)-distal and -proximal protospacer, respectively, while AID10 fused to both termini conferred an additive activity window. We further replaced nSpCas9 with orthogonal or PAM-relaxed Cas9 variants to widen target scopes. Moreover, we devised dual base editors with AID10 located adjacently or distally to the adenine deaminase ABE8e, leading to juxtaposed or spaced cytosine and adenine co-editing at the same target sequence in plant cells. Furthermore, we expanded the application of this toolkit in plants for tunable knockdown of protein-coding genes via creating upstream open reading frame and for loss-of-function analysis of non-coding genes, such as microRNA sponges. Collectively, this toolkit increases the functional diversity and versatility of base editors in basic and applied plant research.
Collapse
Affiliation(s)
- Xiangyu Xiong
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenxiang Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jieping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kehui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chenlong Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian-Feng Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| |
Collapse
|
368
|
Cornean A, Gierten J, Welz B, Mateo JL, Thumberger T, Wittbrodt J. Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction. eLife 2022; 11:e72124. [PMID: 35373735 PMCID: PMC9033269 DOI: 10.7554/elife.72124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/21/2022] [Indexed: 11/18/2022] Open
Abstract
Single nucleotide variants (SNVs) are prevalent genetic factors shaping individual trait profiles and disease susceptibility. The recent development and optimizations of base editors, rubber and pencil genome editing tools now promise to enable direct functional assessment of SNVs in model organisms. However, the lack of bioinformatic tools aiding target prediction limits the application of base editing in vivo. Here, we provide a framework for adenine and cytosine base editing in medaka (Oryzias latipes) and zebrafish (Danio rerio), ideal for scalable validation studies. We developed an online base editing tool ACEofBASEs (a careful evaluation of base-edits), to facilitate decision-making by streamlining sgRNA design and performing off-target evaluation. We used state-of-the-art adenine (ABE) and cytosine base editors (CBE) in medaka and zebrafish to edit eye pigmentation genes and transgenic GFP function with high efficiencies. Base editing in the genes encoding troponin T and the potassium channel ERG faithfully recreated known cardiac phenotypes. Deep-sequencing of alleles revealed the abundance of intended edits in comparison to low levels of insertion or deletion (indel) events for ABE8e and evoBE4max. We finally validated missense mutations in novel candidate genes of congenital heart disease (CHD) dapk3, ube2b, usp44, and ptpn11 in F0 and F1 for a subset of these target genes with genotype-phenotype correlation. This base editing framework applies to a wide range of SNV-susceptible traits accessible in fish, facilitating straight-forward candidate validation and prioritization for detailed mechanistic downstream studies.
Collapse
Affiliation(s)
- Alex Cornean
- Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
- Heidelberg Biosciences International Graduate School (HBIGS)HeidelbergGermany
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
- Department of Pediatric Cardiology, University Hospital HeidelbergHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research)HeidelbergGermany
| | - Bettina Welz
- Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
- Heidelberg Biosciences International Graduate School (HBIGS)HeidelbergGermany
- DZHK (German Centre for Cardiovascular Research)HeidelbergGermany
| | - Juan Luis Mateo
- Deparment of Computer Science, University of OviedoOviedoSpain
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg UniversityHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research)HeidelbergGermany
| |
Collapse
|
369
|
Sun N, Zhao D, Li S, Zhang Z, Bi C, Zhang X. Reconstructed glycosylase base editors GBE2.0 with enhanced C-to-G base editing efficiency and purity. Mol Ther 2022; 30:2452-2463. [DOI: 10.1016/j.ymthe.2022.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 02/25/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022] Open
|
370
|
Chen S, Liu Z, Yu H, Lai L, Li Z. Efficient multi-nucleotide deletions using deaminase-Cas9 fusions in human cells. J Genet Genomics 2022; 49:927-933. [DOI: 10.1016/j.jgg.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/06/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
|
371
|
Hua K, Han P, Zhu JK. Improvement of base editors and prime editors advances precision genome engineering in plants. PLANT PHYSIOLOGY 2022; 188:1795-1810. [PMID: 34962995 PMCID: PMC8968349 DOI: 10.1093/plphys/kiab591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/22/2021] [Indexed: 05/11/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein (Cas)-mediated gene disruption has revolutionized biomedical research as well as plant and animal breeding. However, most disease-causing mutations and agronomically important genetic variations are single base polymorphisms (single-nucleotide polymorphisms) that require precision genome editing tools for correction of the sequences. Although homology-directed repair of double-stranded breaks (DSBs) can introduce precise changes, such repairs are inefficient in differentiated animal and plant cells. Base editing and prime editing are two recently developed genome engineering approaches that can efficiently introduce precise edits into target sites without requirement of DSB formation or donor DNA templates. They have been applied in several plant species with promising results. Here, we review the extensive literature on improving the efficiency, target scope, and specificity of base editors and prime editors in plants. We also highlight recent progress on base editing in plant organellar genomes and discuss how these precision genome editing tools are advancing basic plant research and crop breeding.
Collapse
Affiliation(s)
- Kai Hua
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Peijin Han
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| |
Collapse
|
372
|
Huang Y, Shang M, Liu T, Wang K. High-throughput methods for genome editing: the more the better. PLANT PHYSIOLOGY 2022; 188:1731-1745. [PMID: 35134245 PMCID: PMC8968257 DOI: 10.1093/plphys/kiac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 05/04/2023]
Abstract
During the last decade, targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) technologies, have permitted efficient targeting of genomes, thereby modifying these genomes to offer tremendous opportunities for deciphering gene function and engineering beneficial traits in many biological systems. As a powerful genome-editing tool, the CRISPR/Cas systems, combined with the development of next-generation sequencing and many other high-throughput techniques, have thus been quickly developed into a high-throughput engineering strategy in animals and plants. Therefore, here, we review recent advances in using high-throughput genome-editing technologies in animals and plants, such as the high-throughput design of targeted guide RNA (gRNA), construction of large-scale pooled gRNA, and high-throughput genome-editing libraries, high-throughput detection of editing events, and high-throughput supervision of genome-editing products. Moreover, we outline perspectives for future applications, ranging from medication using gene therapy to crop improvement using high-throughput genome-editing technologies.
Collapse
Affiliation(s)
- Yong Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Meiqi Shang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Tingting Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| |
Collapse
|
373
|
Rallapalli KL, Ranzau BL, Ganapathy KR, Paesani F, Komor AC. Combined Theoretical, Bioinformatic, and Biochemical Analyses of RNA Editing by Adenine Base Editors. CRISPR J 2022; 5:294-310. [PMID: 35353638 DOI: 10.1089/crispr.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adenine base editors (ABEs) have been subjected to multiple rounds of mutagenesis with the goal of optimizing their function as efficient and precise genome editing agents. Despite an ever-expanding data set of ABE mutants and their corresponding DNA or RNA-editing activity, the molecular mechanisms defining these changes remain to be elucidated. In this study, we provide a systematic interpretation of the nature of these mutations using an entropy-based classification model that relies on evolutionary data from extant protein sequences. Using this model in conjunction with experimental analyses, we identify two previously reported mutations that form an epistatic pair in the RNA-editing functional landscape of ABEs. Molecular dynamics simulations reveal the atomistic details of how these two mutations affect substrate-binding and catalytic activity, via both individual and cooperative effects, hence providing insights into the mechanisms through which these two mutations are epistatically coupled.
Collapse
Affiliation(s)
- Kartik L Rallapalli
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| | - Kaushik R Ganapathy
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA.,Materials Science and Engineering, University of California San Diego, La Jolla, California, USA; and University of California San Diego, La Jolla, California, USA.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| |
Collapse
|
374
|
Dimitri A, Herbst F, Fraietta JA. Engineering the next-generation of CAR T-cells with CRISPR-Cas9 gene editing. Mol Cancer 2022; 21:78. [PMID: 35303871 PMCID: PMC8932053 DOI: 10.1186/s12943-022-01559-z] [Citation(s) in RCA: 122] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/04/2022] [Indexed: 12/24/2022] Open
Abstract
Chimeric Antigen Receptor (CAR) T-cells represent a breakthrough in personalized cancer therapy. In this strategy, synthetic receptors comprised of antigen recognition, signaling, and costimulatory domains are used to reprogram T-cells to target tumor cells for destruction. Despite the success of this approach in refractory B-cell malignancies, optimal potency of CAR T-cell therapy for many other cancers, particularly solid tumors, has not been achieved. Factors such as T-cell exhaustion, lack of CAR T-cell persistence, cytokine-related toxicities, and bottlenecks in the manufacturing of autologous products have hampered the safety, effectiveness, and availability of this approach. With the ease and accessibility of CRISPR-Cas9-based gene editing, it is possible to address many of these limitations. Accordingly, current research efforts focus on precision engineering of CAR T-cells with conventional CRISPR-Cas9 systems or novel editors that can install desired genetic changes with or without introduction of a double-stranded break (DSB) into the genome. These tools and strategies can be directly applied to targeting negative regulators of T-cell function, directing therapeutic transgenes to specific genomic loci, and generating reproducibly safe and potent allogeneic universal CAR T-cell products for on-demand cancer immunotherapy. This review evaluates several of the ongoing and future directions of combining next-generation CRISPR-Cas9 gene editing with synthetic biology to optimize CAR T-cell therapy for future clinical trials toward the establishment of a new cancer treatment paradigm.
Collapse
Affiliation(s)
- Alexander Dimitri
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, South Pavilion Expansion (SPE), Room 9-104, 3400 Civic Center Blvd, Bldg. 421, Philadelphia, PA, 19104-5156, USA.,Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Friederike Herbst
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Translational Medical Oncology, National Center for Tumor Diseases, Dresden and German Cancer Research Center, Heidelberg, Germany
| | - Joseph A Fraietta
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, South Pavilion Expansion (SPE), Room 9-104, 3400 Civic Center Blvd, Bldg. 421, Philadelphia, PA, 19104-5156, USA. .,Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
375
|
Nguyen Tran MT, Kc R, Hewitt AW. A Taxonomic and Phylogenetic Classification of Diverse Base Editors. CRISPR J 2022; 5:311-328. [PMID: 35244489 DOI: 10.1089/crispr.2021.0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Base editors mediate the targeted conversion of single nucleobases in a therapeutically relevant manner. Herein, we present a hypothetical taxonomic and phylogenetic framework for the classification of more than 200 different DNA base editors, and we categorize them based on their described properties. Following evaluation of their in situ activity windows, which were derived by cataloguing their activity in published literature, organization is done hierarchically, with specific base editor signatures being subcategorized according to their on-target activity or nonspecific, genome- or transcriptome-wide activity. Based on this categorization, we curate a phylogenetic framework, based on protein homology alignment, and describe a taxonomic structure that clusters base editor variants on their target chemistry, endonuclease component, identity of their deaminase component, and their described properties into discrete taxa. Thus, we establish a hypothetical taxonomic structure that can describe and organize current and potentially future base editing variants into clearly defined groups that are defined by their characteristics. Finally, we summarize our findings into a navigable database (ShinyApp in R) that allows users to select through our repository to nominate ideal base editor candidates as a starting point for further testing in their specific application.
Collapse
Affiliation(s)
- Minh Thuan Nguyen Tran
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia; and The University of Melbourne, Melbourne, Australia
| | - Rajendra Kc
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia; and The University of Melbourne, Melbourne, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia; and The University of Melbourne, Melbourne, Australia.,Centre for Eye Research Australia, The University of Melbourne, Melbourne, Australia
| |
Collapse
|
376
|
Yu SY, Birkenshaw A, Thomson T, Carlaw T, Zhang LH, Ross CJD. Increasing the Targeting Scope of CRISPR Base Editing System Beyond NGG. CRISPR J 2022; 5:187-202. [PMID: 35238621 DOI: 10.1089/crispr.2021.0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genome editing provides a new therapeutic strategy to cure genetic diseases. The recently developed CRISPR-Cas9 base editing technology has shown great potential to repair the majority of pathogenic point mutations in the patient's DNA precisely. Base editor is the fusion of a Cas9 nickase with a base-modifying enzyme that can change a nucleotide on a single strand of DNA without generating double-stranded DNA breaks. However, a major limitation in applying such a system is the prerequisite of a protospacer adjacent motif sequence at the desired position relative to the target site. Progress has been made to increase the targeting scope of base editors by engineering SpCas9 protein variants, establishing systems with broadened editing windows, characterizing new SpCas9 orthologs, and developing prime editing technology. In this review, we discuss recent progress in the development of CRISPR base editing, focusing on its targeting scope, and we provide a workflow for selecting a suitable base editor based on the target nucleotide sequences.
Collapse
Affiliation(s)
- Si-Yue Yu
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Alexandra Birkenshaw
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Tyler Thomson
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Tiffany Carlaw
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Lin-Hua Zhang
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Colin J D Ross
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| |
Collapse
|
377
|
Sidorova OA, Sayed S, Paszkowski-Rogacz M, Seifert M, Camgöz A, Roeder I, Bornhäuser M, Thiede C, Buchholz F. RNAi-Mediated Screen of Primary AML Cells Nominates MDM4 as a Therapeutic Target in NK-AML with DNMT3A Mutations. Cells 2022; 11:cells11050854. [PMID: 35269477 PMCID: PMC8909053 DOI: 10.3390/cells11050854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/22/2022] Open
Abstract
DNA-methyltransferase 3A (DNMT3A) mutations belong to the most frequent genetic aberrations found in adult acute myeloid leukemia (AML). Recent evidence suggests that these mutations arise early in leukemogenesis, marking leukemic progenitors and stem cells, and persist through consolidation chemotherapy, providing a pool for AML relapse. Currently, there are no therapeutic approaches directed specifically against this cell population. To unravel therapeutically actionable targets in mutant DNMT3A-driven AML cells, we have performed a focused RNAi screen in a panel of 30 primary AML samples, all carrying a DNMT3A R882 mutation. As one of the strongest hits, we identified MDM4 as a gene essential for proliferation of primary DNMT3AWT/R882X AML cells. We analyzed a publicly available RNA-Seq dataset of primary normal karyotype (NK) AML samples and found a trend towards MDM4 transcript overexpression particularly in DNMT3A-mutant samples. Moreover, we found that the MDM2/4 inhibitor ALRN-6924 impairs growth of DNMT3AWT/R882X primary cells in vitro by inducing cell cycle arrest through upregulation of p53 target genes. Our results suggest that MDM4 inhibition is a potential target in NK-AML patients bearing DNMT3A R882X mutations.
Collapse
Affiliation(s)
- Olga Alexandra Sidorova
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
| | - Shady Sayed
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, 01307 Dresden, Germany; (M.S.); (I.R.)
| | - Aylin Camgöz
- Hopp Children’s Cancer Center Heidelberg, 69120 Heidelberg, Germany;
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, 01307 Dresden, Germany; (M.S.); (I.R.)
| | - Martin Bornhäuser
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
- National Center for Tumor Diseases (NCT/UCC), 01307 Dresden, Germany
- Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
| | - Christian Thiede
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
- National Center for Tumor Diseases (NCT/UCC), 01307 Dresden, Germany
- Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
- National Center for Tumor Diseases (NCT/UCC), 01307 Dresden, Germany
- Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
- Correspondence:
| |
Collapse
|
378
|
McLure RJ, Radford SE, Brockwell DJ. High-throughput directed evolution: a golden era for protein science. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
379
|
Zhao D, Qian Y, Li J, Li Z, Lai L. Highly efficient A-to-G base editing by ABE8.17 in rabbits. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 27:1156-1163. [PMID: 35282412 PMCID: PMC8888895 DOI: 10.1016/j.omtn.2022.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 01/24/2022] [Indexed: 11/25/2022]
|
380
|
Huang X, Wang Y, Wang N. Base Editors for Citrus Gene Editing. Front Genome Ed 2022; 4:852867. [PMID: 35296063 PMCID: PMC8919994 DOI: 10.3389/fgeed.2022.852867] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/10/2022] [Indexed: 11/22/2022] Open
Abstract
Base editors, such as adenine base editors (ABE) and cytosine base editors (CBE), provide alternatives for precise genome editing without generating double-strand breaks (DSBs), thus avoiding the risk of genome instability and unpredictable outcomes caused by DNA repair. Precise gene editing mediated by base editors in citrus has not been reported. Here, we have successfully adapted the ABE to edit the TATA box in the promoter region of the canker susceptibility gene LOB1 from TATA to CACA in grapefruit (Citrus paradise) and sweet orange (Citrus sinensis). TATA-edited plants are resistant to the canker pathogen Xanthomonas citri subsp. citri (Xcc). In addition, CBE was successfully used to edit the acetolactate synthase (ALS) gene in citrus. ALS-edited plants were resistant to the herbicide chlorsulfuron. Two ALS-edited plants did not show green fluorescence although the starting construct for transformation contains a GFP expression cassette. The Cas9 gene was undetectable in the herbicide-resistant citrus plants. This indicates that the ALS edited plants are transgene-free, representing the first transgene-free gene-edited citrus using the CRISPR technology. In summary, we have successfully adapted the base editors for precise citrus gene editing. The CBE base editor has been used to generate transgene-free citrus via transient expression.
Collapse
|
381
|
Feng S, Wang Z, Li A, Xie X, Liu J, Li S, Li Y, Wang B, Hu L, Yang L, Guo T. Strategies for High-Efficiency Mutation Using the CRISPR/Cas System. Front Cell Dev Biol 2022; 9:803252. [PMID: 35198566 PMCID: PMC8860194 DOI: 10.3389/fcell.2021.803252] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/22/2021] [Indexed: 12/15/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated systems have revolutionized traditional gene-editing tools and are a significant tool for ameliorating gene defects. Characterized by high target specificity, extraordinary efficiency, and cost-effectiveness, CRISPR/Cas systems have displayed tremendous potential for genetic manipulation in almost any organism and cell type. Despite their numerous advantages, however, CRISPR/Cas systems have some inherent limitations, such as off-target effects, unsatisfactory efficiency of delivery, and unwanted adverse effects, thereby resulting in a desire to explore approaches to address these issues. Strategies for improving the efficiency of CRISPR/Cas-induced mutations, such as reducing off-target effects, improving the design and modification of sgRNA, optimizing the editing time and the temperature, choice of delivery system, and enrichment of sgRNA, are comprehensively described in this review. Additionally, several newly emerging approaches, including the use of Cas variants, anti-CRISPR proteins, and mutant enrichment, are discussed in detail. Furthermore, the authors provide a deep analysis of the current challenges in the utilization of CRISPR/Cas systems and the future applications of CRISPR/Cas systems in various scenarios. This review not only serves as a reference for improving the maturity of CRISPR/Cas systems but also supplies practical guidance for expanding the applicability of this technology.
Collapse
Affiliation(s)
- Shuying Feng
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zilong Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Aifang Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xin Xie
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Junjie Liu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Shuxuan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yalan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Baiyan Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lina Hu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lianhe Yang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Tao Guo
- Department of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| |
Collapse
|
382
|
Wang G, Xu Z, Wang F, Huang Y, Xin Y, Liang S, Li B, Si H, Sun L, Wang Q, Ding X, Zhu X, Chen L, Yu L, Lindsey K, Zhang X, Jin S. Development of an efficient and precise adenine base editor (ABE) with expanded target range in allotetraploid cotton (Gossypium hirsutum). BMC Biol 2022; 20:45. [PMID: 35164736 PMCID: PMC8845244 DOI: 10.1186/s12915-022-01232-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/13/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Base editors (BEs) display diverse applications in a variety of plant species such as Arabidopsis, rice, wheat, maize, soybean, and cotton, where they have been used to mediate precise base pair conversions without the collateral generation of undesirable double-stranded breaks (DSB). Studies of single-nucleotide polymorphisms (SNPs) underpinning plant traits are still challenging, particularly in polyploidy species where such SNPs are present in multiple copies, and simultaneous modification of all alleles would be required for functional analysis. Allotetraploid cotton has a number of homoeologous gene pairs located in the A and D sub-genomes with considerable SNPs, and it is desirable to develop adenine base editors (ABEs) for efficient and precise A-to-G single-base editing without DSB in such complex genome. RESULTS We established various ABE vectors based on different engineered adenosine deaminase (TadA) proteins fused to Cas9 variants (dCas9, nCas9), enabling efficient A to G editing up to 64% efficiency on-target sites of the allotetraploid cotton genome. Comprehensive analysis showed that GhABE7.10n exhibited the highest editing efficiency, with the main editing sites specifically located at the position A5 (counting the PAM as positions 21-23). Furthermore, DNA and RNA off-target analysis of cotton plants edited with GhABE7.10n and GhABE7.10d by whole genome and whole-transcriptome sequencing revealed no DNA off-target mutations, while very low-level RNA off-target mutations were detected. A new base editor, namely GhABE7.10dCpf1 (7.10TadA + dCpf1), that recognizes a T-rich PAM, was developed for the first time. Targeted A-to-G substitutions generated a single amino acid change in the cotton phosphatidyl ethanolamine-binding protein (GhPEBP), leading to a compact cotton plant architecture, an ideotype for mechanized harvesting of modern cotton production. CONCLUSIONS Our data illustrate the robustness of adenine base editing in plant species with complex genomes, which provides efficient and precise toolkit for cotton functional genomics and precise molecular breeding.
Collapse
Affiliation(s)
- Guanying Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Zhongping Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Fuqiu Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Yuefan Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Yanfeng Xin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Sijia Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Bo Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Wulumuqi, Xinjaing, 830000, People's Republic of China
| | - Huan Si
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Lin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Qiongqiong Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Xiao Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Xiangqian Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Luo Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Lu Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.
| |
Collapse
|
383
|
Ravi NS, Wienert B, Wyman SK, Bell HW, George A, Mahalingam G, Vu JT, Prasad K, Bandlamudi BP, Devaraju N, Rajendiran V, Syedbasha N, Pai AA, Nakamura Y, Kurita R, Narayanasamy M, Balasubramanian P, Thangavel S, Marepally S, Velayudhan SR, Srivastava A, DeWitt MA, Crossley M, Corn JE, Mohankumar KM. Identification of novel HPFH-like mutations by CRISPR base editing that elevate the expression of fetal hemoglobin. eLife 2022; 11:e65421. [PMID: 35147495 PMCID: PMC8865852 DOI: 10.7554/elife.65421] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Naturally occurring point mutations in the HBG promoter switch hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin in sickle cell patients with hereditary persistence of fetal hemoglobin (HPFH) and ameliorate the clinical severity. Inspired by this natural phenomenon, we tiled the highly homologous HBG proximal promoters using adenine and cytosine base editors that avoid the generation of large deletions and identified novel regulatory regions including a cluster at the -123 region. Base editing at -123 and -124 bp of HBG promoter induced fetal hemoglobin (HbF) to a higher level than disruption of well-known BCL11A binding site in erythroblasts derived from human CD34+ hematopoietic stem and progenitor cells (HSPC). We further demonstrated in vitro that the introduction of -123T > C and -124T > C HPFH-like mutations drives gamma-globin expression by creating a de novo binding site for KLF1. Overall, our findings shed light on so far unknown regulatory elements within the HBG promoter and identified additional targets for therapeutic upregulation of fetal hemoglobin.
Collapse
Affiliation(s)
- Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
- Sree Chitra Tirunal Institute for Medical Sciences and TechnologyThiruvananthapuramIndia
| | - Beeke Wienert
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydneyAustralia
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
| | - Henry William Bell
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydneyAustralia
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
- Sree Chitra Tirunal Institute for Medical Sciences and TechnologyThiruvananthapuramIndia
| | - Gokulnath Mahalingam
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
| | - Jonathan T Vu
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
| | - Kirti Prasad
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
- Manipal Academy of Higher EducationKarnatakaIndia
| | - Bhanu Prasad Bandlamudi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
| | - Nivedhitha Devaraju
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
- Manipal Academy of Higher EducationKarnatakaIndia
| | - Vignesh Rajendiran
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
- Sree Chitra Tirunal Institute for Medical Sciences and TechnologyThiruvananthapuramIndia
| | - Nazar Syedbasha
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
| | - Aswin Anand Pai
- Sree Chitra Tirunal Institute for Medical Sciences and TechnologyThiruvananthapuramIndia
- Department of Haematology, Christian Medical College & HospitalVelloreIndia
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource CenterIbarakiJapan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, JapanTokyoJapan
| | - Muthuraman Narayanasamy
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
- Department of Biochemistry, Christian Medical CollegeVelloreIndia
| | - Poonkuzhali Balasubramanian
- Sree Chitra Tirunal Institute for Medical Sciences and TechnologyThiruvananthapuramIndia
- Department of Haematology, Christian Medical College & HospitalVelloreIndia
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
| | - Srujan Marepally
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
| | - Shaji R Velayudhan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
- Sree Chitra Tirunal Institute for Medical Sciences and TechnologyThiruvananthapuramIndia
- Department of Haematology, Christian Medical College & HospitalVelloreIndia
| | - Alok Srivastava
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
- Sree Chitra Tirunal Institute for Medical Sciences and TechnologyThiruvananthapuramIndia
- Department of Haematology, Christian Medical College & HospitalVelloreIndia
| | - Mark A DeWitt
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los AngelesLos AngelesUnited States
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydneyAustralia
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Institute of Molecular Health Sciences, Department of BiologyZurichSwitzerland
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College CampusVelloreIndia
- Sree Chitra Tirunal Institute for Medical Sciences and TechnologyThiruvananthapuramIndia
| |
Collapse
|
384
|
Li S, Liu L, Sun W, Zhou X, Zhou H. A large-scale genome and transcriptome sequencing analysis reveals the mutation landscapes induced by high-activity adenine base editors in plants. Genome Biol 2022; 23:51. [PMID: 35139891 PMCID: PMC8826654 DOI: 10.1186/s13059-022-02618-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/18/2022] [Indexed: 12/30/2022] Open
Abstract
Background The high-activity adenine base editors (ABEs), engineered with the recently-developed tRNA adenosine deaminases (TadA8e and TadA9), show robust base editing activity but raise concerns about off-target effects. Results In this study, we perform a comprehensive evaluation of ABE8e- and ABE9-induced DNA and RNA mutations in Oryza sativa. Whole-genome sequencing analysis of plants transformed with four ABEs, including SpCas9n-TadA8e, SpCas9n-TadA9, SpCas9n-NG-TadA8e, and SpCas9n-NG-TadA9, reveal that ABEs harboring TadA9 lead to a higher number of off-target A-to-G (A>G) single-nucleotide variants (SNVs), and that those harboring CRISPR/SpCas9n-NG lead to a higher total number of off-target SNVs in the rice genome. An analysis of the T-DNAs carrying the ABEs indicates that the on-target mutations could be introduced before and/or after T-DNA integration into plant genomes, with more off-target A>G SNVs forming after the ABEs had integrated into the genome. Furthermore, we detect off-target A>G RNA mutations in plants with high expression of ABEs but not in plants with low expression of ABEs. The off-target A>G RNA mutations tend to cluster, while off-target A>G DNA mutations rarely clustered. Conclusion Our findings that Cas proteins, TadA variants, temporal expression of ABEs, and expression levels of ABEs contribute to ABE specificity in rice provide insight into the specificity of ABEs and suggest alternative ways to increase ABE specificity besides engineering TadA variants. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02618-w.
Collapse
Affiliation(s)
- Shaofang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Lang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China.,Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Wenxian Sun
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Zhejiang, Hangzhou, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. .,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China.
| |
Collapse
|
385
|
Liu Z, Chen S, Lai L, Li Z. Inhibition of base editors with anti-deaminases derived from viruses. Nat Commun 2022; 13:597. [PMID: 35105899 PMCID: PMC8807840 DOI: 10.1038/s41467-022-28300-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/18/2022] [Indexed: 11/09/2022] Open
Abstract
Cytosine base editors (CBEs), combining cytidine deaminases with the Cas9 nickase (nCas9), enable targeted C-to-T conversions in genomic DNA and are powerful genome-editing tools used in biotechnology and medicine. However, the overexpression of cytidine deaminases in vivo leads to unexpected potential safety risks, such as Cas9-independent off-target effects. This risk makes the development of deaminase off switches for modulating CBE activity an urgent need. Here, we report the repurpose of four virus-derived anti-deaminases (Ades) that efficiently inhibit APOBEC3 deaminase-CBEs. We demonstrate that they antagonize CBEs by inhibiting the APOBEC3 catalytic domain, relocating the deaminases to the extranuclear region or degrading the whole CBE complex. By rationally engineering the deaminase domain, other frequently used base editors, such as CGBE, A&CBE, A&CGBE, rA1-CBE and ABE8e, can be moderately inhibited by Ades, expanding the scope of their applications. As a proof of concept, the Ades in this study dramatically decrease both Cas9-dependent and Cas9-independent off-target effects of CBEs better than traditional anti-CRISPRs (Acrs). Finally, we report the creation of a cell type-specific CBE-ON switch based on a microRNA-responsive Ade vector, showing its practicality. In summary, these natural deaminase-specific Ades are tools that can be used to regulate the genome-engineering functions of BEs.
Collapse
Affiliation(s)
- Zhiquan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Siyu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- Key Laboratory of Zoonosis Research, Ministry of Education, 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 Guang Dong Laboratory (GRMH-GDL), Guangzhou, 510005, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhanjun Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, 130062, China.
| |
Collapse
|
386
|
Bloomer H, Khirallah J, Li Y, Xu Q. CRISPR/Cas9 ribonucleoprotein-mediated genome and epigenome editing in mammalian cells. Adv Drug Deliv Rev 2022; 181:114087. [PMID: 34942274 PMCID: PMC8844242 DOI: 10.1016/j.addr.2021.114087] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/15/2021] [Accepted: 12/16/2021] [Indexed: 02/03/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) system has revolutionized the ability to edit the mammalian genome, providing a platform for the correction of pathogenic mutations and further investigation into gene function. CRISPR reagents can be delivered into the cell as DNA, RNA, or pre-formed ribonucleoproteins (RNPs). RNPs offer numerous advantages over other delivery approaches due to their ability to rapidly target genomic sites and quickly degrade thereafter. Here, we review the production steps and delivery methods for Cas9 RNPs. Additionally, we discuss how RNPs enhance genome and epigenome editing efficiencies, reduce off-target editing activity, and minimize cellular toxicity in clinically relevant mammalian cell types. We include details on a broad range of editing approaches, including novel base and prime editing techniques. Finally, we summarize key challenges for the use of RNPs, and propose future perspectives on the field.
Collapse
Affiliation(s)
- Hanan Bloomer
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, US,School of Medicine and Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, US
| | - Jennifer Khirallah
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, US
| | - Yamin Li
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, US,Corresponding Authors: (Y. Li) and (Q. Xu)
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, US,Corresponding Authors: (Y. Li) and (Q. Xu)
| |
Collapse
|
387
|
Xu R, Qin R, Xie H, Li J, Liu X, Zhu M, Sun Y, Yu Y, Lu P, Wei P. Genome editing with type II-C CRISPR-Cas9 systems from Neisseria meningitidis in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:350-359. [PMID: 34582079 PMCID: PMC8753361 DOI: 10.1111/pbi.13716] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 05/05/2023]
Abstract
Two type II-C Cas9 orthologs (Nm1Cas9 and Nm2Cas9) were recently identified from Neisseria meningitidis and have been extensively used in mammalian cells, but whether these NmCas9 orthologs or other type II-C Cas9 proteins can mediate genome editing in plants remains unclear. In this study, we developed and optimized targeted mutagenesis systems from NmCas9s for plants. Efficient genome editing at the target with N4 GATT and N4 CC protospacer adjacent motifs (PAMs) was achieved with Nm1Cas9 and Nm2Cas9 respectively. These results indicated that a highly active editing system could be developed from type II-C Cas9s with distinct PAM preferences, thus providing a reliable strategy to extend the scope of genome editing in plants. Base editors (BEs) were further developed from the NmCas9s. The editing efficiency of adenine BEs (ABEs) of TadA*-7.10 and cytosine BEs (CBEs) of rat APOBEC1 (rAPO1) or human APOBEC3a (hA3A) were extremely limited, whereas ABEs of TadA-8e and CBEs of Petromyzon marinus cytidine deaminase 1 (PmCDA1) exhibited markedly improved performance on the same targets. In addition, we found that fusion of a single-stranded DNA-binding domain from the human Rad51 protein enhanced the base editing capability of rAPO1-CBEs of NmCas9s. Together, our results suggest that the engineering of NmCas9s or other type II-C Cas9s can provide useful alternatives for crop genome editing.
Collapse
Affiliation(s)
- Rongfang Xu
- College of AgronomyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Ruiying Qin
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Hongjun Xie
- Key Laboratory of Indica Rice Genetics and Breeding in the middle and Lower Reaches of Yangtze River ValleyMinistry of AgricultureHunan Rice Research InstituteChangshaChina
| | - Juan Li
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Xiaoshuang Liu
- College of AgronomyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Mingdong Zhu
- Key Laboratory of Indica Rice Genetics and Breeding in the middle and Lower Reaches of Yangtze River ValleyMinistry of AgricultureHunan Rice Research InstituteChangshaChina
| | - Yang Sun
- State Key Laboratory of Crop Stress Adaptation and ImprovementKey Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifengChina
| | - Yinghong Yu
- Key Laboratory of Indica Rice Genetics and Breeding in the middle and Lower Reaches of Yangtze River ValleyMinistry of AgricultureHunan Rice Research InstituteChangshaChina
| | - Pingli Lu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major DiseasesCollege of Life SciencesAnhui Normal UniversityWuhuChina
| | - Pengcheng Wei
- College of AgronomyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| |
Collapse
|
388
|
Shelake RM, Pramanik D, Kim JY. In Vivo Rapid Investigation of CRISPR-Based Base Editing Components in Escherichia coli (IRI-CCE): A Platform for Evaluating Base Editing Tools and Their Components. Int J Mol Sci 2022; 23:ijms23031145. [PMID: 35163069 PMCID: PMC8834901 DOI: 10.3390/ijms23031145] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/16/2022] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid assessment of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing (GE) tools and their components is a critical aspect for successful GE applications in different organisms. In many bacteria, double-strand breaks (DSBs) generated by CRISPR/Cas tool generally cause cell death due to the lack of an efficient nonhomologous end-joining pathway and restricts its use. CRISPR-based DSB-free base editors (BEs) have been applied for precise nucleotide (nt) editing in bacteria, which does not need to make DSBs. However, optimization of newer BE tools in bacteria is challenging owing to the toxic effects of BE reagents expressed using strong promoters. Improved variants of two main BEs, cytidine base editor (CBE) and adenine base editor (ABE), capable of converting C to T and A to G, respectively, have been recently developed but yet to be tested for editing characteristics in bacteria. Here, we report a platform for in vivo rapid investigation of CRISPR-BE components in Escherichia coli (IRI-CCE) comprising a combination of promoters and terminators enabling the expression of nCas9-based BE and sgRNA to nontoxic levels, eventually leading to successful base editing. We demonstrate the use of IRI-CCE to characterize different variants of CBEs (PmCDA1, evoCDA1, APOBEC3A) and ABEs (ABE8e, ABE9e) for bacteria, exhibiting that each independent BE has its specific editing pattern for a given target site depending on protospacer length. In summary, CRISPR-BE components expressed without lethal effects on cell survival in the IRI-CCE allow an analysis of various BE tools, including cloned biopart modules and sgRNAs.
Collapse
Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Correspondence: (R.M.S.); (J.-Y.K.)
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea
- Correspondence: (R.M.S.); (J.-Y.K.)
| |
Collapse
|
389
|
Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
Collapse
Affiliation(s)
- Tarun S Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada.
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
390
|
Banskota S, Raguram A, Suh S, Du SW, Davis JR, Choi EH, Wang X, Nielsen SC, Newby GA, Randolph PB, Osborn MJ, Musunuru K, Palczewski K, Liu DR. Engineered virus-like particles for efficient in vivo delivery of therapeutic proteins. Cell 2022; 185:250-265.e16. [PMID: 35021064 PMCID: PMC8809250 DOI: 10.1016/j.cell.2021.12.021] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/23/2021] [Accepted: 12/15/2021] [Indexed: 02/08/2023]
Abstract
Methods to deliver gene editing agents in vivo as ribonucleoproteins could offer safety advantages over nucleic acid delivery approaches. We report the development and application of engineered DNA-free virus-like particles (eVLPs) that efficiently package and deliver base editor or Cas9 ribonucleoproteins. By engineering VLPs to overcome cargo packaging, release, and localization bottlenecks, we developed fourth-generation eVLPs that mediate efficient base editing in several primary mouse and human cell types. Using different glycoproteins in eVLPs alters their cellular tropism. Single injections of eVLPs into mice support therapeutic levels of base editing in multiple tissues, reducing serum Pcsk9 levels 78% following 63% liver editing, and partially restoring visual function in a mouse model of genetic blindness. In vitro and in vivo off-target editing from eVLPs was virtually undetected, an improvement over AAV or plasmid delivery. These results establish eVLPs as promising vehicles for therapeutic macromolecule delivery that combine key advantages of both viral and nonviral delivery.
Collapse
Affiliation(s)
- Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Susie Suh
- Gavin Herbert Eye Institute, Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA; Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Samuel W Du
- Gavin Herbert Eye Institute, Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA; Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Elliot H Choi
- Gavin Herbert Eye Institute, Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA; Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Xiao Wang
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah C Nielsen
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Peyton B Randolph
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Mark J Osborn
- Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Kiran Musunuru
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA; Department of Physiology and Biophysics, University of California, Irvine, CA, USA; Department of Chemistry, University of California, Irvine, CA, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
391
|
Adenine base-editing-mediated exon skipping induces gene knockout in cultured pig cells. Biotechnol Lett 2022; 44:59-76. [PMID: 34997407 DOI: 10.1007/s10529-021-03214-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/28/2021] [Indexed: 12/26/2022]
Abstract
Gene-knockout pigs have important applications in agriculture and medicine. Compared with CRISPR/Cas9, Adenine base editor (ABE) convert single A·T pairs to G·C pairs in the genome without generating DNA double-strand breaks, and this method has higher accuracy and biosafety in pig genetic modification. However, the application of ABE in pig gene knockout is limited by protospacer-adjacent motif sequences and the base-editing window. Alternative mRNA splicing is an important mechanism underlying the formation of proteins with diverse functions in eukaryotes. Spliceosome recognizes the conservative sequences of splice donors and acceptors in a precursor mRNA. Mutations in these conservative sequences induce exon skipping, leading to proteins with novel functions or to gene inactivation due to frameshift mutations. In this study, adenine base-editing-mediated exon skipping was used to expand the application of ABE in the generation of gene knockout pigs. We first constructed a modified "all-in-one" ABE vector suitable for porcine somatic cell transfection that contained an ABE for single-base editing and an sgRNA expression cassette. The "all-in-one" ABE vector induced efficient sgRNA-dependent A-to-G conversions in porcine cells during single base-editing of multiple endogenous gene loci. Subsequently, an ABE system was designed for single adenine editing of the conservative splice acceptor site (AG sequence at the 3' end of the intron 5) and splice donor site (GT sequence at the 5' end of the intron 6) in the porcine gene GHR; this method achieved highly efficient A-to-G conversion at the cellular level. Then, porcine single-cell colonies carrying a biallelic A-to-G conversion in the splice acceptor site in the intron 5 of GHR were generated. RT-PCR indicated exon 6 skipped at the mRNA level. Western blotting revealed GHR protein loss, and gene sequencing showed no sgRNA-dependent off-target effects. These results demonstrate accurate adenine base-editing-mediated exon skipping and gene knockout in porcine cells. This is the first proof-of-concept study of adenine base-editing-mediated exon skipping for gene regulation in pigs, and this work provides a new strategy for accurate and safe genetic modification of pigs for agricultural and medical applications.
Collapse
|
392
|
Habib O, Habib G, Hwang GH, Bae S. Comprehensive analysis of prime editing outcomes in human embryonic stem cells. Nucleic Acids Res 2022; 50:1187-1197. [PMID: 35018468 PMCID: PMC8789035 DOI: 10.1093/nar/gkab1295] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
Abstract
Prime editing is a versatile and precise genome editing technique that can directly copy desired genetic modifications into target DNA sites without the need for donor DNA. This technique holds great promise for the analysis of gene function, disease modeling, and the correction of pathogenic mutations in clinically relevant cells such as human pluripotent stem cells (hPSCs). Here, we comprehensively tested prime editing in hPSCs by generating a doxycycline-inducible prime editing platform. Prime editing successfully induced all types of nucleotide substitutions and small insertions and deletions, similar to observations in other human cell types. Moreover, we compared prime editing and base editing for correcting a disease-related mutation in induced pluripotent stem cells derived form a patient with α 1-antitrypsin (A1AT) deficiency. Finally, whole-genome sequencing showed that, unlike the cytidine deaminase domain of cytosine base editors, the reverse transcriptase domain of a prime editor does not lead to guide RNA-independent off-target mutations in the genome. Our results demonstrate that prime editing in hPSCs has great potential for complementing previously developed CRISPR genome editing tools.
Collapse
Affiliation(s)
- Omer Habib
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| | - Gizem Habib
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| | - Gue-Ho Hwang
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| | - Sangsu Bae
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| |
Collapse
|
393
|
Disruption of HIV-1 co-receptors CCR5 and CXCR4 in primary human T cells and hematopoietic stem and progenitor cells using base editing. Mol Ther 2022; 30:130-144. [PMID: 34737067 PMCID: PMC8753564 DOI: 10.1016/j.ymthe.2021.10.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/31/2021] [Accepted: 10/27/2021] [Indexed: 01/07/2023] Open
Abstract
Disruption of CCR5 or CXCR4, the main human immunodeficiency virus type 1 (HIV-1) co-receptors, has been shown to protect primary human CD4+ T cells from HIV-1 infection. Base editing can install targeted point mutations in cellular genomes, and can thus efficiently inactivate genes by introducing stop codons or eliminating start codons without double-stranded DNA break formation. Here, we applied base editors for individual and simultaneous disruption of both co-receptors in primary human CD4+ T cells. Using cytosine base editors we observed premature stop codon introduction in up to 89% of sequenced CCR5 or CXCR4 alleles. Using adenine base editors we eliminated the start codon in CCR5 in up to 95% of primary human CD4+ T cell and up to 88% of CD34+ hematopoietic stem and progenitor cell target alleles. Genome-wide specificity analysis revealed low numbers of off-target mutations that were introduced by base editing, located predominantly in intergenic or intronic regions. We show that our editing strategies prevent transduction with CCR5-tropic and CXCR4-tropic viral vectors in up to 79% and 88% of human CD4+ T cells, respectively. The engineered T cells maintained functionality and overall our results demonstrate the effectiveness of base-editing strategies for efficient and specific ablation of HIV co-receptors in clinically relevant cell types.
Collapse
|
394
|
Ramadier S, Chalumeau A, Felix T, Othman N, Aknoun S, Casini A, Maule G, Masson C, De Cian A, Frati G, Brusson M, Concordet JP, Cavazzana M, Cereseto A, El Nemer W, Amendola M, Wattellier B, Meneghini V, Miccio A. Combination of lentiviral and genome editing technologies for the treatment of sickle cell disease. Mol Ther 2022; 30:145-163. [PMID: 34418541 PMCID: PMC8753569 DOI: 10.1016/j.ymthe.2021.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 01/07/2023] Open
Abstract
Sickle cell disease (SCD) is caused by a mutation in the β-globin gene leading to polymerization of the sickle hemoglobin (HbS) and deformation of red blood cells. Autologous transplantation of hematopoietic stem/progenitor cells (HSPCs) genetically modified using lentiviral vectors (LVs) to express an anti-sickling β-globin leads to some clinical benefit in SCD patients, but it requires high-level transgene expression (i.e., high vector copy number [VCN]) to counteract HbS polymerization. Here, we developed therapeutic approaches combining LV-based gene addition and CRISPR-Cas9 strategies aimed to either knock down the sickle β-globin and increase the incorporation of an anti-sickling globin (AS3) in hemoglobin tetramers, or to induce the expression of anti-sickling fetal γ-globins. HSPCs from SCD patients were transduced with LVs expressing AS3 and a guide RNA either targeting the endogenous β-globin gene or regions involved in fetal hemoglobin silencing. Transfection of transduced cells with Cas9 protein resulted in high editing efficiency, elevated levels of anti-sickling hemoglobins, and rescue of the SCD phenotype at a significantly lower VCN compared to the conventional LV-based approach. This versatile platform can improve the efficacy of current gene addition approaches by combining different therapeutic strategies, thus reducing the vector amount required to achieve a therapeutic VCN and the associated genotoxicity risk.
Collapse
Affiliation(s)
- Sophie Ramadier
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France; Phasics, Bâtiment Explorer, Espace Technologique, Route de l'Orme des Merisiers, 91190 St. Aubin, France
| | - Anne Chalumeau
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France
| | - Tristan Felix
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France
| | - Nadia Othman
- Phasics, Bâtiment Explorer, Espace Technologique, Route de l'Orme des Merisiers, 91190 St. Aubin, France
| | - Sherazade Aknoun
- Phasics, Bâtiment Explorer, Espace Technologique, Route de l'Orme des Merisiers, 91190 St. Aubin, France
| | | | - Giulia Maule
- CIBIO, University of Trento, 38100 Trento, Italy
| | - Cecile Masson
- Paris-Descartes Bioinformatics Platform, Imagine Institute, 75015 Paris, France
| | - Anne De Cian
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, 75015 Paris, France
| | - Giacomo Frati
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France
| | - Megane Brusson
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, 75015 Paris, France
| | - Marina Cavazzana
- Université de Paris, 75015 Paris, France; Imagine Institute, 75015 Paris, France; Biotherapy Department and Clinical Investigation Center, Assistance Publique Hôpitaux de Paris, INSERM, 75015 Paris, France
| | | | - Wassim El Nemer
- Etablissement Français du Sang PACA-Corse, Marseille, France; Aix Marseille Université, EFS, CNRS, ADES, "Biologie des Groupes Sanguins," 13000 Marseille, France; Laboratoire d'Excellence GR-Ex, Paris, France
| | | | - Benoit Wattellier
- Phasics, Bâtiment Explorer, Espace Technologique, Route de l'Orme des Merisiers, 91190 St. Aubin, France
| | - Vasco Meneghini
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France.
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR1163, 75015 Paris, France; Université de Paris, 75015 Paris, France.
| |
Collapse
|
395
|
Dang L, Zhou X, Zhong X, Yu W, Huang S, Liu H, Chen Y, Zhang W, Yuan L, Li L, Huang X, Li G, Liu J, Tong G. Correction of the pathogenic mutation in TGM1 gene by adenine base editing in mutant embryos. Mol Ther 2022; 30:175-183. [PMID: 33974999 PMCID: PMC8753292 DOI: 10.1016/j.ymthe.2021.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/09/2021] [Accepted: 05/05/2021] [Indexed: 01/07/2023] Open
Abstract
A couple diagnosed as carriers for lamellar ichthyosis, an autosomal recessive rare disease, encountered two pregnancy losses. Their blood samples showed the same heterozygous c.607C>T mutation in the TGM1 gene. However, we found that about 98.4% of the sperm had mutations, suggesting possible de novo germline mutation. To explore the probability of correcting this mutation, we used two different adenine base editors (ABEs) combined with related truncated single guide RNA (sgRNA) to repair the pathogenic mutation in mutant zygotes. Our results showed that the editing efficiency was 73.8% for ABEmax-NG combined with 20-bp-length sgRNA and 78.7% for Sc-ABEmax combined with 19-bp-length sgRNA. The whole-genome sequencing (WGS) and deep sequencing analysis demonstrated precise DNA editing. This study reveals the possibility of correcting the genetic mutation in embryos with the ABE system.
Collapse
Affiliation(s)
- Lu Dang
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xueliang Zhou
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiufang Zhong
- Department of Reproductive Center, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wenxia Yu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shisheng Huang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Hanyan Liu
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuanyuan Chen
- Department of Reproductive Center, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wuwen Zhang
- Department of Reproductive Center, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lihua Yuan
- Department of Reproductive Center, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lei Li
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xingxu Huang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Guanglei Li
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Jianqiao Liu
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Guoqing Tong
- Department of Reproductive Center, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| |
Collapse
|
396
|
Liu Z, Chen S, Xie W, Song Y, Li J, Lai L, Li Z. Versatile and efficient in vivo genome editing with compact Streptococcus pasteurianus Cas9. Mol Ther 2022; 30:256-267. [PMID: 34174445 PMCID: PMC8753289 DOI: 10.1016/j.ymthe.2021.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/01/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
Compact CRISPR-Cas9 systems that can be packaged into an adeno-associated virus (AAV) show promise for gene therapy. However, the requirement of protospacer adjacent motifs (PAMs) restricts the target scope. To expand this repertoire, we revisited and optimized a small Cas9 ortholog derived from Streptococcus pasteurianus (SpaCas9) for efficient genome editing in vivo. We found that SpaCas9 enables potent targeting of 5'-NNGYRA-3' PAMs, which are distinct from those recognized by currently used small Cas9s; the Spa-cytosine base editor (CBE) and Spa-adenine base editor (ABE) systems efficiently generated robust C-to-T and A-to-G conversions both in vitro and in vivo. In addition, by exploiting natural variation in the PAM-interacting domain, we engineered three SpaCas9 variants to further expand the targeting scope of compact Cas9 systems. Moreover, mutant mice with efficient disruption of the Tyr gene were successfully generated by microinjection of SpaCas9 mRNA and the corresponding single guide RNA (sgRNA) into zygotes. Notably, all-in-one AAV delivery of SpaCas9 targeting the Pcsk9 gene in adult mouse liver produced efficient genome-editing events and reduced its serum cholesterol. Thus, with distinct PAMs and a small size, SpaCas9 will broaden the CRISPR-Cas9 toolsets for efficient gene modifications and therapeutic applications.
Collapse
Affiliation(s)
- Zhiquan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
| | - Siyu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
| | - Wanhua Xie
- The Precise Medicine Center, Shenyang Medical College, Shenyang 110000, China
| | - Yuning Song
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
| | - Jinze Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
| | - Liangxue Lai
- Key Laboratory of Zoonosis Research, Ministry of Education, 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 Guang Dong Laboratory (GRMH-GDL), Guangzhou 510005, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhanjun Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China.
| |
Collapse
|
397
|
Tu CF, Chuang CK, Yang TS. The application of new breeding technology based on gene editing in pig industry. Anim Biosci 2022; 35:791-803. [PMID: 34991204 PMCID: PMC9066036 DOI: 10.5713/ab.21.0390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/07/2021] [Indexed: 12/02/2022] Open
Abstract
Genome/gene-editing (GE) techniques, characterized by a low technological barrier, high efficiency, and broad application among organisms, are now being employed not only in medical science but also in agriculture/veterinary science. Different engineered CRISPR/Cas9s have been identified to expand the application of this technology. In pig production, GE is a precise new breeding technology (NBT), and promising outcomes in improving economic traits, such as growth, lean or healthy meat production, animal welfare, and disease resistance, have already been documented and reviewed. These promising achievements in porcine gene editing, including the Myostatin gene knockout (KO) in indigenous breeds to improve lean meat production, the uncoupling protein 1 (UCP1) gene knock-in to enhance piglet thermogenesis and survival under cold stress, the generation of GGTA1 and CMP-N-glycolylneuraminic acid hydroxylase (CMAH) gene double KO (dKO) pigs to produce healthy red meat, and the KO or deletion of exon 7 of the CD163 gene to confer resistance to porcine reproductive and respiratory syndrome virus infection, are described in the present article. Other related approaches for such purposes are also discussed. The current trend of global regulations or legislation for GE organisms is that they are exempted from classification as genetically modified organisms (GMOs) if no exogenes are integrated into the genome, according to product-based and not process-based methods. Moreover, an updated case study in the EU showed that current GMO legislation is not fit for purpose in term of NBTs, which contribute to the objectives of the EU’s Green Deal and biodiversity strategies and even meet the United Nations’ sustainable development goals for a more resilient and sustainable agri-food system. The GE pigs generated via NBT will be exempted from classification as GMOs, and their global valorization and commercialization can be foreseen.
Collapse
Affiliation(s)
- Ching-Fu Tu
- Division of Animal Technology, Animal Technology Laboratories, Agricultural Technology Research Institute, Hsinchu City 30093, Taiwan
| | - Chin-Kai Chuang
- Division of Animal Technology, Animal Technology Laboratories, Agricultural Technology Research Institute, Hsinchu City 30093, Taiwan
| | - Tien-Shuh Yang
- Division of Animal Technology, Animal Technology Laboratories, Agricultural Technology Research Institute, Hsinchu City 30093, Taiwan.,Department of Biotechnology and Animal Science, National Ilan University, Yilan City, 26047 Taiwan
| |
Collapse
|
398
|
Abdelnour SA, Xie L, Hassanin AA, Zuo E, Lu Y. The Potential of CRISPR/Cas9 Gene Editing as a Treatment Strategy for Inherited Diseases. Front Cell Dev Biol 2022; 9:699597. [PMID: 34977000 PMCID: PMC8715006 DOI: 10.3389/fcell.2021.699597] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a promising innovative technology for genomic editing that offers scientists the chance to edit DNA structures and change gene function. It has several possible uses consisting of editing inherited deficiencies, treating, and reducing the spread of disorders. Recently, reports have demonstrated the creation of synthetic RNA molecules and supplying them alongside Cas9 into genome of eukaryotes, since distinct specific regions of the genome can be manipulated and targeted. The therapeutic potential of CRISPR/Cas9 technology is great, especially in gene therapy, in which a patient-specific mutation is genetically edited, or in the treating of human disorders that are untreatable with traditional treatments. This review focused on numerous, in vivo, in vitro, and ex vivo uses of the CRISPR/Cas9 technology in human inherited diseases, discovering the capability of this versatile in medicine and examining some of the main limitations for its upcoming use in patients. In addition to introducing a brief impression of the biology of the CRISPR/Cas9 scheme and its mechanisms, we presented the utmost recent progress in the uses of CRISPR/Cas9 technology in editing and treating of human genetic diseases.
Collapse
Affiliation(s)
- Sameh A Abdelnour
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China.,Animal Production Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Long Xie
- Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Abdallah A Hassanin
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Erwei Zuo
- Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| |
Collapse
|
399
|
Li G, Li X, Zhuang S, Wang L, Zhu Y, Chen Y, Sun W, Wu Z, Zhou Z, Chen J, Huang X, Wang J, Li D, Li W, Wang H, Wei W. Gene editing and its applications in biomedicine. SCIENCE CHINA. LIFE SCIENCES 2022; 65:660-700. [PMID: 35235150 PMCID: PMC8889061 DOI: 10.1007/s11427-021-2057-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
The steady progress in genome editing, especially genome editing based on the use of clustered regularly interspaced short palindromic repeats (CRISPR) and programmable nucleases to make precise modifications to genetic material, has provided enormous opportunities to advance biomedical research and promote human health. The application of these technologies in basic biomedical research has yielded significant advances in identifying and studying key molecular targets relevant to human diseases and their treatment. The clinical translation of genome editing techniques offers unprecedented biomedical engineering capabilities in the diagnosis, prevention, and treatment of disease or disability. Here, we provide a general summary of emerging biomedical applications of genome editing, including open challenges. We also summarize the tools of genome editing and the insights derived from their applications, hoping to accelerate new discoveries and therapies in biomedicine.
Collapse
Affiliation(s)
- Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Songkuan Zhuang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China
| | - Liren Wang
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yifan Zhu
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeguang Wu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China.
| | - Dali Li
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, 150001, China.
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
| |
Collapse
|
400
|
Shamshirgaran Y, Liu J, Sumer H, Verma PJ, Taheri-Ghahfarokhi A. Tools for Efficient Genome Editing; ZFN, TALEN, and CRISPR. Methods Mol Biol 2022; 2495:29-46. [PMID: 35696026 DOI: 10.1007/978-1-0716-2301-5_2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The last two decades have marked significant advancement in the genome editing field. Three generations of programmable nucleases (ZFNs, TALENs, and CRISPR-Cas system) have been adopted to introduce targeted DNA double-strand breaks (DSBs) in eukaryotic cells. DNA repair machinery of the cells has been exploited to introduce insertion and deletions (indels) at the targeted DSBs to study function of any gene-of-interest. The resulting indels were generally assumed to be "random" events produced by "error-prone" DNA repair pathways. However, recent advances in computational tools developed to study the Cas9-induced mutations have changed the consensus and implied the "non-randomness" nature of these mutations. Furthermore, CRISPR-centric tools are evolving at an unprecedented pace, for example, base- and prime-editors are the newest developments that have been added to the genome editing toolbox. Altogether, genome editing tools have revolutionized our way of conducting research in life sciences. Here, we present a concise overview of genome editing tools and describe the DNA repair pathways underlying the generation of genome editing outcome.
Collapse
Affiliation(s)
- Yasaman Shamshirgaran
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jun Liu
- Stem Cells and Genome Editing, Genomics and Cellular Sciences, Agriculture Victoria Research, Bundoora, VIC, Australia
| | - Huseyin Sumer
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Paul J Verma
- Aquatics & Livestock Sciences, South Australian Research and Development Institute, Roseworthy, SA, Australia
| | - Amir Taheri-Ghahfarokhi
- Quantitative Biology, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| |
Collapse
|