1
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Li XC, Srinivasan V, Laiker I, Misunou N, Frankel N, Pallares LF, Crocker J. TF-High-Evolutionary: In Vivo Mutagenesis of Gene Regulatory Networks for the Study of the Genetics and Evolution of the Drosophila Regulatory Genome. Mol Biol Evol 2024; 41:msae167. [PMID: 39117360 PMCID: PMC11342961 DOI: 10.1093/molbev/msae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/10/2024] Open
Abstract
Understanding the evolutionary potential of mutations in gene regulatory networks is essential to furthering the study of evolution and development. However, in multicellular systems, genetic manipulation of regulatory networks in a targeted and high-throughput way remains challenging. In this study, we designed TF-High-Evolutionary (HighEvo), a transcription factor (TF) fused with a base editor (activation-induced deaminase), to continuously induce germline mutations at TF-binding sites across regulatory networks in Drosophila. Populations of flies expressing TF-HighEvo in their germlines accumulated mutations at rates an order of magnitude higher than natural populations. Importantly, these mutations accumulated around the targeted TF-binding sites across the genome, leading to distinct morphological phenotypes consistent with the developmental roles of the tagged TFs. As such, this TF-HighEvo method allows the interrogation of the mutational space of gene regulatory networks at scale and can serve as a powerful reagent for experimental evolution and genetic screens focused on the regulatory genome.
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Affiliation(s)
- Xueying C Li
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Ian Laiker
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
| | | | - Nicolás Frankel
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
| | - Luisa F Pallares
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Justin Crocker
- European Molecular Biology Laboratory, Heidelberg, Germany
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2
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Fauser F, Kadam BN, Arangundy-Franklin S, Davis JE, Vaidya V, Schmidt NJ, Lew G, Xia DF, Mureli R, Ng C, Zhou Y, Scarlott NA, Eshleman J, Bendaña YR, Shivak DA, Reik A, Li P, Davis GD, Miller JC. Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells. Nat Commun 2024; 15:1181. [PMID: 38360922 PMCID: PMC10869815 DOI: 10.1038/s41467-024-45100-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Nucleobase editors represent an emerging technology that enables precise single-base edits to the genomes of eukaryotic cells. Most nucleobase editors use deaminase domains that act upon single-stranded DNA and require RNA-guided proteins such as Cas9 to unwind the DNA prior to editing. However, the most recent class of base editors utilizes a deaminase domain, DddAtox, that can act upon double-stranded DNA. Here, we target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers (ZFs). We also identify a broad variety of Toxin-Derived Deaminases (TDDs) orthologous to DddAtox that allow us to fine-tune properties such as targeting density and specificity. TDD-derived ZF base editors enable up to 73% base editing in T cells with good cell viability and favorable specificity.
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Affiliation(s)
| | | | | | | | | | | | - Garrett Lew
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | - Danny F Xia
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | - Colman Ng
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | | | | | | | | | | | - Patrick Li
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
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3
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Singh K, Bhushan B, Kumar S, Singh S, Macadangdang RR, Pandey E, Varma AK, Kumar S. Precision Genome Editing Techniques in Gene Therapy: Current State and Future Prospects. Curr Gene Ther 2024; 24:377-394. [PMID: 38258771 DOI: 10.2174/0115665232279528240115075352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/26/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Precision genome editing is a rapidly evolving field in gene therapy, allowing for the precise modification of genetic material. The CRISPR and Cas systems, particularly the CRISPRCas9 system, have revolutionized genetic research and therapeutic development by enabling precise changes like single-nucleotide substitutions, insertions, and deletions. This technology has the potential to correct disease-causing mutations at their source, allowing for the treatment of various genetic diseases. Programmable nucleases like CRISPR-Cas9, transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs) can be used to restore normal gene function, paving the way for novel therapeutic interventions. However, challenges, such as off-target effects, unintended modifications, and ethical concerns surrounding germline editing, require careful consideration and mitigation strategies. Researchers are exploring innovative solutions, such as enhanced nucleases, refined delivery methods, and improved bioinformatics tools for predicting and minimizing off-target effects. The prospects of precision genome editing in gene therapy are promising, with continued research and innovation expected to refine existing techniques and uncover new therapeutic applications.
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Affiliation(s)
- Kuldeep Singh
- Department of Pharmacology, Rajiv Academy for Pharmacy, Mathura, Uttar Pradesh, India
| | - Bharat Bhushan
- Department of Pharmacology, Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - Sunil Kumar
- Department of Pharmacology, P.K. University, Thanra, Karera, Shivpuri, Madhya Pradesh, India
| | - Supriya Singh
- Department of Pharmaceutics, Babu Banarasi Das Northern India Institute of Technology, Faizabaad road, Lucknow, Uttar Pradesh, India
| | | | - Ekta Pandey
- Department of Chemistry, Bundelkhand Institute of Engineering and Technology, Jhansi, Uttar Pradesh, India
| | - Ajit Kumar Varma
- Department of Pharmaceutics, Rama University, Kanpur, Uttar Pradesh, India
| | - Shivendra Kumar
- Department of Pharmacology, Rajiv Academy for Pharmacy, Mathura, Uttar Pradesh, India
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4
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Hosseini SY, Mallick R, Mäkinen P, Ylä-Herttuala S. Navigating the prime editing strategy to treat cardiovascular genetic disorders in transforming heart health. Expert Rev Cardiovasc Ther 2024; 22:75-89. [PMID: 38494784 DOI: 10.1080/14779072.2024.2328642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
INTRODUCTION After understanding the genetic basis of cardiovascular disorders, the discovery of prime editing (PE), has opened new horizons for finding their cures. PE strategy is the most versatile editing tool to change cardiac genetic background for therapeutic interventions. The optimization of elements, prediction of efficiency, and discovery of the involved genes regulating the process have not been completed. The large size of the cargo and multi-elementary structure makes the in vivo heart delivery challenging. AREAS COVERED Updated from recent published studies, the fundamentals of the PEs, their application in cardiology, potentials, shortcomings, and the future perspectives for the treatment of cardiac-related genetic disorders will be discussed. EXPERT OPINION The ideal PE for the heart should be tissue-specific, regulatable, less immunogenic, high transducing, and safe. However, low efficiency, sup-optimal PE architecture, the large size of required elements, the unclear role of transcriptomics on the process, unpredictable off-target effects, and its context-dependency are subjects that need to be considered. It is also of great importance to see how beneficial or detrimental cell cycle or epigenomic modifier is to bring changes into cardiac cells. The PE delivery is challenging due to the size, multi-component properties of the editors and liver sink.
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Affiliation(s)
- Seyed Younes Hosseini
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Bacteriology and Virology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Rahul Mallick
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Petri Mäkinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
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5
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Sanz-García F, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. The Pseudomonas aeruginosa Resistome: Permanent and Transient Antibiotic Resistance, an Overview. Methods Mol Biol 2024; 2721:85-102. [PMID: 37819517 DOI: 10.1007/978-1-0716-3473-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
One of the most concerning characteristics of Pseudomonas aeruginosa is its low susceptibility to several antibiotics of common use in clinics, as well as its facility to acquire increased resistance levels. Consequently, the study of the antibiotic resistance mechanisms of this bacterium is of relevance for human health. For such a study, different types of resistance should be distinguished. The intrinsic resistome is composed of a set of genes, present in the core genome of P. aeruginosa, which contributes to its characteristic, species-specific, phenotype of susceptibility to antibiotics. Acquired resistance refers to those genetic events, such as the acquisition of mutations or antibiotic resistance genes that reduce antibiotic susceptibility. Finally, antibiotic resistance can be transiently acquired in the presence of specific compounds or under some growing conditions. The current article provides information on methods currently used to analyze intrinsic, mutation-driven, and transient antibiotic resistance in P. aeruginosa.
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Affiliation(s)
| | - Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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6
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Budzko L, Hoffa-Sobiech K, Jackowiak P, Figlerowicz M. Engineered deaminases as a key component of DNA and RNA editing tools. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102062. [PMID: 38028200 PMCID: PMC10661471 DOI: 10.1016/j.omtn.2023.102062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Over recent years, zinc-dependent deaminases have attracted increasing interest as key components of nucleic acid editing tools that can generate point mutations at specific sites in either DNA or RNA by combining a targeting module (such as a catalytically impaired CRISPR-Cas component) and an effector module (most often a deaminase). Deaminase-based molecular tools are already being utilized in a wide spectrum of therapeutic and research applications; however, their medical and biotechnological potential seems to be much greater. Recent reports indicate that the further development of nucleic acid editing systems depends largely on our ability to engineer the substrate specificity and catalytic activity of the editors themselves. In this review, we summarize the current trends and achievements in deaminase engineering. The presented data indicate that the potential of these enzymes has not yet been fully revealed or understood. Several examples show that even relatively minor changes in the structure of deaminases can give them completely new and unique properties.
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Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Hoffa-Sobiech
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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7
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Abstract
DNA-editing enzymes perform chemical reactions on DNA nucleobases. These reactions can change the genetic identity of the modified base or modulate gene expression. Interest in DNA-editing enzymes has burgeoned in recent years due to the advent of clustered regularly interspaced short palindromic repeat-associated (CRISPR-Cas) systems, which can be used to direct their DNA-editing activity to specific genomic loci of interest. In this review, we showcase DNA-editing enzymes that have been repurposed or redesigned and developed into programmable base editors. These include deaminases, glycosylases, methyltransferases, and demethylases. We highlight the astounding degree to which these enzymes have been redesigned, evolved, and refined and present these collective engineering efforts as a paragon for future efforts to repurpose and engineer other families of enzymes. Collectively, base editors derived from these DNA-editing enzymes facilitate programmable point mutation introduction and gene expression modulation by targeted chemical modification of nucleobases.
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Affiliation(s)
- Kartik L Rallapalli
- Department of Chemistry and Biochemistry, 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;
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8
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Lam DK, Feliciano PR, Arif A, Bohnuud T, Fernandez TP, Gehrke JM, Grayson P, Lee KD, Ortega MA, Sawyer C, Schwaegerle ND, Peraro L, Young L, Lee SJ, Ciaramella G, Gaudelli NM. Improved cytosine base editors generated from TadA variants. Nat Biotechnol 2023; 41:686-697. [PMID: 36624149 PMCID: PMC10188367 DOI: 10.1038/s41587-022-01611-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/09/2022] [Indexed: 01/11/2023]
Abstract
Cytosine base editors (CBEs) enable programmable genomic C·G-to-T·A transition mutations and typically comprise a modified CRISPR-Cas enzyme, a naturally occurring cytidine deaminase, and an inhibitor of uracil repair. Previous studies have shown that CBEs utilizing naturally occurring cytidine deaminases may cause unguided, genome-wide cytosine deamination. While improved CBEs that decrease stochastic genome-wide off-targets have subsequently been reported, these editors can suffer from suboptimal on-target performance. Here, we report the generation and characterization of CBEs that use engineered variants of TadA (CBE-T) that enable high on-target C·G to T·A across a sequence-diverse set of genomic loci, demonstrate robust activity in primary cells and cause no detectable elevation in genome-wide mutation. Additionally, we report cytosine and adenine base editors (CABEs) catalyzing both A-to-I and C-to-U editing (CABE-Ts). Together with ABEs, CBE-Ts and CABE-Ts enable the programmable installation of all transition mutations using laboratory-evolved TadA variants with improved properties relative to previously reported CBEs.
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Affiliation(s)
| | | | | | | | | | | | | | - Kin D Lee
- Beam Therapeutics, Cambridge, MA, USA
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9
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Yang SP, Zhu XX, Qu ZX, Chen CY, Wu YB, Wu Y, Luo ZD, Wang XY, He CY, Fang JW, Wang LQ, Hong GL, Zheng ST, Zeng JM, Yan AF, Feng J, Liu L, Zhang XL, Zhang LG, Miao K, Tang DS. Production of MSTN knockout porcine cells using adenine base-editing-mediated exon skipping. In Vitro Cell Dev Biol Anim 2023:10.1007/s11626-023-00763-5. [PMID: 37099179 DOI: 10.1007/s11626-023-00763-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/24/2023] [Indexed: 04/27/2023]
Abstract
Gene-knockout pigs have important applications in agriculture and medicine. Compared with CRISPR/Cas9 and cytosine base editing (CBE) technologies, adenine base editing (ABE) shows better safety and accuracy in gene modification. However, because of the characteristics of gene sequences, the ABE system cannot be widely used in gene knockout. Alternative splicing of mRNA is an important biological mechanism in eukaryotes for the formation of proteins with different functional activities. The splicing apparatus recognizes conserved sequences of the 5' end splice donor and 3' end splice acceptor motifs of introns in pre-mRNA that can trigger exon skipping, leading to the production of new functional proteins, or causing gene inactivation through frameshift mutations. This study aimed to construct a MSTN knockout pig by inducing exon skipping with the aid of the ABE system to expand the application of the ABE system for the preparation of knockout pigs. In this study, first, we constructed ABEmaxAW and ABE8eV106W plasmid vectors and found that their editing efficiencies at the targets were at least sixfold and even 260-fold higher than that of ABEmaxAW by contrasting the editing efficiencies at the gene targets of endogenous CD163, IGF2, and MSTN in pigs. Subsequently, we used the ABE8eV106W system to realize adenine base (the base of the antisense strand is thymine) editing of the conserved splice donor sequence (5'-GT) of intron 2 of the porcine MSTN gene. A porcine single-cell clone carrying a homozygous mutation (5'-GC) in the conserved sequence (5'-GT) of the intron 2 splice donor of the MSTN gene was successfully generated after drug selection. Unfortunately, the MSTN gene was not expressed and, therefore, could not be characterized at this level. No detectable genomic off-target edits were identified by Sanger sequencing. In this study, we verified that the ABE8eV106W vector had higher editing efficiency and could expand the editing scope of ABE. Additionally, we successfully achieved the precise modification of the alternative splice acceptor of intron 2 of the porcine MSTN gene, which may provide a new strategy for gene knockout in pigs.
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Affiliation(s)
- Shuai-Peng Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, 528225, China
| | - Xiang-Xing Zhu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, 528225, China.
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China.
| | - Zi-Xiao Qu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, 528225, China
| | - Cai-Yue Chen
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Yao-Bing Wu
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Yue Wu
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Zi-Dan Luo
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Xin-Yi Wang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Chu-Yu He
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Jia-Wen Fang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Ling-Qi Wang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Guang-Long Hong
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Shu-Tao Zheng
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Jie-Mei Zeng
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Ai-Fen Yan
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Juan Feng
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Lian Liu
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Xiao-Li Zhang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Li-Gang Zhang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Kai Miao
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.
| | - Dong-Sheng Tang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, 528225, China.
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China.
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10
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Liu H, Zhu Y, Li M, Gu Z. Precise genome editing with base editors. MEDICAL REVIEW (2021) 2023; 3:75-84. [PMID: 37724105 PMCID: PMC10471085 DOI: 10.1515/mr-2022-0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/01/2023] [Indexed: 09/20/2023]
Abstract
Single-nucleotide variants account for about half of known pathogenic genetic variants in human. Genome editing strategies by reversing pathogenic point mutations with minimum side effects have great therapeutic potential and are now being actively pursued. The emerge of precise and efficient genome editing strategies such as base editing and prime editing provide powerful tools for nucleotide conversion without inducing double-stranded DNA breaks (DSBs), which have shown great potential for curing genetic disorders. A diverse toolkit of base editors has been developed to improve the editing efficiency and accuracy in different context of application. Here, we summarized the evolving of base editors (BEs), their limitations and future perspective of base editing-based therapeutic strategies.
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Affiliation(s)
- Hongcai Liu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu Province, China
| | - Yao Zhu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu Province, China
| | - Minjie Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu Province, China
| | - Zhimin Gu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu Province, China
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11
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Yoshida R, Nakamura S. Association of TP53 clonal hematopoiesis with indeterminate potential with the development of myeloid neoplasms after rucaparib treatment. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1292. [PMID: 36618808 PMCID: PMC9816858 DOI: 10.21037/atm-2022-65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/21/2022] [Indexed: 11/23/2022]
Affiliation(s)
- Reiko Yoshida
- Institute for Clinical Genetics and Genomics, Showa University, Tokyo, Japan
| | - Seigo Nakamura
- Institute for Clinical Genetics and Genomics, Showa University, Tokyo, Japan
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12
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Willis JCW, Silva-Pinheiro P, Widdup L, Minczuk M, Liu DR. Compact zinc finger base editors that edit mitochondrial or nuclear DNA in vitro and in vivo. Nat Commun 2022; 13:7204. [PMID: 36418298 PMCID: PMC9684478 DOI: 10.1038/s41467-022-34784-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
DddA-derived cytosine base editors (DdCBEs) use programmable DNA-binding TALE repeat arrays, rather than CRISPR proteins, a split double-stranded DNA cytidine deaminase (DddA), and a uracil glycosylase inhibitor to mediate C•G-to-T•A editing in nuclear and organelle DNA. Here we report the development of zinc finger DdCBEs (ZF-DdCBEs) and the improvement of their editing performance through engineering their architectures, defining improved ZF scaffolds, and installing DddA activity-enhancing mutations. We engineer variants with improved DNA specificity by integrating four strategies to reduce off-target editing. We use optimized ZF-DdCBEs to install or correct disease-associated mutations in mitochondria and in the nucleus. Leveraging their small size, we use a single AAV9 to deliver into heart, liver, and skeletal muscle in post-natal mice ZF-DdCBEs that efficiently install disease-associated mutations. While off-target editing of ZF-DdCBEs is likely too high for therapeutic applications, these findings demonstrate a compact, all-protein base editing research tool for precise editing of organelle or nuclear DNA without double-strand DNA breaks.
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Affiliation(s)
- Julian C W Willis
- 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
| | | | - Lily Widdup
- 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
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - 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.
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13
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Zhou J, Liu Y, Wei Y, Zheng S, Gou S, Chen T, Yang Y, Lan T, Chen M, Liao Y, Zhang Q, Tang C, Liu Y, Wu Y, Peng X, Gao M, Wang J, Zhang K, Lai L, Zou Q. Eliminating predictable DNA off-target effects of cytosine base editor by using dual guiders including sgRNA and TALE. Mol Ther 2022; 30:2443-2451. [PMID: 35443934 PMCID: PMC9263286 DOI: 10.1016/j.ymthe.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/07/2022] [Accepted: 04/16/2022] [Indexed: 11/30/2022] Open
Abstract
Predictable DNA off-target effect is one of the major safety concerns for the application of cytosine base editors (CBEs). To eliminate Cas9-dependent DNA off-target effects, we designed a novel effective CBE system with dual guiders by combining CRISPR with transcription activator-like effector (TALE). In this system, Cas9 nickase (nCas9) and cytosine deaminase are guided to the same target site to conduct base editing by single-guide RNA (sgRNA) and TALE, respectively. However, if nCas9 is guided to a wrong site by sgRNA, it will not generate base editing due to the absence of deaminase. Similarly, when deaminase is guided to a wrong site by TALE, base editing will not occur due to the absence of single-stranded DNA. In this way, Cas9- and TALE-dependent DNA off-target effects could be completely eliminated. Furthermore, by fusing TALE with YE1, a cytidine deaminase with minimal Cas9-independent off-target effect, we established a novel CBE that could induce efficient C-to-T conversion without detectable Cas9- or TALE-dependent DNA off-target mutations.
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Affiliation(s)
- Jizeng Zhou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China; School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Yang Liu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yuhui Wei
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shuwen Zheng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Shixue Gou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yang Yang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Ting Lan
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yuan Liao
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Quanjun Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China
| | - Chengcheng Tang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yu Liu
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yunqin Wu
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Xiaohua Peng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Minghui Gao
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Junwei Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kun Zhang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China; School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China.
| | - Liangxue Lai
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China; CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China.
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14
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Jie-Liu, Xu JZ, Rao ZM, Zhang WG. Industrial production of L-lysine in Corynebacterium glutamicum: progress and prospects. Microbiol Res 2022; 262:127101. [DOI: 10.1016/j.micres.2022.127101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/11/2022] [Accepted: 06/22/2022] [Indexed: 11/24/2022]
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15
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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%.
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16
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Haroon M, Wang X, Afzal R, Zafar MM, Idrees F, Batool M, Khan AS, Imran M. Novel Plant Breeding Techniques Shake Hands with Cereals to Increase Production. PLANTS (BASEL, SWITZERLAND) 2022; 11:1052. [PMID: 35448780 PMCID: PMC9025237 DOI: 10.3390/plants11081052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 06/01/2023]
Abstract
Cereals are the main source of human food on our planet. The ever-increasing food demand, continuously changing environment, and diseases of cereal crops have made adequate production a challenging task for feeding the ever-increasing population. Plant breeders are striving their hardest to increase production by manipulating conventional breeding methods based on the biology of plants, either self-pollinating or cross-pollinating. However, traditional approaches take a decade, space, and inputs in order to make crosses and release improved varieties. Recent advancements in genome editing tools (GETs) have increased the possibility of precise and rapid genome editing. New GETs such as CRISPR/Cas9, CRISPR/Cpf1, prime editing, base editing, dCas9 epigenetic modification, and several other transgene-free genome editing approaches are available to fill the lacuna of selection cycles and limited genetic diversity. Over the last few years, these technologies have led to revolutionary developments and researchers have quickly attained remarkable achievements. However, GETs are associated with various bottlenecks that prevent the scaling development of new varieties that can be dealt with by integrating the GETs with the improved conventional breeding methods such as speed breeding, which would take plant breeding to the next level. In this review, we have summarized all these traditional, molecular, and integrated approaches to speed up the breeding procedure of cereals.
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Affiliation(s)
- Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an 716000, China
| | - Rabail Afzal
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Chinese Academy of Agricultural Science, Anyang 455000, China
| | - Fahad Idrees
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Maria Batool
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Abdul Saboor Khan
- Institute of Plant Sciences, University of Cologne, 50667 Cologne, Germany
| | - Muhammad Imran
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou 510642, China
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17
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Elimination of Cas9-dependent off-targeting of adenine base editor by using TALE to separately guide deaminase to target sites. Cell Discov 2022; 8:28. [PMID: 35322006 PMCID: PMC8942999 DOI: 10.1038/s41421-022-00384-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/06/2022] [Indexed: 12/02/2022] Open
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18
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Alquézar B, Bennici S, Carmona L, Gentile A, Peña L. Generation of Transfer-DNA-Free Base-Edited Citrus Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:835282. [PMID: 35371165 PMCID: PMC8965368 DOI: 10.3389/fpls.2022.835282] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
To recover transgenic citrus plants in the most efficient manner, the use of selection marker genes is essential. In this work, it was shown that the mutated forms of the acetolactate synthase (ALS) gene in combination with the herbicide selection agent imazapyr (IMZ) added to the selection medium may be used to achieve this goal. This approach enables the development of cisgenic regenerants, namely, plants without the incorporation of those bacterial genes currently employed for transgenic selection, and additionally it allows the generation of edited, non-transgenic plants with altered endogenous ALS genes leading to IMZ resistance. In this work, the citrus mutants, in which ALS has been converted into IMZ-resistant forms using a base editor system, were recovered after cocultivation of the explants with Agrobacterium tumefaciens carrying a cytidine deaminase fused to nSpCas9 in the T-DNA and selecting regenerants in the culture medium supplemented with IMZ. Analysis of transgene-free plants indicated that the transient expression of the T-DNA genes was sufficient to induce ALS mutations and thus generate IMZ-resistant shoots at 11.7% frequency. To our knowledge, this is the first report of T-DNA-free edited citrus plants. Although further optimization is required to increase edition efficiency, this methodology will allow generating new citrus varieties with improved organoleptic/agronomic features without the need to use foreign genes.
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Affiliation(s)
- Berta Alquézar
- Laboratório de Biotecnologia Vegetal, Pesquisa, and Desenvolvimento, Fundo de Defesa da Citricultura (Fundecitrus), Araraquara, Brazil
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Stefania Bennici
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Lourdes Carmona
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
| | - Alessandra Gentile
- Department of Agriculture, Food, and Environment, University of Catania, Catania, Italy
| | - Leandro Peña
- Laboratório de Biotecnologia Vegetal, Pesquisa, and Desenvolvimento, Fundo de Defesa da Citricultura (Fundecitrus), Araraquara, Brazil
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
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19
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Abstract
DNA synthesis technology has progressed to the point that it is now practical to synthesize entire genomes. Quite a variety of methods have been developed, first to synthesize single genes but ultimately to massively edit or write from scratch entire genomes. Synthetic genomes can essentially be clones of native sequences, but this approach does not teach us much new biology. The ability to endow genomes with novel properties offers special promise for addressing questions not easily approachable with conventional gene-at-a-time methods. These include questions about evolution and about how genomes are fundamentally wired informationally, metabolically, and genetically. The techniques and technologies relating to how to design, build, and deliver big DNA at the genome scale are reviewed here. A fuller understanding of these principles may someday lead to the ability to truly design genomes from scratch.
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Affiliation(s)
- Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Joel S Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , , .,Department of Biomedical Engineering, New York University Tandon School of Engineering, New York, NY 11201, USA
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20
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Wang Y, Liu Y, Zheng P, Sun J, Wang M. Microbial Base Editing: A Powerful Emerging Technology for Microbial Genome Engineering. Trends Biotechnol 2020; 39:165-180. [PMID: 32680590 DOI: 10.1016/j.tibtech.2020.06.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 02/08/2023]
Abstract
Genome engineering is crucial for answering fundamental questions about, and exploring practical applications of, microorganisms. Various microbial genome-engineering tools, including CRISPR/Cas-enhanced homologous recombination (HR), have been developed, with ever-improving simplicity, efficiency, and applicability. Recently, a powerful emerging technology based on CRISPR/Cas-nucleobase deaminase fusions, known as base editing, opened new avenues for microbial genome engineering. Base editing enables nucleotide transition without inducing lethal double-stranded (ds)DNA cleavage, adding foreign donor DNA, or depending on inefficient HR. Here, we review ongoing efforts to develop and apply base editing to engineer industrially and clinically relevant microorganisms. We also summarize bioinformatics tools that would greatly facilitate guide (g)RNA design and sequencing data analysis and discuss the future challenges and prospects associated with this technology.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Ye Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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21
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Csörgő B, Nyerges A, Pál C. Targeted mutagenesis of multiple chromosomal regions in microbes. Curr Opin Microbiol 2020; 57:22-30. [PMID: 32599531 PMCID: PMC7613694 DOI: 10.1016/j.mib.2020.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/20/2022]
Abstract
Directed evolution allows the effective engineering of proteins, biosynthetic pathways, and cellular functions. Traditional plasmid-based methods generally subject one or occasionally multiple genes-of-interest to mutagenesis, require time-consuming manual interventions, and the genes that are subjected to mutagenesis are outside of their native genomic context. Other methods mutagenize the whole genome unselectively which may distort the outcome. Recent recombineering- and CRISPR-based technologies radically change this field by allowing exceedingly high mutation rates at multiple, predefined loci in their native genomic context. In this review, we focus on recent technologies that potentially allow accelerated tunable mutagenesis at multiple genomic loci in the native genomic context of these target sequences. These technologies will be compared by four main criteria, including the scale of mutagenesis, portability to multiple microbial species, off-target mutagenesis, and cost-effectiveness. Finally, we discuss how these technical advances open new avenues in basic research and biotechnology.
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Affiliation(s)
- Bálint Csörgő
- Department of Microbiology and Immunology, University of California, San Francisco, 94143, San Francisco, CA, USA; Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Akos Nyerges
- Synthetic and Systems Biology Unit, Biological Research Centre, 6726, Szeged, Hungary; Department of Genetics, Harvard Medical School, 02115, Boston, MA, USA
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Biological Research Centre, 6726, Szeged, Hungary.
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22
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Mok BY, de Moraes MH, Zeng J, Bosch DE, Kotrys AV, Raguram A, Hsu F, Radey MC, Peterson SB, Mootha VK, Mougous JD, Liu DR. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 2020; 583:631-637. [PMID: 32641830 PMCID: PMC7381381 DOI: 10.1038/s41586-020-2477-4] [Citation(s) in RCA: 390] [Impact Index Per Article: 97.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 05/26/2020] [Indexed: 12/21/2022]
Abstract
Bacterial toxins represent a vast reservoir of biochemical diversity that can be repurposed for biomedical applications. Such proteins include a group of predicted interbacterial toxins of the deaminase superfamily, members of which have found application in gene-editing techniques1,2. Because previously described cytidine deaminases operate on single-stranded nucleic acids3, their use in base editing requires the unwinding of double-stranded DNA (dsDNA)-for example by a CRISPR-Cas9 system. Base editing within mitochondrial DNA (mtDNA), however, has thus far been hindered by challenges associated with the delivery of guide RNA into the mitochondria4. As a consequence, manipulation of mtDNA to date has been limited to the targeted destruction of the mitochondrial genome by designer nucleases9,10.Here we describe an interbacterial toxin, which we name DddA, that catalyses the deamination of cytidines within dsDNA. We engineered split-DddA halves that are non-toxic and inactive until brought together on target DNA by adjacently bound programmable DNA-binding proteins. Fusions of the split-DddA halves, transcription activator-like effector array proteins, and a uracil glycosylase inhibitor resulted in RNA-free DddA-derived cytosine base editors (DdCBEs) that catalyse C•G-to-T•A conversions in human mtDNA with high target specificity and product purity. We used DdCBEs to model a disease-associated mtDNA mutation in human cells, resulting in changes in respiration rates and oxidative phosphorylation. CRISPR-free DdCBEs enable the precise manipulation of mtDNA, rather than the elimination of mtDNA copies that results from its cleavage by targeted nucleases, with broad implications for the study and potential treatment of mitochondrial disorders.
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Affiliation(s)
- Beverly Y Mok
- 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
| | - Marcos H de Moraes
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jun Zeng
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Dustin E Bosch
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Anna V Kotrys
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - 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
| | - FoSheng Hsu
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Matthew C Radey
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA.
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 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.
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23
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Luo Y, Ge M, Wang B, Sun C, Wang J, Dong Y, Xi JJ. CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1. Microb Cell Fact 2020; 19:93. [PMID: 32334589 PMCID: PMC7183636 DOI: 10.1186/s12934-020-01345-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022] Open
Abstract
Background CRISPR/Cas9 systems have been repurposed as canonical genome editing tools in a variety of species, but no application for the model strain Rhodobacter sphaeroides 2.4.1 was unveiled. Results Here we showed two kinds of programmable base editing systems, cytosine base editors (CBEs) and adenine base editors (ABEs), generated by fusing endonuclease Cas9 variant to cytosine deaminase PmCDA1 or heterodimer adenine deaminase TadA–TadA*, respectively. Using CBEs, we were able to obtain C-to-T mutation of single and double targets following the first induction step, with the efficiency of up to 97% and 43%; while the second induction step was needed in the case of triple target, with the screening rate of 47%. Using ABEs, we were only able to gain A-to-G mutation of single target after the second induction step, with the screening rate of 30%. Additionally, we performed a knockout analysis to identify the genes responsible for coenzyme Q10 biosynthesis and found that ubiF, ubiA, ubiG, and ubiX to be the most crucial ones. Conclusions Together, CBEs and ABEs serve as alternative methods for genetic manipulation in Rhodobacter sphaeroides and will shed light on the fundamental research of other bacteria that are hard to be directly edited by Cas9-sgRNA.
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Affiliation(s)
- Yufeng Luo
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Mei Ge
- Shanghai Laiyi Center for Biopharmaceutical R&D, 800 Dongchuan Road, Shanghai, 200240, China
| | - Bolun Wang
- Department of Biomedical Engineering, State Key Laboratory of Natural and Biomimetic Drugs, College of Engineering, Peking University, Beijing, 100871, China
| | - Changhong Sun
- Beijing Viewsolid Biotech Co. Ltd, Beijing, 100071, China
| | - Junyi Wang
- Department of Biomedical Engineering, State Key Laboratory of Natural and Biomimetic Drugs, College of Engineering, Peking University, Beijing, 100871, China
| | - Yuyang Dong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, GA, 30332, USA
| | - Jianzhong Jeff Xi
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China. .,Department of Biomedical Engineering, State Key Laboratory of Natural and Biomimetic Drugs, College of Engineering, Peking University, Beijing, 100871, China.
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24
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Zhang Y, Zhang H, Wang Z, Wu Z, Wang Y, Tang N, Xu X, Zhao S, Chen W, Ji Q. Programmable adenine deamination in bacteria using a Cas9-adenine-deaminase fusion. Chem Sci 2020; 11:1657-1664. [PMID: 32206285 PMCID: PMC7069399 DOI: 10.1039/c9sc03784e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/06/2020] [Indexed: 12/26/2022] Open
Abstract
Precise genetic manipulation is vital to studying bacterial physiology, but is difficult to achieve in some bacterial species due to the weak intrinsic homologous recombination (HR) capacity and lack of a compatible exogenous HR system. Here we report the establishment of a rapid and efficient method for directly converting adenine to guanine in bacterial genomes using the fusion of an adenine deaminase and a Cas9 nickase. The method achieves the conversion of adenine to guanine via an enzymatic deamination reaction and a subsequent DNA replication process rather than HR, which is utilized in conventional bacterial genetic manipulation methods, thereby substantially simplifying the genome editing process. A systematic screening targeting the possibly editable adenine sites of cntBC, the importer of the staphylopine/metal complex in Staphylococcus aureus, pinpoints key residues for metal importation, demonstrating that application of the system would greatly facilitate the genomic engineering of bacteria.
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Affiliation(s)
- Ya Zhang
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China . ;
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Hongyuan Zhang
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China . ;
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Zhipeng Wang
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China . ;
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Zhaowei Wu
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China . ;
| | - Yu Wang
- College of Life Science and Engineering , Jiangxi Agricultural University , Nanchang 330045 , China
| | - Na Tang
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China . ;
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Xuexia Xu
- iHuman Institute , ShanghaiTech University , Shanghai 201210 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Suwen Zhao
- iHuman Institute , ShanghaiTech University , Shanghai 201210 , China
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Weizhong Chen
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China . ;
| | - Quanjiang Ji
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China . ;
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25
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Lee HK, Smith HE, Liu C, Willi M, Hennighausen L. Cytosine base editor 4 but not adenine base editor generates off-target mutations in mouse embryos. Commun Biol 2020; 3:19. [PMID: 31925293 PMCID: PMC6952419 DOI: 10.1038/s42003-019-0745-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/16/2019] [Indexed: 11/09/2022] Open
Abstract
Deaminase base editing has emerged as a tool to install or correct point mutations in the genomes of living cells in a wide range of organisms. However, the genome-wide off-target effects introduced by base editors in the mammalian genome have been examined in only one study. Here, we have investigated the fidelity of cytosine base editor 4 (BE4) and adenine base editors (ABE) in mouse embryos using unbiased whole-genome sequencing of a family-based trio cohort. The same sgRNA was used for BE4 and ABE. We demonstrate that BE4-edited mice carry an excess of single-nucleotide variants and deletions compared to ABE-edited mice and controls. Therefore, an optimization of cytosine base editors is required to improve its fidelity. While the remarkable fidelity of ABE has implications for a wide range of applications, the occurrence of rare aberrant C-to-T conversions at specific target sites needs to be addressed.
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Affiliation(s)
- Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, 20892, USA.
| | - Harold E Smith
- Genomics Core, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Michaela Willi
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, 20892, USA.
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, 20892, USA.
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26
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Liu LD, Huang M, Dai P, Liu T, Fan S, Cheng X, Zhao Y, Yeap LS, Meng FL. Intrinsic Nucleotide Preference of Diversifying Base Editors Guides Antibody Ex Vivo Affinity Maturation. Cell Rep 2019; 25:884-892.e3. [PMID: 30355495 DOI: 10.1016/j.celrep.2018.09.090] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/13/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
Base editors (BEs) are emerging tools used for precision correction or diversifying mutation. It provides a potential way to recreate somatic hypermutations (SHM) for generating high-affinity antibody, which is usually screened from antigen-challenged animal models or synthetic combinatorial libraries. By comparing somatic mutations in the same genomic context, we screened engineered deaminases and CRISPR-deaminase coupling approaches and updated diversifying base editors (DBEs) to generate SHM. The deaminase used in DBEs retains its intrinsic nucleotide preference and mutates cytidines at its preferred motifs. DBE with AID targets the same hotspots as physiological AID does in vivo, while DBE with other deaminases generates distinct mutation profiles from the same DNA substrate. Downstream DNA repair pathways further diversified the sequence, while Cas9-nickase restricted mutation spreading. Finally, application of DBE in an antibody display system achieved antibody affinity maturation ex vivo. Our findings provide insight of DBE working mechanism and an alternative antibody engineering approach.
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Affiliation(s)
- Liu Daisy Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Min Huang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Tingting Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shuangshuang Fan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Xueqian Cheng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
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27
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Molla KA, Yang Y. CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications. Trends Biotechnol 2019; 37:1121-1142. [PMID: 30995964 DOI: 10.1016/j.tibtech.2019.03.008] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Kutubuddin A Molla
- Department of Plant Pathology and Environmental Microbiology, and Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology, and Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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28
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29
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Andreazza S, Samstag CL, Sanchez-Martinez A, Fernandez-Vizarra E, Gomez-Duran A, Lee JJ, Tufi R, Hipp MJ, Schmidt EK, Nicholls TJ, Gammage PA, Chinnery PF, Minczuk M, Pallanck LJ, Kennedy SR, Whitworth AJ. Mitochondrially-targeted APOBEC1 is a potent mtDNA mutator affecting mitochondrial function and organismal fitness in Drosophila. Nat Commun 2019; 10:3280. [PMID: 31337756 PMCID: PMC6650417 DOI: 10.1038/s41467-019-10857-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 06/06/2019] [Indexed: 12/22/2022] Open
Abstract
Somatic mutations in the mitochondrial genome (mtDNA) have been linked to multiple disease conditions and to ageing itself. In Drosophila, knock-in of a proofreading deficient mtDNA polymerase (POLG) generates high levels of somatic point mutations and also small indels, but surprisingly limited impact on organismal longevity or fitness. Here we describe a new mtDNA mutator model based on a mitochondrially-targeted cytidine deaminase, APOBEC1. mito-APOBEC1 acts as a potent mutagen which exclusively induces C:G>T:A transitions with no indels or mtDNA depletion. In these flies, the presence of multiple non-synonymous substitutions, even at modest heteroplasmy, disrupts mitochondrial function and dramatically impacts organismal fitness. A detailed analysis of the mutation profile in the POLG and mito-APOBEC1 models reveals that mutation type (quality) rather than quantity is a critical factor in impacting organismal fitness. The specificity for transition mutations and the severe phenotypes make mito-APOBEC1 an excellent mtDNA mutator model for ageing research.
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Affiliation(s)
- Simonetta Andreazza
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Colby L Samstag
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Alvaro Sanchez-Martinez
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Erika Fernandez-Vizarra
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Aurora Gomez-Duran
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Juliette J Lee
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Roberta Tufi
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Michael J Hipp
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | | | - Thomas J Nicholls
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Payam A Gammage
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Leo J Pallanck
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Scott R Kennedy
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander J Whitworth
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.
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30
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Tang J, Lee T, Sun T. Single-nucleotide editing: From principle, optimization to application. Hum Mutat 2019; 40:2171-2183. [PMID: 31131955 DOI: 10.1002/humu.23819] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/30/2019] [Accepted: 05/23/2019] [Indexed: 12/26/2022]
Abstract
Cytosine base editors (CBEs) and adenine base editors (ABEs), which are generally composed of an engineered deaminase and a catalytically impaired CRISPR-Cas9 variant, are new favorite tools for single base substitution in cells and organisms. In this review, we summarize the principle of base-editing systems and elaborate on the evolution of different platforms of CBEs and ABEs, including their deaminase, Cas9 variants, and editing outcomes. Moreover, we highlight their applications in mouse and human cells and discuss the challenges and prospects of base editors. The ABE- and CBE systems have been used in gene silencing, pathogenic gene correction, and functional genetic screening. Single base editing is becoming a new promising genetic tool in biomedical research and gene therapy.
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Affiliation(s)
- Jinling Tang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Trevor Lee
- Department of Cell and Developmental Biology, Weill Medical College, Cornell University, New York, New York
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
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31
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WareJoncas Z, Campbell JM, Martínez-Gálvez G, Gendron WAC, Barry MA, Harris PC, Sussman CR, Ekker SC. Precision gene editing technology and applications in nephrology. Nat Rev Nephrol 2018; 14:663-677. [PMID: 30089813 PMCID: PMC6591726 DOI: 10.1038/s41581-018-0047-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The expanding field of precision gene editing is empowering researchers to directly modify DNA. Gene editing is made possible using synonymous technologies: a DNA-binding platform to molecularly locate user-selected genomic sequences and an associated biochemical activity that serves as a functional editor. The advent of accessible DNA-targeting molecular systems, such as zinc-finger nucleases, transcription activator-like effectors (TALEs) and CRISPR-Cas9 gene editing systems, has unlocked the ability to target nearly any DNA sequence with nucleotide-level precision. Progress has also been made in harnessing endogenous DNA repair machineries, such as non-homologous end joining, homology-directed repair and microhomology-mediated end joining, to functionally manipulate genetic sequences. As understanding of how DNA damage results in deletions, insertions and modifications increases, the genome becomes more predictably mutable. DNA-binding platforms such as TALEs and CRISPR can also be used to make locus-specific epigenetic changes and to transcriptionally enhance or suppress genes. Although many challenges remain, the application of precision gene editing technology in the field of nephrology has enabled the generation of new animal models of disease as well as advances in the development of novel therapeutic approaches such as gene therapy and xenotransplantation.
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Affiliation(s)
- Zachary WareJoncas
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jarryd M Campbell
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - William A C Gendron
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Michael A Barry
- Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA
| | - Peter C Harris
- Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA
| | - Caroline R Sussman
- Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA.
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32
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Sakuma T, Yamamoto T. Acceleration of cancer science with genome editing and related technologies. Cancer Sci 2018; 109:3679-3685. [PMID: 30315615 PMCID: PMC6272086 DOI: 10.1111/cas.13832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/30/2018] [Accepted: 10/09/2018] [Indexed: 12/26/2022] Open
Abstract
Genome editing includes various edits of the genome, such as short insertions and deletions, substitutions, and chromosomal rearrangements including inversions, duplications, and translocations. These variations are based on single or multiple DNA double-strand break (DSB)-triggered in cellulo repair machineries. In addition to these "conventional" genome editing strategies, tools enabling customized, site-specific recognition of particular nucleic acid sequences have been coming into wider use; for example, single base editing without DSB introduction, epigenome editing with recruitment of epigenetic modifiers, transcriptome engineering using RNA editing systems, and in vitro detection of specific DNA and RNA sequences. In this review, we provide a quick overview of the current state of genome editing and related technologies that multilaterally contribute to cancer science.
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Affiliation(s)
- Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan
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33
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Tan ZY, Huang T, Ngeow J. 65 YEARS OF THE DOUBLE HELIX: The advancements of gene editing and potential application to hereditary cancer. Endocr Relat Cancer 2018; 25:T141-T158. [PMID: 29980644 DOI: 10.1530/erc-18-0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/10/2018] [Indexed: 12/26/2022]
Abstract
Hereditary cancer predisposition syndromes are associated with germline mutations that lead to increased vulnerability for an individual to develop cancers. Such germline mutations in tumour suppressor genes, oncogenes and genes encoding for proteins essential in DNA repair pathways and cell cycle control can cause overall chromosomal instability in the genome and increase risk in developing cancers. Gene correction of these germline mutations to restore normal protein functions is anticipated as a new therapeutic option. This can be achieved through disruption of gain-of-function pathogenic mutation, restoration of loss-of-function mutation, addition of a transgene essential for cell function and single nucleotide changes. Genome editing tools are applicable to precise gene correction. Development of genome editing tools comes in two waves. The first wave focuses on improving targeting specificity and editing efficiency of nucleases, and the second wave of gene editing draws on innovative engineering of fusion proteins combining deactivated nucleases and other enzymes that are able to create limitless functional molecular tools. This gene editing advancement is going to impact medicine, particularly in hereditary cancers. In this review, we discuss the application of gene editing as an early intervention and possible treatment for hereditary cancers, by highlighting a selection of highly penetrant cancer syndromes as examples of how this may be achieved in clinical practice.
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Affiliation(s)
- Zi Ying Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Institute of Molecular and Cell Biology, Singapore
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Institute of Molecular and Cell Biology, Singapore
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School Singapore, Singapore
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34
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Jiang W, Feng S, Huang S, Yu W, Li G, Yang G, Liu Y, Zhang Y, Zhang L, Hou Y, Chen J, Chen J, Huang X. BE-PLUS: a new base editing tool with broadened editing window and enhanced fidelity. Cell Res 2018; 28:855-861. [PMID: 29875396 DOI: 10.1038/s41422-018-0052-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 05/07/2018] [Accepted: 05/16/2018] [Indexed: 12/26/2022] Open
Abstract
Base editor (BE), containing a cytidine deaminase and catalytically defective Cas9, has been widely used to perform base editing. However, the narrow editing window of BE limits its utility. Here, we developed a new editing technology named as base editor for programming larger C to U (T) scope (BE-PLUS) by fusing 10 copies of GCN4 peptide to nCas9(D10A) for recruiting scFv-APOBEC-UGI-GB1 to the target sites. The new system achieves base editing with a broadened window, resulting in an increased genome-targeting scope. Interestingly, the new system yielded much fewer unwanted indels and non-C-to-T conversions. We also demonstrated its potential use in gene disruption across the whole genome through induction of stop codons (iSTOP). Taken together, the BE-PLUS system offers a new editing tool with increased editing window and enhanced fidelity.
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Affiliation(s)
- Wen Jiang
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Songjie Feng
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201210, Shanghai, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Wenxia Yu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Guang Yang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Yajing Liu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201210, Shanghai, China
| | - Yu Zhang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Lei Zhang
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201210, Shanghai, China
| | - Yu Hou
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Jia Chen
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Jieping Chen
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
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35
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Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance. Proc Natl Acad Sci U S A 2018; 115:E5726-E5735. [PMID: 29871954 PMCID: PMC6016788 DOI: 10.1073/pnas.1801646115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology.
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36
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Abstract
PURPOSE OF REVIEW This review describes the recent progress in nuclease-based therapeutic applications for inherited heart diseases in vitro, highlights the development of the most recent genome editing technologies and discusses the associated challenges for clinical translation. RECENT FINDINGS Inherited cardiovascular disorders are passed from generation to generation. Over the past decade, considerable progress has been made in understanding the genetic basis of inherited heart diseases. The timely emergence of genome editing technologies using engineered programmable nucleases has revolutionized the basic research of inherited cardiovascular diseases and holds great promise for the development of targeted therapies. The genome editing toolbox is rapidly expanding, and new tools have been recently added that significantly expand the capabilities of engineered nucleases. Newer classes of versatile engineered nucleases, such as the "base editors," have been recently developed, offering the potential for efficient and precise therapeutic manipulation of the human genome.
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37
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Zheng K, Wang Y, Li N, Jiang FF, Wu CX, Liu F, Chen HC, Liu ZF. Highly efficient base editing in bacteria using a Cas9-cytidine deaminase fusion. Commun Biol 2018; 1:32. [PMID: 30271918 PMCID: PMC6123677 DOI: 10.1038/s42003-018-0035-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/21/2018] [Indexed: 12/02/2022] Open
Abstract
The ability to precisely edit individual bases of bacterial genomes would accelerate the investigation of the function of genes. Here we utilized a nickase Cas9-cytidine deaminase fusion protein to direct the conversion of cytosine to thymine within prokaryotic cells, resulting in high mutagenesis frequencies in Escherichia coli and Brucella melitensis. Our study suggests that CRISPR/Cas9-guided base-editing is a viable alternative approach to generate mutant bacterial strains. Ke Zheng and colleagues repurposed a nickase Cas9-cytidine deaminase fusion protein to effectively direct the conversion of cytosine to thymine on bacterial genome. This study suggests that CRISPR/Cas9-guided base-editing can be used to generate viable mutant bacterial strains.
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Affiliation(s)
- Ke Zheng
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yang Wang
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Na Li
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang-Fang Jiang
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang-Xian Wu
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Liu
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huan-Chun Chen
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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38
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Tang W, Liu DR. Rewritable multi-event analog recording in bacterial and mammalian cells. Science 2018; 360:eaap8992. [PMID: 29449507 PMCID: PMC5898985 DOI: 10.1126/science.aap8992] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/22/2017] [Accepted: 02/08/2018] [Indexed: 12/26/2022]
Abstract
We present two CRISPR-mediated analog multi-event recording apparatus (CAMERA) systems that use base editors and Cas9 nucleases to record cellular events in bacteria and mammalian cells. The devices record signal amplitude or duration as changes in the ratio of mutually exclusive DNA sequences (CAMERA 1) or as single-base modifications (CAMERA 2). We achieved recording of multiple stimuli in bacteria or mammalian cells, including exposure to antibiotics, nutrients, viruses, light, and changes in Wnt signaling. When recording to multicopy plasmids, reliable readout requires as few as 10 to 100 cells. The order of stimuli can be recorded through an overlapping guide RNA design, and memories can be erased and re-recorded over multiple cycles. CAMERA systems serve as "cell data recorders" that write a history of endogenous or exogenous signaling events into permanent DNA sequence modifications in living cells.
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Affiliation(s)
- Weixin Tang
- Merkin Institute for Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, and Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - David R Liu
- Merkin Institute for Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, and Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
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39
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Zhang C, Quan R, Wang J. Development and application of CRISPR/Cas9 technologies in genomic editing. Hum Mol Genet 2018; 27:R79-R88. [DOI: 10.1093/hmg/ddy120] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Cui Zhang
- Institute of Cell and Development Biology, College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Renfu Quan
- Institute of Orthopedics, Xiaoshan Traditional Chinese Medical Hospital, Hangzhou, Zhejiang, China
| | - Jinfu Wang
- Institute of Cell and Development Biology, College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang, P.R. China
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40
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Liang P, Zhang X, Chen Y, Huang J. Developmental history and application of CRISPR in human disease. J Gene Med 2018. [PMID: 28623876 DOI: 10.1002/jgm.2963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-editing tools are programmable artificial nucleases, mainly including zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeat (CRISPR). By recognizing and cleaving specific DNA sequences, genome-editing tools make it possible to generate site-specific DNA double-strand breaks (DSBs) in the genome. DSBs will then be repaired by either error-prone nonhomologous end joining or high-fidelity homologous recombination mechanisms. Through these two different mechanisms, endogenous genes can be knocked out or precisely repaired/modified. Rapid developments in genome-editing tools, especially CRISPR, have revolutionized human disease models generation, for example, various zebrafish, mouse, rat, pig, monkey and human cell lines have been constructed. Here, we review the developmental history of CRISPR and its application in studies of human diseases. In addition, we also briefly discussed the therapeutic application of CRISPR in the near future.
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Affiliation(s)
- Puping Liang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiya Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuxi Chen
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Junjiu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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41
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Banno S, Nishida K, Arazoe T, Mitsunobu H, Kondo A. Deaminase-mediated multiplex genome editing in Escherichia coli. Nat Microbiol 2018; 3:423-429. [PMID: 29403014 DOI: 10.1038/s41564-017-0102-6] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022]
Abstract
In eukaryotes, the CRISPR-Cas9 system has now been widely used as a revolutionary genome engineering tool1, 2. However, in prokaryotes, the use of nuclease-mediated genome editing tools has been limited to negative selection for the already modified cells because of its lethality3, 4. Here, we report on deaminase-mediated targeted nucleotide editing (Target-AID) 5 adopted in Escherichia coli. Cytidine deaminase PmCDA1 fused to the nuclease-deficient CRISPR-Cas9 system achieved specific point mutagenesis at the target sites in E. coli by introducing cytosine mutations without compromising cell growth. The cytosine-to-thymine substitutions were induced mainly within an approximately five-base window of target sequences on the protospacer adjacent motif-distal side, which can be shifted depending on the length of the single guide RNA sequence. Use of a uracil DNA glycosylase inhibitor 6 in combination with a degradation tag (LVA tag) 7 resulted in a robustly high mutation efficiency, which allowed simultaneous multiplex editing of six different genes. The major multi-copy transposase genes that consist of at least 41 loci were also simultaneously edited by using four target sequences. As this system does not rely on any additional or host-dependent factors, it may be readily applicable to a wide range of bacteria.
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Affiliation(s)
- Satomi Banno
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Hyogo, Japan
| | - Keiji Nishida
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Hyogo, Japan.
| | - Takayuki Arazoe
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Hyogo, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Hitoshi Mitsunobu
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Hyogo, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Hyogo, Japan.
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan.
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42
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Wang Y, Liu Y, Liu J, Guo Y, Fan L, Ni X, Zheng X, Wang M, Zheng P, Sun J, Ma Y. MACBETH: Multiplex automated Corynebacterium glutamicum base editing method. Metab Eng 2018; 47:200-210. [PMID: 29580925 DOI: 10.1016/j.ymben.2018.02.016] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/27/2018] [Accepted: 02/28/2018] [Indexed: 11/27/2022]
Abstract
CRISPR/Cas9 or Cpf1-introduced double strand break dramatically decreases bacterial cell survival rate, which hampers multiplex genome editing in bacteria. In addition, the requirement of a foreign DNA template for each target locus is labor demanding and may encounter more GMO related regulatory hurdle in industrial applications. Herein, we developed a multiplex automated Corynebacterium glutamicum base editing method (MACBETH) using CRISPR/Cas9 and activation-induced cytidine deaminase (AID), without foreign DNA templates, achieving single-, double-, and triple-locus editing with efficiencies up to 100%, 87.2% and 23.3%, respectively. In addition, MACBETH was applied to generate a combinatorial gene inactivation library for improving glutamate production, and pyk&ldhA double inactivation strain was found to improve glutamate production by 3-fold. Finally, MACBETH was automated with an integrated robotic system, which would enable us to generate thousands of rationally engineered strains per month for metabolic engineering of C. glutamicum. As a proof of concept demonstration, the automation platform was used to construct an arrayed genome-scale gene inactivation library of 94 transcription factors with 100% success rate. Therefore, MACBETH would be a powerful tool for multiplex and automated bacterial genome editing in future studies and industrial applications.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ye Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Liwen Fan
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiaomei Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; School of Life Science, University of Science and Technology of China, Hefei 230026, China.
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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43
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Chew WL. Immunity to CRISPR Cas9 and Cas12a therapeutics. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10. [PMID: 29083112 DOI: 10.1002/wsbm.1408] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 09/08/2017] [Accepted: 09/10/2017] [Indexed: 12/27/2022]
Abstract
Genome-editing therapeutics are poised to treat human diseases. As we enter clinical trials with the most promising CRISPR-Cas9 and CRISPR-Cas12a (Cpf1) modalities, the risks associated with administering these foreign biomolecules into human patients become increasingly salient. Preclinical discovery with CRISPR-Cas9 and CRISPR-Cas12a systems and foundational gene therapy studies indicate that the host immune system can mount undesired responses against the administered proteins and nucleic acids, the gene-edited cells, and the host itself. These host defenses include inflammation via activation of innate immunity, antibody induction in humoral immunity, and cell death by T-cell-mediated cytotoxicity. If left unchecked, these immunological reactions can curtail therapeutic benefits and potentially lead to mortality. Ways to assay and reduce the immunogenicity of Cas9 and Cas12a proteins are therefore critical for ensuring patient safety and treatment efficacy, and for bringing us closer to realizing the vision of permanent genetic cures. WIREs Syst Biol Med 2018, 10:e1408. doi: 10.1002/wsbm.1408 This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Translational, Genomic, and Systems Medicine > Translational Medicine Translational, Genomic, and Systems Medicine > Therapeutic Methods.
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Affiliation(s)
- Wei Leong Chew
- Synthetic Biology, Genome Institute of Singapore, Singapore, Singapore
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44
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Abstract
Recent exponential advances in genome sequencing and engineering technologies have enabled an unprecedented level of interrogation into the impact of DNA variation (genotype) on cellular function (phenotype). Furthermore, these advances have also prompted realistic discussion of writing and radically re-writing complex genomes. In this Perspective, we detail the motivation for large-scale engineering, discuss the progress made from such projects in bacteria and yeast and describe how various genome-engineering technologies will contribute to this effort. Finally, we describe the features of an ideal platform and provide a roadmap to facilitate the efficient writing of large genomes.
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Affiliation(s)
- Raj Chari
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts, 02115, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle, Boston, Massachusetts, 02115, USA
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45
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Recent advances in DNA-free editing and precise base editing in plants. Emerg Top Life Sci 2017; 1:161-168. [PMID: 33525763 DOI: 10.1042/etls20170021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/13/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022]
Abstract
Genome-editing technologies based on the CRISPR (clustered regularly interspaced short palindromic repeat) system have been widely used in plants to investigate gene function and improve crop traits. The recently developed DNA-free delivery methods and precise base-editing systems provide new opportunities for plant genome engineering. In this review, we describe the novel DNA-free genome-editing methods in plants. These methods reduce off-target effects and may alleviate regulatory concern about genetically modified plants. We also review applications of base-editing systems, which are highly effective in generating point mutations and are of great value for introducing agronomically valuable traits. Future perspectives for DNA-free editing and base editing are also discussed.
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46
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Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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47
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Hess GT, Tycko J, Yao D, Bassik MC. Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes. Mol Cell 2017; 68:26-43. [PMID: 28985508 PMCID: PMC5997582 DOI: 10.1016/j.molcel.2017.09.029] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022]
Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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Affiliation(s)
- Gaelen T Hess
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - David Yao
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA.
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48
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Beyond Native Cas9: Manipulating Genomic Information and Function. Trends Biotechnol 2017; 35:983-996. [DOI: 10.1016/j.tibtech.2017.06.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/22/2017] [Accepted: 06/08/2017] [Indexed: 02/07/2023]
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49
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Billon P, Bryant EE, Joseph SA, Nambiar TS, Hayward SB, Rothstein R, Ciccia A. CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons. Mol Cell 2017; 67:1068-1079.e4. [PMID: 28890334 PMCID: PMC5610906 DOI: 10.1016/j.molcel.2017.08.008] [Citation(s) in RCA: 243] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/20/2017] [Accepted: 08/14/2017] [Indexed: 12/21/2022]
Abstract
Standard CRISPR-mediated gene disruption strategies rely on Cas9-induced DNA double-strand breaks (DSBs). Here, we show that CRISPR-dependent base editing efficiently inactivates genes by precisely converting four codons (CAA, CAG, CGA, and TGG) into STOP codons without DSB formation. To facilitate gene inactivation by induction of STOP codons (iSTOP), we provide access to a database of over 3.4 million single guide RNAs (sgRNAs) for iSTOP (sgSTOPs) targeting 97%-99% of genes in eight eukaryotic species, and we describe a restriction fragment length polymorphism (RFLP) assay that allows the rapid detection of iSTOP-mediated editing in cell populations and clones. To simplify the selection of sgSTOPs, our resource includes annotations for off-target propensity, percentage of isoforms targeted, prediction of nonsense-mediated decay, and restriction enzymes for RFLP analysis. Additionally, our database includes sgSTOPs that could be employed to precisely model over 32,000 cancer-associated nonsense mutations. Altogether, this work provides a comprehensive resource for DSB-free gene disruption by iSTOP.
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MESH Headings
- Animals
- Arabidopsis/genetics
- Arabidopsis/metabolism
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Codon, Nonsense
- Codon, Terminator
- Computational Biology
- DNA Restriction Enzymes/genetics
- DNA Restriction Enzymes/metabolism
- Databases, Genetic
- Gene Editing/methods
- Gene Expression Regulation, Fungal
- Gene Expression Regulation, Neoplastic
- Gene Expression Regulation, Plant
- Gene Silencing
- HEK293 Cells
- Humans
- Mice
- Neoplasms/genetics
- Neoplasms/metabolism
- Polymorphism, Restriction Fragment Length
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Rats
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Transfection
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Affiliation(s)
- Pierre Billon
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Eric E Bryant
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Sarah A Joseph
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.
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50
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Pineda M, Moghadam F, Ebrahimkhani MR, Kiani S. Engineered CRISPR Systems for Next Generation Gene Therapies. ACS Synth Biol 2017; 6:1614-1626. [PMID: 28558198 DOI: 10.1021/acssynbio.7b00011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An ideal in vivo gene therapy platform provides safe, reprogrammable, and precise strategies which modulate cell and tissue gene regulatory networks with a high temporal and spatial resolution. Clustered regularly interspaced short palindromic repeats (CRISPR), a bacterial adoptive immune system, and its CRISPR-associated protein 9 (Cas9), have gained attention for the ability to target and modify DNA sequences on demand with unprecedented flexibility and precision. The precision and programmability of Cas9 is derived from its complexation with a guide-RNA (gRNA) that is complementary to a desired genomic sequence. CRISPR systems open-up widespread applications including genetic disease modeling, functional screens, and synthetic gene regulation. The plausibility of in vivo genetic engineering using CRISPR has garnered significant traction as a next generation in vivo therapeutic. However, there are hurdles that need to be addressed before CRISPR-based strategies are fully implemented. Some key issues center on the controllability of the CRISPR platform, including minimizing genomic-off target effects and maximizing in vivo gene editing efficiency, in vivo cellular delivery, and spatial-temporal regulation. The modifiable components of CRISPR systems: Cas9 protein, gRNA, delivery platform, and the form of CRISPR system delivered (DNA, RNA, or ribonucleoprotein) have recently been engineered independently to design a better genome engineering toolbox. This review focuses on evaluating CRISPR potential as a next generation in vivo gene therapy platform and discusses bioengineering advancements that can address challenges associated with clinical translation of this emerging technology.
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Affiliation(s)
- Michael Pineda
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Farzaneh Moghadam
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Mo R. Ebrahimkhani
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
- Center for Regenerative
Medicine, Mayo Clinic, Phoenix, Arizona 85054, United States
| | - Samira Kiani
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
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