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Irfan M, Majeed H, Iftikhar T, Ravi PK. A review on molecular scissoring with CRISPR/Cas9 genome editing technology. Toxicol Res (Camb) 2024; 13:tfae105. [PMID: 39006883 PMCID: PMC11240166 DOI: 10.1093/toxres/tfae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Genome editing is a technology to make specific changes in the DNA of a cell or an organism. It has significantly altered the landscape of life sciences, facilitating the establishment of exceedingly customized genetic modifications. Among various genome editing technologies, the CRISPR/Cas9 system, a specific endonuclease induces a double stranded DNA break and enabling modifications to the genome, has surfaced as a formidable and adaptable instrument. Its significance cannot be overstated, as it not only allows for the manipulation of genomes in model organisms but also holds great potential for revolutionary advances in medicine, particularly in treating genetic diseases. This review paper explores the remarkable journey of CRISPR/Cas9, its natural function, mechanisms, and transformative impact on genome editing and finally the use of artificial intelligence and other intelligent manufacturing tools used. The introduction provides the background on genome editing, emphasizing the emergence and significance of CRISPR/Cas9. Subsequent sections comprehensively elucidate its natural function, disease modeling, agriculture, and biotechnology, address therapeutic applications, and ongoing clinical trials while also discussing prospects and ethical implications. We summarized the key findings, indicating that CRISPR/Cas9 has empowered the creation of disease-specific animal models. This provides invaluable insights into pathogenic mechanisms and opens new avenues for drug discovery, reaffirming the transformative impact of CRISPR/Cas9 on genome editing. Finally we discussed the importance of continued research and collaboration for comprehensive utilization of the inherent capabilities of this molecular precision tool in shaping forthcoming advancements.
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Affiliation(s)
- Muskan Irfan
- Department of Biotechnology, University of Management and Technology (UMT), Lahore, Sialkot Campus, Sialkot 51310, Pakistan
| | - Hammad Majeed
- Department of Chemistry, University of Management and Technology (UMT), Lahore, Sialkot Campus, Sialkot 51310, Pakistan
| | - Tehreema Iftikhar
- Applied Botany Lab, Department of Botany, Government College University, 54000, Lahore, Pakistan
| | - Pritam Kumar Ravi
- Computer Applications Department, Ganesh Lal Agarwal College, Nilamber-Pitamber University, Jharkhand, 822101, India
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Alipanahi R, Safari L, Khanteymoori A. CRISPR genome editing using computational approaches: A survey. FRONTIERS IN BIOINFORMATICS 2023; 2:1001131. [PMID: 36710911 PMCID: PMC9875887 DOI: 10.3389/fbinf.2022.1001131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing has been widely used in various cell types and organisms. To make genome editing with Clustered regularly interspaced short palindromic repeats far more precise and practical, we must concentrate on the design of optimal gRNA and the selection of appropriate Cas enzymes. Numerous computational tools have been created in recent years to help researchers design the best gRNA for Clustered regularly interspaced short palindromic repeats researches. There are two approaches for designing an appropriate gRNA sequence (which targets our desired sites with high precision): experimental and predicting-based approaches. It is essential to reduce off-target sites when designing an optimal gRNA. Here we review both traditional and machine learning-based approaches for designing an appropriate gRNA sequence and predicting off-target sites. In this review, we summarize the key characteristics of all available tools (as far as possible) and compare them together. Machine learning-based tools and web servers are believed to become the most effective and reliable methods for predicting on-target and off-target activities of Clustered regularly interspaced short palindromic repeats in the future. However, these predictions are not so precise now and the performance of these algorithms -especially deep learning one's-depends on the amount of data used during training phase. So, as more features are discovered and incorporated into these models, predictions become more in line with experimental observations. We must concentrate on the creation of ideal gRNA and the choice of suitable Cas enzymes in order to make genome editing with Clustered regularly interspaced short palindromic repeats far more accurate and feasible.
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Affiliation(s)
| | - Leila Safari
- Department of Computer Engineering, University of Zanjan, Zanjan, Iran,*Correspondence: Leila Safari,
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Singh P, Ali SA. Impact of CRISPR-Cas9-Based Genome Engineering in Farm Animals. Vet Sci 2021; 8:122. [PMID: 34209174 PMCID: PMC8309983 DOI: 10.3390/vetsci8070122] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/26/2022] Open
Abstract
Humans are sorely over-dependent on livestock for their daily basic need of food in the form of meat, milk, and eggs. Therefore, genetic engineering and transgenesis provide the opportunity for more significant gains and production in a short span of time. One of the best strategies is the genetic alteration of livestock to enhance the efficiency of food production (e.g., meat and milk), animal health, and welfare (animal population and disease). Moreover, genome engineering in the bovine is majorly focused on subjects such as disease resistance (e.g., tuberculosis), eradicate allergens (e.g., beta-lactoglobulin knock-out), products generation (e.g., meat from male and milk from female), male or female birth specifically (animal sexing), the introduction of valuable traits (e.g., stress tolerance and disease resistance) and their wellbeing (e.g., hornlessness). This review addressed the impressive genome engineering method CRISPR, its fundamental principle for generating highly efficient target-specific guide RNA, and the accompanying web-based tools. However, we have covered the remarkable roadmap of the CRISPR method from its conception to its use in cattle. Additionally, we have updated the comprehensive information on CRISPR-based gene editing in cattle.
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Affiliation(s)
| | - Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal 132001, India;
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Xiang X, Zhao X, Pan X, Dong Z, Yu J, Li S, Liang X, Han P, Qu K, Jensen JB, Farup J, Wang F, Petersen TS, Bolund L, Teng H, Lin L, Luo Y. Efficient correction of Duchenne muscular dystrophy mutations by SpCas9 and dual gRNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:403-415. [PMID: 33868784 PMCID: PMC8039775 DOI: 10.1016/j.omtn.2021.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/10/2021] [Indexed: 12/17/2022]
Abstract
CRISPR gene therapy is one promising approach for treatment of Duchenne muscular dystrophy (DMD), which is caused by a large spectrum of mutations in the dystrophin gene. To broaden CRISPR gene editing strategies for DMD treatment, we report the efficient restoration of dystrophin expression in induced myotubes by SpCas9 and dual guide RNAs (gRNAs). We first sequenced 32 deletion junctions generated by this editing method and revealed that non-homologous blunt-end joining represents the major indel type. Based on this predictive repair outcome, efficient in-frame deletion of a part of DMD exon 51 was achieved in HEK293T cells with plasmids expressing SpCas9 and dual gRNAs. More importantly, we further corrected a frameshift mutation in human DMD (exon45del) fibroblasts with SpCas9-dual gRNA ribonucleoproteins. The edited DMD fibroblasts were transdifferentiated into myotubes by lentiviral-mediated overexpression of a human MYOD transcription factor. Restoration of DMD expression at both the mRNA and protein levels was confirmed in the induced myotubes. With further development, the combination of SpCas9-dual gRNA-corrected DMD patient fibroblasts and transdifferentiation may provide a valuable therapeutic strategy for DMD.
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Affiliation(s)
- Xi Xiang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Xiaoying Zhao
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Zhanying Dong
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Jiaying Yu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Siyuan Li
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xue Liang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Jonas Brorson Jensen
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Jean Farup
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Fei Wang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | | | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Huajing Teng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
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Wang J, Zhang X, Cheng L, Luo Y. An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools. RNA Biol 2020; 17:13-22. [PMID: 31533522 PMCID: PMC6948960 DOI: 10.1080/15476286.2019.1669406] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/06/2019] [Accepted: 09/14/2019] [Indexed: 12/18/2022] Open
Abstract
The CRISPR-Cas9 system has become the most promising and versatile tool for genetic manipulation applications. Albeit the technology has been broadly adopted by both academic and pharmaceutic societies, the activity (on-target) and specificity (off-target) of CRISPR-Cas9 are decisive factors for any application of the technology. Several in silico gRNA activity and specificity predicting models and web tools have been developed, making it much more convenient and precise for conducting CRISPR gene editing studies. In this review, we present an overview and comparative analysis of machine and deep learning (MDL)-based algorithms, which are believed to be the most effective and reliable methods for the prediction of CRISPR gRNA on- and off-target activities. As an increasing number of sequence features and characteristics are discovered and are incorporated into the MDL models, the prediction outcome is getting closer to experimental observations. We also introduced the basic principle of CRISPR activity and specificity and summarized the challenges they faced, aiming to facilitate the CRISPR communities to develop more accurate models for applying.
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Affiliation(s)
- Jun Wang
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Lixin Cheng
- Department of Critical Care Medicine, Shenzhen People’s Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Yonglun Luo
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biomedicine, Aarhus University, Denmark
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