1
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Coorey BA, Gold WA. Breaking Boundaries in the Brain-Advances in Editing Tools for Neurogenetic Disorders. Front Genome Ed 2021; 3:623519. [PMID: 34713252 PMCID: PMC8525368 DOI: 10.3389/fgeed.2021.623519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
Monogenic neurological disorders are devastating, affecting hundreds of millions of people globally and present a substantial burden to individuals, carers, and healthcare systems. These disorders are predominantly caused by inherited or de novo variants that result in impairments to nervous system development, neurodegeneration, or impaired neuronal function. No cure exists for these disorders with many being refractory to medication. However, since monogenic neurological disorders have a single causal factor, they are also excellent targets for innovative, therapies such as gene therapy. Despite this promise, gene transfer therapies are limited in that they are only suitable for neurogenetic disorders that fit within the technological reach of these therapies. The limitations include the size of the coding region of the gene, the regulatory control of expression (dosage sensitivity), the mode of expression (e.g., dominant negative) and access to target cells. Gene editing therapies are an alternative strategy to gene transfer therapy as they have the potential of overcoming some of these hurdles, enabling the retention of physiological expression of the gene and offers precision medicine-based therapies where individual variants can be repaired. This review focusses on the existing gene editing technologies for neurogenetic disorders and how these propose to overcome the challenges common to neurogenetic disorders with gene transfer therapies as well as their own challenges.
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Affiliation(s)
- Bronte A Coorey
- School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia.,Molecular Neurobiology Research Laboratory, Kid's Research, Children's Hospital at Westmead, Westmead, NSW, Australia.,Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Wendy A Gold
- School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia.,Molecular Neurobiology Research Laboratory, Kid's Research, Children's Hospital at Westmead, Westmead, NSW, Australia.,Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine and Health, Camperdown, NSW, Australia.,Molecular Neurobiology, The Children's Medical Research Institute, Westmead, NSW, Australia
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2
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Greenfield A. Making sense of heritable human genome editing: Scientific and ethical considerations. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:1-28. [PMID: 34175039 DOI: 10.1016/bs.pmbts.2020.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genome editing, particularly the use of CRISPR-Cas9-based methodologies, is revolutionizing biology through its impacts on research and the translation of these into applications in biomedicine. Somatic genome editing aimed at treating individuals with disease raises some significant ethical issues, but proposed heritable interventions, through the use of genome editing in gametes or embryos, raise a number of distinct social, ethical and political issues. This review will consider some proposed uses of heritable human genome editing (HHGE) and several of the objections to these that have been raised. Making sense of such proposed uses requires viewing HHGE as an assisted reproductive technology (ART) that, like preimplantation genetic testing (PGT) and mitochondrial replacement techniques (MRT), aims to prevent disease transmission during sexual reproduction, rather than acting as a therapy for an existing individual. Applications beyond the paradigm of disease prevention raise even more difficult scientific and ethical questions. Here, I will discuss various themes that are prominent in discussions of the science and ethics of HHGE, including impacts on human dignity and society, the language of HHGE used for public dialogue and the governance of HHGE.
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Affiliation(s)
- Andy Greenfield
- MRC Mammalian Genetics Unit, Harwell Institute, Oxfordshire, United Kingdom.
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3
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Genome-Wide Analysis of Off-Target CRISPR/Cas9 Activity in Single-Cell-Derived Human Hematopoietic Stem and Progenitor Cell Clones. Genes (Basel) 2020; 11:genes11121501. [PMID: 33322084 PMCID: PMC7762975 DOI: 10.3390/genes11121501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/28/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)-mediated genome editing holds remarkable promise for the treatment of human genetic diseases. However, the possibility of off-target Cas9 activity remains a concern. To address this issue using clinically relevant target cells, we electroporated Cas9 ribonucleoprotein (RNP) complexes (independently targeted to two different genomic loci, the CXCR4 locus on chromosome 2 and the AAVS1 locus on chromosome 19) into human mobilized peripheral blood-derived hematopoietic stem and progenitor cells (HSPCs) and assessed the acquisition of somatic mutations in an unbiased, genome-wide manner via whole genome sequencing (WGS) of single-cell-derived HSPC clones. Bioinformatic analysis identified >20,000 total somatic variants (indels, single nucleotide variants, and structural variants) distributed among Cas9-treated and non-Cas9-treated control HSPC clones. Statistical analysis revealed no significant difference in the number of novel non-targeted indels among the samples. Moreover, data analysis showed no evidence of Cas9-mediated indel formation at 623 predicted off-target sites. The median number of novel single nucleotide variants was slightly elevated in Cas9 RNP-recipient sample groups compared to baseline, but did not reach statistical significance. Structural variants were rare and demonstrated no clear causal connection to Cas9-mediated gene editing procedures. We find that the collective somatic mutational burden observed within Cas9 RNP-edited human HSPC clones is indistinguishable from naturally occurring levels of background genetic heterogeneity.
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4
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Burgio G, Teboul L. Anticipating and Identifying Collateral Damage in Genome Editing. Trends Genet 2020; 36:905-914. [PMID: 33039248 PMCID: PMC7658041 DOI: 10.1016/j.tig.2020.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023]
Abstract
Genome editing has powerful applications in research, healthcare, and agriculture. However, the range of possible molecular events resulting from genome editing has been underestimated and the technology remains unpredictable on, and away from, the target locus. This has considerable impact in providing a safe approach for therapeutic genome editing, agriculture, and other applications. This opinion article discusses how to anticipate and detect those editing events by a combination of assays to capture all possible genomic changes. It also discusses strategies for preventing unwanted effects, critical to appraise the benefit or risk associated with the use of the technology. Anticipating and verifying the result of genome editing are essential for the success for all applications.
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Affiliation(s)
- Gaëtan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, ACT 2603, Australia.
| | - Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Campus, Didcot, OX11 0RD, UK.
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5
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Clement K, Hsu JY, Canver MC, Joung JK, Pinello L. Technologies and Computational Analysis Strategies for CRISPR Applications. Mol Cell 2020; 79:11-29. [PMID: 32619467 PMCID: PMC7497852 DOI: 10.1016/j.molcel.2020.06.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 03/12/2020] [Accepted: 06/05/2020] [Indexed: 12/21/2022]
Abstract
The CRISPR-Cas system offers a programmable platform for eukaryotic genome and epigenome editing. The ability to perform targeted genetic and epigenetic perturbations enables researchers to perform a variety of tasks, ranging from investigating questions in basic biology to potentially developing novel therapeutics for the treatment of disease. While CRISPR systems have been engineered to target DNA and RNA with increased precision, efficiency, and flexibility, assays to identify off-target editing are becoming more comprehensive and sensitive. Furthermore, techniques to perform high-throughput genome and epigenome editing can be paired with a variety of readouts and are uncovering important cellular functions and mechanisms. These technological advances drive and are driven by accompanying computational approaches. Here, we briefly present available CRISPR technologies and review key computational advances and considerations for various CRISPR applications. In particular, we focus on the analysis of on- and off-target editing and CRISPR pooled screen data.
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Affiliation(s)
- Kendell Clement
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Y Hsu
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew C Canver
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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6
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Teboul L, Herault Y, Wells S, Qasim W, Pavlovic G. Variability in Genome Editing Outcomes: Challenges for Research Reproducibility and Clinical Safety. Mol Ther 2020; 28:1422-1431. [PMID: 32243835 PMCID: PMC7264426 DOI: 10.1016/j.ymthe.2020.03.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome editing tools have already revolutionized biomedical research and are also expected to have an important impact in the clinic. However, their extensive use in research has revealed much unpredictability, both off and on target, in the outcome of their application. We discuss the challenges associated with this unpredictability, both for research and in the clinic. For the former, an extensive validation of the model is essential. For the latter, potential unpredicted activity does not preclude the use of these tools but requires that molecular evidence to underpin the relevant risk:benefit evaluation is available. Safe and successful clinical application will also depend on the mode of delivery and the cellular context.
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Affiliation(s)
- Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Campus, Didcot OX11 0RD, Oxon, UK.
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-Institut Clinique de la Souris, Celphedia, Strasbourg 67404, France
| | - Sara Wells
- The Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Campus, Didcot OX11 0RD, Oxon, UK
| | - Waseem Qasim
- Great Ormond Street Institute of Child Health, NIHR Biomedical Research Centre, London WC1N 1EH, UK.
| | - Guillaume Pavlovic
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-Institut Clinique de la Souris, Celphedia, Strasbourg 67404, France.
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7
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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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8
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Luo X, He Y, Zhang C, He X, Yan L, Li M, Hu T, Hu Y, Jiang J, Meng X, Ji W, Zhao X, Zheng P, Xu S, Su B. Trio deep-sequencing does not reveal unexpected off-target and on-target mutations in Cas9-edited rhesus monkeys. Nat Commun 2019; 10:5525. [PMID: 31797925 PMCID: PMC6892871 DOI: 10.1038/s41467-019-13481-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 11/08/2019] [Indexed: 12/16/2022] Open
Abstract
CRISPR-Cas9 is a widely-used genome editing tool, but its off-target effect and on-target complex mutations remain a concern, especially in view of future clinical applications. Non-human primates (NHPs) share close genetic and physiological similarities with humans, making them an ideal preclinical model for developing Cas9-based therapies. However, to our knowledge no comprehensive in vivo off-target and on-target assessment has been conducted in NHPs. Here, we perform whole genome trio sequencing of Cas9-treated rhesus monkeys. We only find a small number of de novo mutations that can be explained by expected spontaneous mutations, and no unexpected off-target mutations (OTMs) were detected. Furthermore, the long-read sequencing data does not detect large structural variants in the target region.
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Affiliation(s)
- Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 100101, Beijing, China
- Kunming Primate Research Center, Chinese Academy of Sciences, 650223, Kunming, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 100101, Beijing, China
- Kunming Primate Research Center, Chinese Academy of Sciences, 650223, Kunming, China
| | - Chao Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, 200031, Shanghai, China
| | - Xiechao He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Kunming Primate Research Center, Chinese Academy of Sciences, 650223, Kunming, China
| | - Lanzhen Yan
- Kunming Primate Research Center, Chinese Academy of Sciences, 650223, Kunming, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, 650203, Kunming, China
| | - Min Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Ting Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Yan Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Jin Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaoyu Meng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Weizhi Ji
- Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, China
| | - Xudong Zhao
- Kunming Primate Research Center, Chinese Academy of Sciences, 650223, Kunming, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, 650203, Kunming, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, 200031, Shanghai, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
- Collaborative Innovation Centre of Genetics and Development, 200438, Shanghai, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.
- Kunming Primate Research Center, Chinese Academy of Sciences, 650223, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.
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9
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Wang D, Zhang C, Wang B, Li B, Wang Q, Liu D, Wang H, Zhou Y, Shi L, Lan F, Wang Y. Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning. Nat Commun 2019; 10:4284. [PMID: 31537810 PMCID: PMC6753114 DOI: 10.1038/s41467-019-12281-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 07/24/2019] [Indexed: 12/16/2022] Open
Abstract
Highly specific Cas9 nucleases derived from SpCas9 are valuable tools for genome editing, but their wide applications are hampered by a lack of knowledge governing guide RNA (gRNA) activity. Here, we perform a genome-scale screen to measure gRNA activity for two highly specific SpCas9 variants (eSpCas9(1.1) and SpCas9-HF1) and wild-type SpCas9 (WT-SpCas9) in human cells, and obtain indel rates of over 50,000 gRNAs for each nuclease, covering ~20,000 genes. We evaluate the contribution of 1,031 features to gRNA activity and develope models for activity prediction. Our data reveals that a combination of RNN with important biological features outperforms other models for activity prediction. We further demonstrate that our model outperforms other popular gRNA design tools. Finally, we develop an online design tool DeepHF for the three Cas9 nucleases. The database, as well as the designer tool, is freely accessible via a web server, http://www.DeepHF.com/ .
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Affiliation(s)
- Daqi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Chengdong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Bei Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Qiang Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Dong Liu
- Co-innovation Center of Neuroregeneration, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Hongyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
- Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, 200011, China
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
- Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Feng Lan
- Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Disease, Capital Medical University, Beijing, 100029, China.
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China.
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10
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Choi K, Shim J, Ko N, Park J. No excessive mutations in transcription activator-like effector nuclease-mediated α-1,3-galactosyltransferase knockout Yucatan miniature pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:360-372. [PMID: 31480150 PMCID: PMC6946973 DOI: 10.5713/ajas.19.0480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Specific genomic sites can be recognized and permanently modified by genome editing. The discovery of endonucleases has advanced genome editing in pigs, attenuating xenograft rejection and cross-species disease transmission. However, off-target mutagenesis caused by these nucleases is a major barrier to putative clinical applications. Furthermore, off-target mutagenesis by genome editing has not yet been addressed in pigs. METHODS Here, we generated genetically inheritable α-1,3-galactosyltransferase (GGTA1) knockout Yucatan miniature pigs by combining transcription activator-like effector nuclease (TALEN) and nuclear transfer. For precise estimation of genomic mutations induced by TALEN in GGTA1 knockout pigs, we obtained the whole-genome sequence of the donor cells for use as an internal control genome. RESULTS In-depth whole-genome sequencing analysis demonstrated that TALEN-mediated GGTA1 knockout pigs had a comparable mutation rate to homologous recombination-treated pigs and wild-type strain controls. RNA sequencing analysis associated with genomic mutations revealed that TALEN-induced off-target mutations had no discernable effect on RNA transcript abundance. CONCLUSION Therefore, TALEN appears to be a precise and safe tool for generating genome-edited pigs, and the TALEN-mediated GGTA1 knockout Yucatan miniature pigs produced in this study can serve as a safe and effective organ and tissue resource for clinical applications.
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Affiliation(s)
| | - Joohyun Shim
- Optipharm Inc., Cheongju 28158, Korea.,Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Nayoung Ko
- Optipharm Inc., Cheongju 28158, Korea.,Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Joonghoon Park
- Department of International Agricultural Technology, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea.,Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
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11
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Miano JM, Long X, Lyu Q. CRISPR links to long noncoding RNA function in mice: A practical approach. Vascul Pharmacol 2019; 114:1-12. [PMID: 30822570 PMCID: PMC6435418 DOI: 10.1016/j.vph.2019.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/29/2022]
Abstract
Next generation sequencing has uncovered a trove of short noncoding RNAs (e.g., microRNAs) and long noncoding RNAs (lncRNAs) that act as molecular rheostats in the control of diverse homeostatic processes. Meanwhile, the tsunamic emergence of clustered regularly interspaced short palindromic repeats (CRISPR) editing has transformed our influence over all DNA-carrying entities, heralding global CRISPRization. This is evident in biomedical research where the ease and low-cost of CRISPR editing has made it the preferred method of manipulating the mouse genome, facilitating rapid discovery of genome function in an in vivo context. Here, CRISPR genome editing components are updated for elucidating lncRNA function in mice. Various strategies are highlighted for understanding the function of lncRNAs residing in intergenic sequence space, as host genes that harbor microRNAs or other genes, and as natural antisense, overlapping or intronic genes. Also discussed is CRISPR editing of mice carrying human lncRNAs as well as the editing of competing endogenous RNAs. The information described herein should assist labs in the rigorous design of experiments that interrogate lncRNA function in mice where complex disease processes can be modeled thus accelerating translational discovery.
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Affiliation(s)
- Joseph M Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America.
| | - Xiaochun Long
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, United States of America
| | - Qing Lyu
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
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12
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Houston RD, Macqueen DJ. Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding. Anim Genet 2019; 50:3-14. [PMID: 30426521 PMCID: PMC6492011 DOI: 10.1111/age.12748] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
Abstract
Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high-quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole-genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome-wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance.
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Affiliation(s)
- R. D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianEH25 9RGUK
| | - D. J. Macqueen
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUK
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13
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Gurumurthy CB, Lloyd KCK. Generating mouse models for biomedical research: technological advances. Dis Model Mech 2019; 12:dmm029462. [PMID: 30626588 PMCID: PMC6361157 DOI: 10.1242/dmm.029462] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, new methods and procedures have been developed to generate genetically engineered mouse models of human disease. This At a Glance article highlights several recent technical advances in mouse genome manipulation that have transformed our ability to manipulate and study gene expression in the mouse. We discuss how conventional gene targeting by homologous recombination in embryonic stem cells has given way to more refined methods that enable allele-specific manipulation in zygotes. We also highlight advances in the use of programmable endonucleases that have greatly increased the feasibility and ease of editing the mouse genome. Together, these and other technologies provide researchers with the molecular tools to functionally annotate the mouse genome with greater fidelity and specificity, as well as to generate new mouse models using faster, simpler and less costly techniques.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
| | - Kevin C Kent Lloyd
- Department of Surgery, School of Medicine, University of California, Davis, CA 95618, USA
- Mouse Biology Program, University of California, Davis, CA 95618, USA
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14
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Abstract
Genome editing holds remarkable promise to transform human medicine as new therapies that can directly address the genetic causes of disease. However, concerns remain about possible undesired biological consequences of genome editors, particularly the introduction of unintended 'off-target' mutations. Here, we discuss both important considerations for therapeutic genome editing and our understanding of the functional impact of undesired off-target mutations. An important challenge for the future will be the development of new approaches for predicting and defining the probable function of unintended genome-editing mutations, which will inspire confidence in the next generation of promising genome-editing therapies.
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Affiliation(s)
- Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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15
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas-based genome editing technology has enabled manipulation of the embryonic genome. Unbiased whole genome sequencing comparing parents to progeny has revealed that the rate of Cas9-induced mutagenesis in mouse embryos is indistinguishable from the background rate of de novo mutation. However, establishing the best practice to confirm on-target alleles of interest remains a challenge. We believe that improvement in editing strategies and screening methods for founder mice will contribute to the generation of quality-controlled animals, thereby ensuring reproducibility of results in animal studies and advancing the 3Rs (replacement, reduction, and refinement).
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Affiliation(s)
- Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan
| | - Kenichi Nakashima
- Gene Engineering Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan
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16
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Vogel KM, Ouagrham-Gormley SB. Anticipating Emerging Biotechnology Threats: A case study of CRISPR. Politics Life Sci 2018; 37:203-219. [PMID: 31120699 DOI: 10.1017/pls.2018.21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This article discusses the contingencies and complexities of CRISPR. It outlines key problems regarding off-target effects and replication of experimental work that are important to consider in light of CRISPR's touted ease of use and diffusion. In light of literature on the sociotechnical dimensions of the life sciences and biotechnology and literature on former bioweapons programs, this article argues that we need more detailed empirical case studies of the social and technical factors shaping CRISPR and related gene-editing techniques in order to better understand how they may be different from other advances in biotechnology-or whether similar features remain. This information will be critical to better inform intelligence practitioners and policymakers about the security implications of new gene-editing techniques.
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17
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Miao K, Zhang X, Su SM, Zeng J, Huang Z, Chan UI, Xu X, Deng CX. Optimizing CRISPR/Cas9 technology for precise correction of the Fgfr3-G374R mutation in achondroplasia in mice. J Biol Chem 2018; 294:1142-1151. [PMID: 30487289 DOI: 10.1074/jbc.ra118.006496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/26/2018] [Indexed: 12/13/2022] Open
Abstract
CRISPR/Cas9 is a powerful technology widely used for genome editing, with the potential to be used for correcting a wide variety of deleterious disease-causing mutations. However, the technique tends to generate more indels (insertions and deletions) than precise modifications at the target sites, which might not resolve the mutation and could instead exacerbate the initial genetic disruption. We sought to develop an improved protocol for CRISPR/Cas9 that would correct mutations without unintended consequences. As a case study, we focused on achondroplasia, a common genetic form of dwarfism defined by missense mutation in the Fgfr3 gene that results in glycine to arginine substitution at position 374 in mice in fibroblast growth factor receptor 3 (Fgfr3-G374R), which corresponds to G380R in humans. First, we designed a GFP reporter system that can evaluate the cutting efficiency and specificity of single guide RNAs (sgRNAs). Using the sgRNA selected based on our GFP reporter system, we conducted targeted therapy of achondroplasia in mice. We found that we achieved higher frequency of precise correction of the Fgfr3-G374R mutation using Cas9 protein rather than Cas9 mRNA. We further demonstrated that targeting oligos of 100 and 200 nucleotides precisely corrected the mutation at equal efficiency. We showed that our strategy completely suppressed phenotypes of achondroplasia and whole genome sequencing detected no off-target effects. These data indicate that improved protocols can enable the precise CRISPR/Cas9-mediated correction of individual mutations with high fidelity.
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Affiliation(s)
- Kai Miao
- Cancer Center, Faculty of Health Sciences, Macau SAR; Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR
| | - Xin Zhang
- Cancer Center, Faculty of Health Sciences, Macau SAR; Transgenic and Knockout Core, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Sek Man Su
- Cancer Center, Faculty of Health Sciences, Macau SAR; Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR
| | - Jianming Zeng
- Cancer Center, Faculty of Health Sciences, Macau SAR; Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR
| | - Zebin Huang
- Cancer Center, Faculty of Health Sciences, Macau SAR; Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR
| | - Un In Chan
- Cancer Center, Faculty of Health Sciences, Macau SAR; Transgenic and Knockout Core, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Xiaoling Xu
- Cancer Center, Faculty of Health Sciences, Macau SAR; Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR; Transgenic and Knockout Core, Faculty of Health Sciences, University of Macau, Macau SAR, China.
| | - Chu-Xia Deng
- Cancer Center, Faculty of Health Sciences, Macau SAR; Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR.
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18
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Razzouk S. CRISPR-Cas9: A cornerstone for the evolution of precision medicine. Ann Hum Genet 2018; 82:331-357. [PMID: 30014471 DOI: 10.1111/ahg.12271] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 12/20/2022]
Abstract
Modern genetic therapy incorporates genomic testing and genome editing. It is the finest approach for precision medicine. Genome editing is a state-of-the-art technology to manipulate gene expression thus generating a particular genotype. It encompasses multiple programmable nuclease-based approaches leading to genetic changes. Not surprisingly, this method triggered internationally a wide array of controversies in the scientific community and in the public since it transforms the human genome. Given its importance, the pace of this technology is exceptionally fast. In this report, we introduce one aspect of genome editing, the CRISPR/Cas9 system, highlight its potential to correct genetic mutations and explore its utility in clinical setting. Our goal is to enlighten health care providers about genome editing and incite them to take part of this vital debate.
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Affiliation(s)
- Sleiman Razzouk
- Adjunct Faculty, Department of Periodontology and Implant Dentistry, New York University College of Dentistry, New York.,Private Practice, Beirut, Lebanon
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19
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Montoliu L, Whitelaw CBA. Unexpected mutations were expected and unrelated to CRISPR-Cas9 activity. Transgenic Res 2018; 27:315-319. [PMID: 29855762 DOI: 10.1007/s11248-018-0081-2] [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] [Received: 04/06/2018] [Accepted: 05/26/2018] [Indexed: 12/26/2022]
Abstract
The scientific journal Nature Methods have just retracted a publication that reported numerous unexpected mutations after a CRISPR-Cas9 experiment based on collecting whole genome sequencing information from one control and two experimental genome edited mice. In the intervening 10 months since publication the data presented have been strongly contested and criticized by the scientific and biotech communities, through publications, open science channels and social networks. The criticism focused on the animal used as control, which was derived from the same mouse strain as the experimental individuals but from an unrelated sub-colony, hence control and experimental mice were genetically divergent. The most plausible explanation for the vast majority of the reported unexpected mutations were the expected underlying genetic polymorphisms that normally accumulate in two different colonies of the same mouse strain which occur as a result of spontaneous mutations and genetic drift. Therefore, the reported mutations were most likely not related to CRISPR-Cas9 activity.
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Affiliation(s)
- Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC), Biomedical Research Networking Centre Consortium on Rare Diseases (CIBERER-ISCIII), Darwin 3, 28049, Madrid, Spain.
| | - C Bruce A Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.
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20
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Abstract
The CRISPR-CRISPR-associated (Cas) nuclease system offers the ability to perform unprecedented functional genetic experiments and the promise of therapy for a variety of genetic disorders. The understanding of factors contributing to CRISPR targeting efficacy and specificity continues to evolve. As CRISPR systems rely on Watson-Crick base pairing to ultimately mediate genomic cleavage, it logically follows that genetic variation would affect CRISPR targeting by increasing or decreasing sequence homology at on-target and off-target sites or by altering protospacer adjacent motifs. Numerous efforts have been made to document the extent of human genetic variation, which can serve as resources to understand and mitigate the effect of genetic variation on CRISPR targeting. Here, we review efforts to elucidate the effect of human genetic variation on CRISPR targeting at on-target and off-target sites with considerations for laboratory experiments and clinical translation of CRISPR-based therapies.
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Affiliation(s)
- Matthew C. Canver
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - J. Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
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21
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Affiliation(s)
- Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
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