151
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Li G, Zhang X, Ou H, Wang H, Liu D, Yang H, Wu Z. PIK-75 promotes homology-directed DNA repair. J Genet Genomics 2019; 46:141-144. [PMID: 30935856 DOI: 10.1016/j.jgg.2019.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/19/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Guoling Li
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xianwei Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Hao Ou
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Haoqiang Wang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Huaqiang Yang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhenfang Wu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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152
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Koebis M, Urata S, Shinoda Y, Okabe S, Yamasoba T, Nakao K, Aiba A, Furuichi T. LAMP5 in presynaptic inhibitory terminals in the hindbrain and spinal cord: a role in startle response and auditory processing. Mol Brain 2019; 12:20. [PMID: 30867010 PMCID: PMC6416879 DOI: 10.1186/s13041-019-0437-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
Lysosome-associated membrane protein 5 (LAMP5) is a mammalian ortholog of the Caenorhabditis elegans protein, UNC-46, which functions as a sorting factor to localize the vesicular GABA transporter UNC-47 to synaptic vesicles. In the mouse forebrain, LAMP5 is expressed in a subpopulation of GABAergic neurons in the olfactory bulb and the striato-nigral system, where it is required for fine-tuning of GABAergic synaptic transmission. Here we focus on the prominent expression of LAMP5 in the brainstem and spinal cord and suggest a role for LAMP5 in these brain regions. LAMP5 was highly expressed in several brainstem nuclei involved with auditory processing including the cochlear nuclei, the superior olivary complex, nuclei of the lateral lemniscus and grey matter in the spinal cord. It was localized exclusively in inhibitory synaptic terminals, as has been reported in the forebrain. In the absence of LAMP5, localization of the vesicular inhibitory amino acid transporter (VIAAT) was unaltered in the lateral superior olive and the ventral cochlear nuclei, arguing against a conserved role for LAMP5 in trafficking VIAAT. Lamp5 knockout mice showed no overt behavioral abnormality but an increased startle response to auditory and tactile stimuli. In addition, LAMP5 deficiency led to a larger intensity-dependent increase of wave I, II and V peak amplitude of auditory brainstem response. Our results indicate that LAMP5 plays a pivotal role in sensorimotor processing in the brainstem and spinal cord.
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Affiliation(s)
- Michinori Koebis
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Shinji Urata
- Department of Otolaryngology, Faculty of Medicine, The University of Tokyo, Tokyo, 113-8655 Japan
| | - Yo Shinoda
- Department of Environmental Health, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392 Japan
| | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Tatsuya Yamasoba
- Department of Otolaryngology, Faculty of Medicine, The University of Tokyo, Tokyo, 113-8655 Japan
| | - Kazuki Nakao
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Teiichi Furuichi
- Department of Applied Biological Sciences, Tokyo University of Science, Chiba, 278-8510 Japan
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153
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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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154
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Rui Y, Wilson DR, Green JJ. Non-Viral Delivery To Enable Genome Editing. Trends Biotechnol 2019; 37:281-293. [PMID: 30278987 PMCID: PMC6378131 DOI: 10.1016/j.tibtech.2018.08.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 12/27/2022]
Abstract
Genome-editing technologies such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENS), and the clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein system have revolutionized biological research. Each biotechnology consists of a DNA-binding protein that can be programmed to recognize and initiate double-strand breaks (DSBs) for site-specific gene modification. These technologies have the potential to be harnessed to cure diseases caused by aberrant gene expression. To be successful therapeutically, their functionality depends on their safe and efficient delivery into the cell nucleus. This review discusses the challenges in the delivery of genome-editing tools, and highlights recent innovations in non-viral delivery that have potential to overcome these limitations and advance the translation of genome editing towards patient care.
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Affiliation(s)
- Yuan Rui
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; These authors contributed equally
| | - David R Wilson
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Institute for Nanobiotechnology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; These authors contributed equally
| | - Jordan J Green
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Institute for Nanobiotechnology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Departments of Materials Science and Engineering and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA; Departments of Ophthalmology, Oncology, and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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155
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Zhou S, Chen Y, Gong X, Jin J, Li H. Site-specific integration of light chain and heavy chain genes of antibody into CHO-K1 stable hot spot and detection of antibody and fusion protein expression level. Prep Biochem Biotechnol 2019; 49:384-390. [DOI: 10.1080/10826068.2019.1573196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Songtao Zhou
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yun Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Xiaohai Gong
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Huazhong Li
- School of Biotechnology, Jiangnan University, Wuxi, China
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156
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Effects of the Prdx2 depletion on blood pressure and life span in spontaneously hypertensive rats. Hypertens Res 2019; 42:610-617. [PMID: 30655626 DOI: 10.1038/s41440-019-0207-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 01/12/2023]
Abstract
Oxidative stress is involved in the pathogenesis of hypertension and hypertensive organ damage. Our previous study suggested that stroke-prone spontaneously hypertensive rats (SHRSP) exhibited greater oxidative stress than SHR and that the stroke incidence was significantly greater in SHRSP than SHR. Therefore, we hypothesized that oxidative stress was responsible for the stroke susceptibility in SHRSP. The present study constructed Prdx2 (a gene coding an antioxidative enzyme)-knockout (KO) SHR to examine whether Prdx2 knockout would make SHR more vulnerable to hypertensive organ damage, including stroke. Prdx2-KO SHR were created using CRISPR/CAS9 for genome editing. Eight-week-old male SHR and Prdx2-KO SHR were fed 1% NaCl for 2 months to induce blood pressure (BP) changes and stroke occurrence. The baseline BP was significantly greater in KO SHR, and this difference disappeared after salt loading. The life span of KO SHR was significantly reduced compared to that of SHR despite no differences in BP under salt-loading. However, no stroke was observed in KO SHR. The severity of hypertensive renal and cardiac injuries did not differ significantly between the two strains, but oxidative stress, evaluated using urinary isoprostane excretion and DHE staining, was greater in KO SHR. These results indicated that the Prdx2-depletion caused a shorter life span and modest BP increase in SHR via increased oxidative stress. The pathophysiological roles of oxidative stress in this model should be clarified in future studies.
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157
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Ittiprasert W, Mann VH, Karinshak SE, Coghlan A, Rinaldi G, Sankaranarayanan G, Chaidee A, Tanno T, Kumkhaek C, Prangtaworn P, Mentink-Kane MM, Cochran CJ, Driguez P, Holroyd N, Tracey A, Rodpai R, Everts B, Hokke CH, Hoffmann KF, Berriman M, Brindley PJ. Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni. eLife 2019; 8:41337. [PMID: 30644357 PMCID: PMC6355194 DOI: 10.7554/elife.41337] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/12/2018] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas9-based genome editing has yet to be reported in species of the Platyhelminthes. We tested this approach by targeting omega-1 (ω1) of Schistosoma mansoni as proof of principle. This secreted ribonuclease is crucial for Th2 polarization and granuloma formation. Schistosome eggs were exposed to Cas9 complexed with guide RNA complementary to ω1 by electroporation or by transduction with lentiviral particles. Some eggs were also transfected with a single stranded donor template. Sequences of amplicons from gene-edited parasites exhibited Cas9-catalyzed mutations including homology directed repaired alleles, and other analyses revealed depletion of ω1 transcripts and the ribonuclease. Gene-edited eggs failed to polarize Th2 cytokine responses in macrophage/T-cell co-cultures, while the volume of pulmonary granulomas surrounding ω1-mutated eggs following tail-vein injection into mice was vastly reduced. Knock-out of ω1 and the diminished levels of these cytokines following exposure showcase the novel application of programmed gene editing for functional genomics in schistosomes. Schistosomiasis is a tropical disease that can cause serious health problems, including damage to the liver and kidneys, infertility and bladder cancer. Nearly a quarter billion people are currently infected, mostly in poor regions of sub-Saharan Africa, the Philippines and Brazil. A freshwater worm known as Schistosoma mansoni causes the disease. These parasites enter the human body by burrowing into the skin; once in the bloodstream, they move to various organs where they rapidly start to reproduce. Their eggs release several molecules, including a protein known as omega-1 ribonuclease, which can damage the surrounding tissues. A gene editing technique called CRISPR/Cas9 allows scientists to precisely target and then deactivate the genetic information a cell needs to produce a given protein. While the tool has been used in other species before, it was unknown if it could be applied to S. mansoni. Here, Ittiprasert et al. harnessed CRISPR/Cas9 to deactivate the gene that codes for omega-1 ribonuclease and create parasites that do not produce the protein, or only very little of it. The experiments showed that mice infected with the gene-edited worm eggs displayed far fewer symptoms of schistosomiasis compared to those that carry the non-edited parasites. Alongside this work, Arunsan et al. used CRISPR/Cas9 to inactivate a gene in another species of worm that can cause liver cancer in humans. Together, these findings demonstrate for the first time that the gene editing method can be adapted for use in parasitic flatworms, which are a major public health problem in tropical climates. This tool should help scientists understand how the parasites invade and damage our bodies, and provide new ideas for treatment and disease control.
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Affiliation(s)
- Wannaporn Ittiprasert
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States.,Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | - Victoria H Mann
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States.,Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | - Shannon E Karinshak
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | - Avril Coghlan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gabriel Rinaldi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Apisit Chaidee
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Toshihiko Tanno
- Department of Surgery, University of Maryland, Baltimore, United States.,Institute of Human Virology, University of Maryland, Baltimore, United States
| | - Chutima Kumkhaek
- Cellular and Molecular Therapeutics Laboratory, National Heart, Lungs and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Pannathee Prangtaworn
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States.,Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Christina J Cochran
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | - Patrick Driguez
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Rutchanee Rodpai
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Bart Everts
- Department of Parasitology, Leiden University Medical Center, Leiden, Netherlands
| | - Cornelis H Hokke
- Department of Parasitology, Leiden University Medical Center, Leiden, Netherlands
| | - Karl F Hoffmann
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Paul J Brindley
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
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158
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Li M, Liu X, Dai S, Xiao H, Wang D. High Efficiency Targeting of Non-coding Sequences Using CRISPR/Cas9 System in Tilapia. G3 (BETHESDA, MD.) 2019; 9:287-295. [PMID: 30482801 PMCID: PMC6325910 DOI: 10.1534/g3.118.200883] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/21/2018] [Indexed: 01/14/2023]
Abstract
The CRISPR/Cas9 has been successfully applied for disruption of protein coding sequences in a variety of organisms. The majority of the animal genome is actually non-coding sequences, which are key regulators associated with various biological processes. In this study, to understand the biological significance of these sequences, we used one or dual gRNA guided Cas9 nuclease to achieve specific deletion of non-coding sequences including microRNA and 3' untranslated region (UTR) in tilapia, which is an important fish for studying sex determination and evolution. Co-injection of fertilized eggs with single gRNA targeting seed region of miRNA and Cas9 mRNA resulted in indel mutations. Further, co-injection of fertilized eggs with dual gRNAs and Cas9 mRNA led to the removal of the fragment between the two target loci, yielding maximum efficiency of 11%. This highest genomic deletion efficiency was further improved up to 19% using short ssDNA as a donor. The deletions can be transmitted through the germline to the next generation at average efficiency of 8.7%. Cas9-vasa 3'-UTR was used to increase the efficiency of germline transmission of non-coding sequence deletion up to 14.9%. In addition, the 3'-UTR of the vasa gene was successfully deleted by dual gRNAs. Deletion of vasa 3'-UTR resulted in low expression level of vasa mRNA in the gonad when compared with the control. To summarize, the improved CRISPR/Cas9 system provided a powerful platform that can assist to easily generate desirable non-coding sequences mutants in non-model fish tilapia to discovery their functions.
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Affiliation(s)
- Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xingyong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Shengfei Dai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Hesheng Xiao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
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159
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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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160
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Brinkman EK, van Steensel B. Rapid Quantitative Evaluation of CRISPR Genome Editing by TIDE and TIDER. Methods Mol Biol 2019; 1961:29-44. [PMID: 30912038 DOI: 10.1007/978-1-4939-9170-9_3] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Current genome editing tools enable targeted mutagenesis of selected DNA sequences in many species. However, the efficiency and the type of introduced mutations by the genome editing method are largely dependent on the target site. As a consequence, the outcome of the editing operation is difficult to predict. Therefore, a quick assay to quantify the frequency of mutations is vital for a proper assessment of genome editing actions. We developed two methods that are rapid, cost-effective, and readily applicable: (1) TIDE, which can accurately identify and quantify insertions and deletions (indels) that arise after introduction of double strand breaks (DSBs); (2) TIDER, which is suited for template-mediated editing events including point mutations. Both methods only require a set of PCR reactions and standard Sanger sequencing runs. The sequence traces are analyzed by the TIDE or TIDER algorithm (available at https://tide.nki.nl or https://deskgen.com ). The routine is easy, fast, and provides much more detailed information than current enzyme-based assays. TIDE and TIDER accelerate testing and designing of DSB-based genome editing strategies.
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Affiliation(s)
- Eva Karina Brinkman
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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161
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Klimke A, Güttler S, Kuballa P, Janzen S, Ortmann S, Flora A. Use of CRISPR/Cas9 for the Modification of the Mouse Genome. Methods Mol Biol 2019; 1953:213-230. [PMID: 30912024 DOI: 10.1007/978-1-4939-9145-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The use of CRISPR/Cas9 to modify the mouse genome has gained immense interest in the past few years since it allows the direct modification of embryos, bypassing the need of labor-intensive procedures for the manipulation of embryonic stem cells. By shortening the overall timelines and reducing the costs for the generation of new genetically modified mouse lines (Li et al., Nat Biotechnol 31: 681-683, 2013), this technology has rapidly become a major tool for in vivo drug discovery applications.
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Affiliation(s)
| | | | | | | | | | - Adriano Flora
- PerkinElmer chemagen Technologie GmbH, Baesweiler, Germany.
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162
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Abstract
Transgenic mouse models can be subdivided into two main categories based on genomic location: (1) targeted genomic manipulation and (2) random integration into the genome. Despite the potential confounding insertional mutagenesis and host locus-dependent expression, random integration transgenics allowed for rapid in vivo assessment of gene/protein function. Since precise genomic manipulation required the time-consuming prerequisite of first generating genetically modified embryonic stem cells, the rapid nature of generating random integration transgenes remained a strong benefit outweighing various disadvantages. The advent of targetable nucleases, such as CRISPR/Cas9, has eliminated the prerequisite of first generating genetically modified embryonic stem cells for some types of targeted genomic mutations. This chapter outlines the generation of mouse models with targeted genomic manipulation using the CRISPR/Cas9 system directly into single cell mouse embryos.
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Affiliation(s)
- Greg J Scott
- Knockout Mouse Core, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Artiom Gruzdev
- Knockout Mouse Core, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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163
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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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164
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Ran Y, Patron N, Kay P, Wong D, Buchanan M, Cao Y, Sawbridge T, Davies JP, Mason J, Webb SR, Spangenberg G, Ainley WM, Walsh TA, Hayden MJ. Zinc finger nuclease-mediated precision genome editing of an endogenous gene in hexaploid bread wheat (Triticum aestivum) using a DNA repair template. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2088-2101. [PMID: 29734518 PMCID: PMC6230953 DOI: 10.1111/pbi.12941] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/03/2018] [Accepted: 04/17/2018] [Indexed: 05/07/2023]
Abstract
Sequence-specific nucleases have been used to engineer targeted genome modifications in various plants. While targeted gene knockouts resulting in loss of function have been reported with relatively high rates of success, targeted gene editing using an exogenously supplied DNA repair template and site-specific transgene integration has been more challenging. Here, we report the first application of zinc finger nuclease (ZFN)-mediated, nonhomologous end-joining (NHEJ)-directed editing of a native gene in allohexaploid bread wheat to introduce, via a supplied DNA repair template, a specific single amino acid change into the coding sequence of acetohydroxyacid synthase (AHAS) to confer resistance to imidazolinone herbicides. We recovered edited wheat plants having the targeted amino acid modification in one or more AHAS homoalleles via direct selection for resistance to imazamox, an AHAS-inhibiting imidazolinone herbicide. Using a cotransformation strategy based on chemical selection for an exogenous marker, we achieved a 1.2% recovery rate of edited plants having the desired amino acid change and a 2.9% recovery of plants with targeted mutations at the AHAS locus resulting in a loss-of-function gene knockout. The latter results demonstrate a broadly applicable approach to introduce targeted modifications into native genes for nonselectable traits. All ZFN-mediated changes were faithfully transmitted to the next generation.
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Affiliation(s)
- Yidong Ran
- Genovo Biotechnology Co. LtdTianjinChina
| | | | - Pippa Kay
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Debbie Wong
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Margaret Buchanan
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Ying‐Ying Cao
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Tim Sawbridge
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| | | | - John Mason
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| | | | - German Spangenberg
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| | | | | | - Matthew J. Hayden
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
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165
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Yamamoto Y, Gerbi SA. Making ends meet: targeted integration of DNA fragments by genome editing. Chromosoma 2018; 127:405-420. [PMID: 30003320 PMCID: PMC6330168 DOI: 10.1007/s00412-018-0677-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/25/2018] [Accepted: 06/28/2018] [Indexed: 12/27/2022]
Abstract
Targeted insertion of large pieces of DNA is an important goal of genetic engineering. However, this goal has been elusive since classical methods for homology-directed repair are inefficient and often not feasible in many systems. Recent advances are described here that enable site-specific genomic insertion of relatively large DNA with much improved efficiency. Using the preferred repair pathway in the cell of nonhomologous end-joining, DNA of up to several kb could be introduced with remarkably good precision by the methods of HITI and ObLiGaRe with an efficiency up to 30-40%. Recent advances utilizing homology-directed repair (methods of PITCh; short homology arms including ssODN; 2H2OP) have significantly increased the efficiency for DNA insertion, often to 40-50% or even more depending on the method and length of DNA. The remaining challenges of integration precision and off-target site insertions are summarized. Overall, current advances provide major steps forward for site-specific insertion of large DNA into genomes from a broad range of cells and organisms.
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Affiliation(s)
- Yutaka Yamamoto
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall room 260, 185 Meeting Street, Providence, RI, 02912, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall room 260, 185 Meeting Street, Providence, RI, 02912, USA.
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166
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Lee SH, Kim S, Hur JK. CRISPR and Target-Specific DNA Endonucleases for Efficient DNA Knock-in in Eukaryotic Genomes. Mol Cells 2018; 41:943-952. [PMID: 30486613 PMCID: PMC6277560 DOI: 10.14348/molcells.2018.0408] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/08/2018] [Accepted: 11/08/2018] [Indexed: 01/23/2023] Open
Abstract
The discovery and mechanistic understanding of target-specific genome engineering technologies has led to extremely effective and specific genome editing in higher organisms. Target-specific genetic modification technology is expected to have a leading position in future gene therapy development, and has a ripple effect on various basic and applied studies. However, several problems remain and hinder efficient and specific editing of target genomic loci. The issues are particularly critical in precise targeted insertion of external DNA sequences into genomes. Here, we discuss some recent efforts to overcome such problems and present a perspective of future genome editing technologies.
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Affiliation(s)
- Seung Hwan Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Sunghyun Kim
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul 02447,
Korea
| | - Junho K Hur
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul 02447,
Korea
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167
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Fujiki S, Aoi S, Funato T, Sato Y, Tsuchiya K, Yanagihara D. Adaptive hindlimb split-belt treadmill walking in rats by controlling basic muscle activation patterns via phase resetting. Sci Rep 2018; 8:17341. [PMID: 30478405 PMCID: PMC6255885 DOI: 10.1038/s41598-018-35714-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022] Open
Abstract
To investigate the adaptive locomotion mechanism in animals, a split-belt treadmill has been used, which has two parallel belts to produce left–right symmetric and asymmetric environments for walking. Spinal cats walking on the treadmill have suggested the contribution of the spinal cord and associated peripheral nervous system to the adaptive locomotion. Physiological studies have shown that phase resetting of locomotor commands involving a phase shift occurs depending on the types of sensory nerves and stimulation timing, and that muscle activation patterns during walking are represented by a linear combination of a few numbers of basic temporal patterns despite the complexity of the activation patterns. Our working hypothesis was that resetting the onset timings of basic temporal patterns based on the sensory information from the leg, especially extension of hip flexors, contributes to adaptive locomotion on the split-belt treadmill. Our hypothesis was examined by conducting forward dynamic simulations using a neuromusculoskeletal model of a rat walking on a split-belt treadmill with its hindlimbs and by comparing the simulated motions with the measured motions of rats.
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Affiliation(s)
- Soichiro Fujiki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
| | - Shinya Aoi
- Department of Aeronautics and Astronautics, Graduate School of Engineering, Kyoto University, Kyoto daigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan
| | - Tetsuro Funato
- Department of Mechanical Engineering and Intelligent Systems, Graduate School of Informatics and Engineering, The University of Electro-communications, 1-5-1 Chofugaoka, Chofu-shi, Tokyo, 182-8585, Japan
| | - Yota Sato
- Department of Mechanical Engineering and Intelligent Systems, Graduate School of Informatics and Engineering, The University of Electro-communications, 1-5-1 Chofugaoka, Chofu-shi, Tokyo, 182-8585, Japan
| | - Kazuo Tsuchiya
- Department of Aeronautics and Astronautics, Graduate School of Engineering, Kyoto University, Kyoto daigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan
| | - Dai Yanagihara
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
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168
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Mizuno N, Mizutani E, Sato H, Kasai M, Ogawa A, Suchy F, Yamaguchi T, Nakauchi H. Intra-embryo Gene Cassette Knockin by CRISPR/Cas9-Mediated Genome Editing with Adeno-Associated Viral Vector. iScience 2018; 9:286-297. [PMID: 30447647 PMCID: PMC6240711 DOI: 10.1016/j.isci.2018.10.030] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/24/2018] [Accepted: 10/29/2018] [Indexed: 12/20/2022] Open
Abstract
Intra-embryo genome editing by CRISPR/Cas9 enables easy generation of gene-modified animals by non-homologous end joining (NHEJ)-mediated frameshift mutations or homology-directed repair (HDR)-mediated point mutations. However, large modifications, such as gene replacement or gene fusions, are still difficult to introduce in embryos without costly micromanipulators. Moreover, micromanipulation techniques for intra-embryo genome editing have been established in only a small set of animals. To overcome these issues, we developed a method of large-fragment DNA knockin without micromanipulation. In this study, we successfully delivered the knockin donor DNA into zygotes by adeno-associated virus (AAV) without removing the zona pellucida, and we succeeded in both large-DNA fragment knockin and whole exon exchange with electroporation of CRISPR/Cas9 ribonucleoprotein. By this method, we can exchange large DNA fragments conveniently in various animal species without micromanipulation.
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Affiliation(s)
- Naoaki Mizuno
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Eiji Mizutani
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Hideyuki Sato
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Mariko Kasai
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Aki Ogawa
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Fabian Suchy
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomoyuki Yamaguchi
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan.
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan; Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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169
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Boel A, De Saffel H, Steyaert W, Callewaert B, De Paepe A, Coucke PJ, Willaert A. CRISPR/Cas9-mediated homology-directed repair by ssODNs in zebrafish induces complex mutational patterns resulting from genomic integration of repair-template fragments. Dis Model Mech 2018; 11:11/10/dmm035352. [PMID: 30355591 PMCID: PMC6215429 DOI: 10.1242/dmm.035352] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/31/2018] [Indexed: 12/30/2022] Open
Abstract
Targeted genome editing by CRISPR/Cas9 is extremely well fitted to generate gene disruptions, although precise sequence replacement by CRISPR/Cas9-mediated homology-directed repair (HDR) suffers from low efficiency, impeding its use for high-throughput knock-in disease modeling. In this study, we used next-generation sequencing (NGS) analysis to determine the efficiency and reliability of CRISPR/Cas9-mediated HDR using several types of single-stranded oligodeoxynucleotide (ssODN) repair templates for the introduction of disease-relevant point mutations in the zebrafish genome. Our results suggest that HDR rates are strongly determined by repair-template composition, with the most influential factor being homology-arm length. However, we found that repair using ssODNs does not only lead to precise sequence replacement but also induces integration of repair-template fragments at the Cas9 cut site. We observed that error-free repair occurs at a relatively constant rate of 1-4% when using different repair templates, which was sufficient for transmission of point mutations to the F1 generation. On the other hand, erroneous repair mainly accounts for the variability in repair rate between the different repair templates. To further improve error-free HDR rates, elucidating the mechanism behind this erroneous repair is essential. We show that the error-prone nature of ssODN-mediated repair, believed to act via synthesis-dependent strand annealing (SDSA), is most likely due to DNA synthesis errors. In conclusion, caution is warranted when using ssODNs for the generation of knock-in models or for therapeutic applications. We recommend the application of in-depth NGS analysis to examine both the efficiency and error-free nature of HDR events. This article has an associated First Person interview with the first author of the paper. Summary: NGS-based analysis reveals that CRISPR/Cas9-induced double-strand-break repair using single-stranded repair templates is error prone in zebrafish, resulting in complex patterns of integrated repair-template fragments.
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Affiliation(s)
- Annekatrien Boel
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Hanna De Saffel
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Anne De Paepe
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Paul J Coucke
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Andy Willaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
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170
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Leidy-Davis T, Cheng K, Goodwin LO, Morgan JL, Juan WC, Roca X, Ong ST, Bergstrom DE. Viable Mice with Extensive Gene Humanization (25-kbp) Created Using Embryonic Stem Cell/Blastocyst and CRISPR/Zygote Injection Approaches. Sci Rep 2018; 8:15028. [PMID: 30301924 PMCID: PMC6177426 DOI: 10.1038/s41598-018-33408-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/28/2018] [Indexed: 02/06/2023] Open
Abstract
Here, we describe an expansion of the typical DNA size limitations associated with CRISPR knock-in technology, more specifically, the physical extent to which mouse genomic DNA can be replaced with donor (in this case, human) DNA at an orthologous locus by zygotic injection. Driving our efforts was the desire to create a whole animal model that would replace 17 kilobase pairs (kbp) of the mouse Bcl2l11 gene with the corresponding 25-kbp segment of human BCL2L11, including a conditionally removable segment (2.9-kbp) of intron 2, a cryptic human exon immediately 3' of this, and a native human exon some 20 kbp downstream. Using two methods, we first carried out the replacement by employing a combination of bacterial artificial chromosome recombineering, classic embryonic stem cell (ESC) targeting, dual selection, and recombinase-driven cassette removal (ESC/Blastocyst Approach). Using a unique second method, we employed the same vector (devoid of its selectable marker cassettes), microinjecting it along with redundant single guide RNAs (sgRNAs) and Cas9 mRNA into mouse zygotes (CRISPR/Zygote Approach). In both instances, we were able to achieve humanization of Bcl2l11 to the extent designed, remove all selection cassettes, and demonstrate the functionality of the conditionally removable, loxP-flanked, 2.9-kbp intronic segment.
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Affiliation(s)
| | - Kai Cheng
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA
- Genetically Engineered Models and Services, Charles River Laboratories, Wilmington, USA
| | - Leslie O Goodwin
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA
| | - Judith L Morgan
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA
- Center for Biometric Analysis, The Jackson Laboratory, Bar Harbor, USA
| | - Wen Chun Juan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- MSD Pharma (Singapore) Private Limited, Singapore, Republic of Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - S Tiong Ong
- Cancer and Stem Cell Biology Signature Research Programme, Duke-NUS Medical School, Singapore, Republic of Singapore
- Department of Haematology, Singapore General Hospital, Singapore, Republic of Singapore
- Department of Medical Oncology, National Cancer Centre, Singapore, Republic of Singapore
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - David E Bergstrom
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, ME, USA.
- Cancer Center, The Jackson Laboratory, Bar Harbor, ME, USA.
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171
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Wang Y, Zhu P, Wang J, Zhu X, Luo J, Meng S, Wu J, Ye B, He L, Du Y, He L, Chen R, Tian Y, Fan Z. Long noncoding RNA lncHand2 promotes liver repopulation via c-Met signaling. J Hepatol 2018; 69:861-872. [PMID: 29653123 DOI: 10.1016/j.jhep.2018.03.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/14/2018] [Accepted: 03/24/2018] [Indexed: 01/20/2023]
Abstract
BACKGROUND & AIMS Long noncoding RNAs (lncRNAs) play important roles in various biological processes, regulating gene expression by diverse mechanisms. However, how lncRNAs regulate liver repopulation is unknown. Herein, we aimed to identify lncRNAs that regulate liver repopulation and elucidate the signaling pathways involved. METHODS Herein, we performed 70% partial hepatectomy in wild-type and gene knockout mice. We then performed transcriptomic analyses to identify a divergent lncRNA termed lncHand2 that is highly expressed during liver regeneration. RESULTS LncHand2 is constitutively expressed in the nuclei of pericentral hepatocytes in mouse and human livers. LncHand2 knockout abrogates liver regeneration and repopulation capacity. Mechanistically, lncHand2 recruits the Ino80 remodeling complex to initiate expression of Nkx1-2 in trans, which triggers c-Met (Met) expression in hepatocytes. Finally, knockout of both Nkx1-2 and c-Met causes more severe liver injury and poorer repopulation ability. Thus, lncHand2 promotes liver repopulation via initiating Nkx1-2-induced c-Met signaling. CONCLUSIONS Our findings reveal that lncHand2 acts as a critical mediator regulating liver repopulation. It does this by inducing Nkx1-2 expression, which in turn triggers c-Met signaling. LAY SUMMARY Long noncoding RNAs play important roles in various biological processes. While long noncoding RNAs do not directly code proteins, they can regulate gene expression by diverse mechanisms. We identified the long noncoding RNA, termed lncHand2 because of its proximity to the gene Hand2, to be an important determinant of liver regeneration through c-Met signaling.
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Affiliation(s)
- Yanying Wang
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingping Zhu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Zhu
- CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianjun Luo
- CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu Meng
- CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayi Wu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Buqing Ye
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Luyun He
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Du
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei He
- Department of Hepatobiliary Surgery, PLA General Hospital, Beijing 100853, China
| | - Runsheng Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yong Tian
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of RNA Biology; Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zusen Fan
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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172
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Sumiyama K, Matsumoto N, Garçon-Yoshida J, Ukai H, Ueda HR, Tanaka Y. Easy and efficient production of completely embryonic-stem-cell-derived mice using a micro-aggregation device. PLoS One 2018; 13:e0203056. [PMID: 30231034 PMCID: PMC6145547 DOI: 10.1371/journal.pone.0203056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/14/2018] [Indexed: 01/09/2023] Open
Abstract
There is an increasing demand for genetically modified mice produced without crossing, for rapid phenotypic screening studies at the organismal level. For this purpose, generation of completely embryonic-stem-cell (ESC)-derived chimeric mice without crossing is now possible using a microinjection or aggregation method with 3i culture medium. However, the microinjection of ESCs into blastocyst, morula, or 8-cell-stage embryos requires a highly skilled operator. The aggregation method is an easier alternative, but the conventional aggregation protocol still requires special skills. To make the aggregation method easier and more precise, here we developed a micro-aggregation device. Unlike conventional 3-dimensional culture, which uses hanging-drop devices for aggregation, we fabricated a polystyrene funnel-like structure to smoothly drop ESCs into a small area (300-μm in diameter) at the bottom of the device. The bottom area was designed so that the surface tension of the liquid-air interface prevents the cells from falling. After aggregation, the cells can be recovered by simply exerting pressure on the liquid from the top. The microdevice can be set upon a regular 96-well plate, so it is compatible with multichannel pipette use or machine operation. Using the microdevice, we successfully obtained chimeric blastocysts, which when transplanted resulted in completely ESC-derived chimeric mice with high efficiency. By changing the number of ESCs in the aggregate, we found that the optimum number of co-cultured ESCs was around 90~120 per embryo. Under this condition, the efficiency of generating completely ESC-derived mice was the same or better than that of the injection method. These results indicated that our microdevice can be used to produce completely ESC-derived chimeric mice easily and with a high success rate, and thus represents a promising alternative to the conventional microinjection or aggregation method, especially for high-throughput, parallel experimental applications.
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Affiliation(s)
- Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 1–3 Yamadaoka, Suita, Osaka, Japan
- * E-mail: (KS); (YT)
| | - Naomi Matsumoto
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 1–3 Yamadaoka, Suita, Osaka, Japan
| | - Junko Garçon-Yoshida
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1–3 Yamadaoka, Suita, Osaka, Japan
| | - Hideki Ukai
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1–3 Yamadaoka, Suita, Osaka, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1–3 Yamadaoka, Suita, Osaka, Japan
- Department of Systems Pharmacology, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Yo Tanaka
- Laboratory for Integrated Biodevice, RIKEN Center for Biosystems Dynamics Research, 1–3 Yamadaoka, Suita, Osaka, Japan
- * E-mail: (KS); (YT)
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173
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Gurumurthy CB, Perez-Pinera P. Technological advances in integrating multi-kilobase DNA sequences into genomes. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018. [DOI: 10.1016/j.cobme.2018.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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174
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Mason DM, Weber CR, Parola C, Meng SM, Greiff V, Kelton WJ, Reddy ST. High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis. Nucleic Acids Res 2018; 46:7436-7449. [PMID: 29931269 PMCID: PMC6101513 DOI: 10.1093/nar/gky550] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022] Open
Abstract
Antibody engineering is often performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offer advantages associated with expression in their final therapeutic format (full-length glycosylated IgG); however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR). HDM leverages oligonucleotides with degenerate codons to generate site-directed mutagenesis libraries in mammalian cells. By improving HDR to a robust efficiency of 15-35% and combining mammalian display screening with next-generation sequencing, we validated this approach can be used for key applications in antibody engineering at high-throughput: rational library construction, novel variant discovery, affinity maturation and deep mutational scanning (DMS). We anticipate that HDM will be a valuable tool for engineering and optimizing antibodies in mammalian cells, and eventually enable directed evolution of other complex proteins and cellular therapeutics.
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Affiliation(s)
- Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
- Life Science Graduate School, Systems Biology, ETH Zürich, University of Zurich, Zurich 8057, Switzerland
| | - Simon M Meng
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - William J Kelton
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
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175
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Karlgren M, Simoff I, Keiser M, Oswald S, Artursson P. CRISPR-Cas9: A New Addition to the Drug Metabolism and Disposition Tool Box. Drug Metab Dispos 2018; 46:1776-1786. [PMID: 30126863 DOI: 10.1124/dmd.118.082842] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/03/2018] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9), i.e., CRISPR-Cas9, has been extensively used as a gene-editing technology during recent years. Unlike earlier technologies for gene editing or gene knockdown, such as zinc finger nucleases and RNA interference, CRISPR-Cas9 is comparably easy to use, affordable, and versatile. Recently, CRISPR-Cas9 has been applied in studies of drug absorption, distribution, metabolism, and excretion (ADME) and for ADME model generation. To date, about 50 papers have been published describing in vitro or in vivo CRISPR-Cas9 gene editing of ADME and ADME-related genes. Twenty of these papers describe gene editing of clinically relevant genes, such as ATP-binding cassette drug transporters and cytochrome P450 drug-metabolizing enzymes. With CRISPR-Cas9, the ADME tool box has been substantially expanded. This new technology allows us to develop better and more predictive in vitro and in vivo ADME models and map previously underexplored ADME genes and gene families. In this mini-review, we give an overview of the CRISPR-Cas9 technology and summarize recent applications of CRISPR-Cas9 within the ADME field. We also speculate about future applications of CRISPR-Cas9 in ADME research.
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Affiliation(s)
- M Karlgren
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - I Simoff
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - M Keiser
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - S Oswald
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - P Artursson
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
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176
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Nishiyama J. Genome editing in the mammalian brain using the CRISPR-Cas system. Neurosci Res 2018; 141:4-12. [PMID: 30076877 DOI: 10.1016/j.neures.2018.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/24/2022]
Abstract
Recent advances in genome editing technologies such as the clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease Cas9 have enabled the rapid and efficient modification of endogenous genomes in a variety of cell types, accelerating biomedical research. In particular, precise genome editing in somatic cells in vivo allows for the rapid generation of genetically modified cells in living animals and holds great promise for the possibility of directly correcting genetic defects associated with human diseases. However, because of the limited efficiency and suitability of these technologies in the brain, especially in postmitotic neurons, the practical application of genome editing technologies has been largely limited in the field of neuroscience. Recent technological advances overcome significant challenges facing genome editing in the brain and have enabled us to precisely edit the genome in both mitotic cells and mature postmitotic neurons in vitro and in vivo, providing powerful means for studying gene function and dysfunction in the brain. This review highlights the development of genome editing technologies for the brain and discusses their applications, limitations, and future challenges.
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Affiliation(s)
- Jun Nishiyama
- Max Planck Florida Institute for Neuroscience, One Max Planck Way, Jupiter, FL 33458, USA.
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177
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Roy B, Zhao J, Yang C, Luo W, Xiong T, Li Y, Fang X, Gao G, Singh CO, Madsen L, Zhou Y, Kristiansen K. CRISPR/Cascade 9-Mediated Genome Editing-Challenges and Opportunities. Front Genet 2018; 9:240. [PMID: 30026755 PMCID: PMC6042012 DOI: 10.3389/fgene.2018.00240] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/18/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and Cascade 9 (also known as Cas9, CRISPR associated protein 9) confer protection against invading viruses or plasmids. The CRISPR/Cascade 9 system constitutes one of the most powerful genome technologies available to researchers today. So far, this technology has enabled efficient genome editing and modification in several model organisms and has successfully been used in biomedicine and biomedical engineering. However, challenges for efficient and safe genetic manipulation in several organisms persist. Here, we review functional approaches and future challenges associated with the use of the CRISPR/Cascade 9 genome editing system and discuss opportunities, ethical issues and future directions within this field.
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Affiliation(s)
| | - Jing Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Chao Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wen Luo
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Teng Xiong
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Guanjun Gao
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Chabungbam O Singh
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Lise Madsen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Institute of Marine Research, Bergen, Norway
| | - Yong Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Karsten Kristiansen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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178
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New Turns for High Efficiency Knock-In of Large DNA in Human Pluripotent Stem Cells. Stem Cells Int 2018; 2018:9465028. [PMID: 30057628 PMCID: PMC6051061 DOI: 10.1155/2018/9465028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 04/22/2018] [Accepted: 05/13/2018] [Indexed: 12/26/2022] Open
Abstract
The groundbreaking CRISPR technology is revolutionizing biomedical research with its superior simplicity, high efficiency, and robust accuracy. Recent technological advances by a coupling CRISPR system with various DNA repair mechanisms have further opened up new opportunities to overcome existing challenges in knocking-in foreign DNA in human pluripotent stem cells, including embryonic stem cells (ESC) and induced pluripotent stem cells (iPSC). In this review, we summarized the very recent development of CRISPR-based knock-in strategies and discussed the results obtained as well as potential applications in human ESC and iPSC.
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179
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Floris M, Olla S, Schlessinger D, Cucca F. Genetic-Driven Druggable Target Identification and Validation. Trends Genet 2018; 34:558-570. [PMID: 29803319 PMCID: PMC6088790 DOI: 10.1016/j.tig.2018.04.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/13/2018] [Accepted: 04/23/2018] [Indexed: 12/19/2022]
Abstract
Choosing the right biological target is the critical primary decision for the development of new drugs. Systematic genetic association testing of both human diseases and quantitative traits, along with resultant findings of coincident associations between them, is becoming a powerful approach to infer drug targetable candidates and generate in vitro tests to identify compounds that can modulate them therapeutically. Here, we discuss opportunities and challenges, and infer criteria for the optimal use of genetic findings in the drug discovery pipeline.
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Affiliation(s)
- Matteo Floris
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy; IRGB-CNR, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Stefania Olla
- IRGB-CNR, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Francesco Cucca
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy; IRGB-CNR, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
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180
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He D, Zhang J, Wu W, Yi N, He W, Lu P, Li B, Yang N, Wang D, Xue Z, Zhang P, Fan G, Zhu X. A novel immunodeficient rat model supports human lung cancer xenografts. FASEB J 2018; 33:140-150. [PMID: 29944447 DOI: 10.1096/fj.201800102rr] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Patient-derived xenograft (PDX) animal models allow the exogenous growth of human tumors, offering an irreplaceable preclinical tool for oncology research. Mice are the most commonly used host for human PDX models, however their small body size limits the xenograft growth, sample collection, and drug evaluation. Therefore, we sought to develop a novel rat model that could overcome many of these limitations. We knocked out Rag1, Rag2, and Il2rg in Sprague Dawley (SD) rats by clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 technology. The development of lymphoid organs is significantly impaired in Rag1-/-Rag2-/-Il2rg-/Y (designated as SD-RG) rats. Consequently, SD-RG rats are severely immunodeficient with an absence of mature T, B, and NK cells in the immune system. After subcutaneous injection of tumor cell lines of different origin, such as NCI-H460, U-87MG, and MDA-MB-231, the tumors grow significantly faster and larger in SD-RG rats than in nonobese diabetic- Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice. Most important of all, we successfully established a PDX model of lung squamous cell carcinoma in which the grafts recapitulate the histopathologic features of the primary tumor for several passages. In conclusion, the severely immunodeficient SD-RG rats support fast growth of PDX compared with mice, thus holding great potential to serve as a new model for oncology research.-He, D., Zhang, J., Wu, W., Yi, N., He, W., Lu, P., Li, B., Yang, N., Wang, D., Xue, Z., Zhang, P., Fan, G., Zhu, X. A novel immunodeficient rat model supports human lung cancer xenografts.
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Affiliation(s)
- Di He
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Junhui Zhang
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Wanwan Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ning Yi
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Wen He
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Ping Lu
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Bin Li
- Alphacait AL Biotech Company, Hangzhou, China
| | - Nan Yang
- PharmaLegacy Laboratories Company, Shanghai, China; and
| | - Di Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhigang Xue
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University Suzhou Institute, Tongji University School of Medicine, Shanghai, China
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guoping Fan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Xianmin Zhu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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181
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Codner GF, Mianné J, Caulder A, Loeffler J, Fell R, King R, Allan AJ, Mackenzie M, Pike FJ, McCabe CV, Christou S, Joynson S, Hutchison M, Stewart ME, Kumar S, Simon MM, Agius L, Anstee QM, Volynski KE, Kullmann DM, Wells S, Teboul L. Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants. BMC Biol 2018; 16:70. [PMID: 29925374 PMCID: PMC6011369 DOI: 10.1186/s12915-018-0530-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/09/2018] [Indexed: 01/22/2023] Open
Abstract
Background Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing have led to the use of long single-stranded DNA (lssDNA) molecules for generating conditional mutations. However, there is still limited available data on the efficiency and reliability of this method. Results We generated conditional mouse alleles using lssDNA donor templates and performed extensive characterization of the resulting mutations. We observed that the use of lssDNA molecules as donors efficiently yielded founders bearing the conditional allele, with seven out of nine projects giving rise to modified alleles. However, rearranged alleles including nucleotide changes, indels, local rearrangements and additional integrations were also frequently generated by this method. Specifically, we found that alleles containing unexpected point mutations were found in three of the nine projects analyzed. Alleles originating from illegitimate repairs or partial integration of the donor were detected in eight projects. Furthermore, additional integrations of donor molecules were identified in four out of the seven projects analyzed by copy counting. This highlighted the requirement for a thorough allele validation by polymerase chain reaction, sequencing and copy counting of the mice generated through this method. We also demonstrated the feasibility of using lssDNA donors to generate thus far problematic point mutations distant from active CRISPR cutting sites by targeting two distinct genes (Gckr and Rims1). We propose a strategy to perform extensive quality control and validation of both types of mouse models generated using lssDNA donors. Conclusion lssDNA donors reproducibly generate conditional alleles and can be used to introduce point mutations away from CRISPR/Cas9 cutting sites in mice. However, our work demonstrates that thorough quality control of new models is essential prior to reliably experimenting with mice generated by this method. These advances in genome editing techniques shift the challenge of mutagenesis from generation to the validation of new mutant models. Electronic supplementary material The online version of this article (10.1186/s12915-018-0530-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma F Codner
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Joffrey Mianné
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Jorik Loeffler
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Rachel Fell
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Ruairidh King
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Alasdair J Allan
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Matthew Mackenzie
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Fran J Pike
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | | | | | - Sam Joynson
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Marie Hutchison
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | | | - Saumya Kumar
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Michelle M Simon
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Loranne Agius
- Institute of Cellular Medicine and Ageing and Health, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Quentin M Anstee
- Institute of Cellular Medicine and Ageing and Health, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Kirill E Volynski
- UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Dimitri M Kullmann
- UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK.
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182
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Lanza DG, Gaspero A, Lorenzo I, Liao L, Zheng P, Wang Y, Deng Y, Cheng C, Zhang C, Seavitt JR, DeMayo FJ, Xu J, Dickinson ME, Beaudet AL, Heaney JD. Comparative analysis of single-stranded DNA donors to generate conditional null mouse alleles. BMC Biol 2018; 16:69. [PMID: 29925370 PMCID: PMC6011517 DOI: 10.1186/s12915-018-0529-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/09/2018] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The International Mouse Phenotyping Consortium is generating null allele mice for every protein-coding gene in the genome and characterizing these mice to identify gene-phenotype associations. While CRISPR/Cas9-mediated null allele production in mice is highly efficient, generation of conditional alleles has proven to be more difficult. To test the feasibility of using CRISPR/Cas9 gene editing to generate conditional knockout mice for this large-scale resource, we employed Cas9-initiated homology-driven repair (HDR) with short and long single stranded oligodeoxynucleotides (ssODNs and lssDNAs). RESULTS Using pairs of single guide RNAs and short ssODNs to introduce loxP sites around a critical exon or exons, we obtained putative conditional allele founder mice, harboring both loxP sites, for 23 out of 30 targeted genes. LoxP sites integrated in cis in at least one mouse for 18 of 23 genes. However, loxP sites were mutagenized in 4 of the 18 in cis lines. HDR efficiency correlated with Cas9 cutting efficiency but was minimally influenced by ssODN homology arm symmetry. By contrast, using pairs of guides and single lssDNAs to introduce loxP-flanked exons, conditional allele founders were generated for all four genes targeted, although one founder was found to harbor undesired mutations within the lssDNA sequence interval. Importantly, when employing either ssODNs or lssDNAs, random integration events were detected. CONCLUSIONS Our studies demonstrate that Cas9-mediated HDR with pairs of ssODNs can generate conditional null alleles at many loci, but reveal inefficiencies when applied at scale. In contrast, lssDNAs are amenable to high-throughput production of conditional alleles when they can be employed. Regardless of the single-stranded donor utilized, it is essential to screen for sequence errors at sites of HDR and random insertion of donor sequences into the genome.
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Affiliation(s)
- Denise G Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Angelina Gaspero
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
| | - Isabel Lorenzo
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Lan Liao
- Department of Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
- Genetically Engineered Mouse Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Ping Zheng
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Ying Wang
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yu Deng
- Lester and Sue Smith Breast Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Chonghui Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
- Department of Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Chuansheng Zhang
- Department of Neuroscience, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
| | - Francesco J DeMayo
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Jianming Xu
- Department of Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
- Genetically Engineered Mouse Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA.
- Mouse ES Cell Core, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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183
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Wen W, Cheng X, Fu Y, Meng F, Zhang JP, Zhang L, Li XL, Yang Z, Xu J, Zhang F, Botimer GD, Yuan W, Sun C, Cheng T, Zhang XB. High-Level Precise Knockin of iPSCs by Simultaneous Reprogramming and Genome Editing of Human Peripheral Blood Mononuclear Cells. Stem Cell Reports 2018; 10:1821-1834. [PMID: 29754960 PMCID: PMC5989814 DOI: 10.1016/j.stemcr.2018.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/13/2022] Open
Abstract
We have developed an improved episomal vector system for efficient generation of integration-free induced pluripotent stem cells (iPSCs) from peripheral blood mononuclear cells. More recently, we reported that the use of an optimized CRISPR-Cas9 system together with a double-cut donor increases homology-directed repair-mediated precise gene knockin efficiency by 5- to 10-fold. Here, we report the integration of blood cell reprogramming and genome editing in a single step. We found that expression of Cas9 and KLF4 using a single vector significantly increases genome editing efficiency, and addition of SV40LT further enhances knockin efficiency. After these optimizations, genome editing efficiency of up to 40% in the bulk iPSC population can be achieved without any selection. Most of the edited cells show characteristics of iPSCs and genome integrity. Our improved approach, which integrates reprogramming and genome editing, should expedite both basic research and clinical applications of precision and regenerative medicine.
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Affiliation(s)
- Wei Wen
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Xinxin Cheng
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Yawen Fu
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Feiying Meng
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Jian-Ping Zhang
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Lu Zhang
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Xiao-Lan Li
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Zhixue Yang
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Jing Xu
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Gary D Botimer
- Department of Orthopaedic Surgery, Loma Linda University, Loma Linda, CA, USA
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, Tianjin, China
| | - Changkai Sun
- School of Biomedical Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China; Research Center for the Control Engineering of Translational Precision Medicine, Dalian University of Technology, Dalian 116024, China; State Key Laboratory of Fine Chemicals, Dalian R&D Center for Stem Cell and Tissue Engineering, Dalian University of Technology, Dalian 116024, China; Liaoning Provincial Key Laboratory of Cerebral Diseases, Institute for Brain Disorders, Dalian Medical University, Dalian 116044, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Tianjin, China; Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China; Collaborative Innovation Center for Cancer Medicine, Tianjin, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, Tianjin, China; Department of Medicine, Loma Linda University, Loma Linda, CA, USA.
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184
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Brinkman EK, Kousholt AN, Harmsen T, Leemans C, Chen T, Jonkers J, van Steensel B. Easy quantification of template-directed CRISPR/Cas9 editing. Nucleic Acids Res 2018; 46:e58. [PMID: 29538768 PMCID: PMC6007333 DOI: 10.1093/nar/gky164] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/13/2018] [Accepted: 02/22/2018] [Indexed: 11/21/2022] Open
Abstract
Template-directed CRISPR/Cas9 editing is a powerful tool for introducing subtle mutations in genomes. However, the success rate of incorporation of the desired mutations at the target site is difficult to predict and therefore must be empirically determined. Here, we adapted the widely used TIDE method for quantification of templated editing events, including point mutations. The resulting TIDER method is a rapid, cheap and accessible tool for testing and optimization of template-directed genome editing strategies. A free web tool for TIDER data analysis is available at http://tide.nki.nl.
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Affiliation(s)
- Eva K Brinkman
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Arne N Kousholt
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Tim Harmsen
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Christ Leemans
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Tao Chen
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
- Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
- Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
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185
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Chen Y, Spitzer S, Agathou S, Karadottir RT, Smith A. Gene Editing in Rat Embryonic Stem Cells to Produce In Vitro Models and In Vivo Reporters. Stem Cell Reports 2018; 9:1262-1274. [PMID: 29020614 PMCID: PMC5639479 DOI: 10.1016/j.stemcr.2017.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/13/2022] Open
Abstract
Rat embryonic stem cells (ESCs) offer the potential for sophisticated genome engineering in this valuable biomedical model species. However, germline transmission has been rare following conventional homologous recombination and clonal selection. Here, we used the CRISPR/Cas9 system to target genomic mutations and insertions. We first evaluated utility for directed mutagenesis and recovered clones with biallelic deletions in Lef1. Mutant cells exhibited reduced sensitivity to glycogen synthase kinase 3 inhibition during self-renewal. We then generated a non-disruptive knockin of dsRed at the Sox10 locus. Two clones produced germline chimeras. Comparative expression of dsRed and SOX10 validated the fidelity of the reporter. To illustrate utility, live imaging of dsRed in neonatal brain slices was employed to visualize oligodendrocyte lineage cells for patch-clamp recording. Overall, these results show that CRISPR/Cas9 gene editing technology in germline-competent rat ESCs is enabling for in vitro studies and for generating genetically modified rats. Gene mutation and homologous recombination in rat ESCs using CRISPR/Cas9 Lef1 mutants exhibit predicted loss of hypersensitivity to GSK3 inhibition Sox10 knockin rat provides a vital reporter of neural crest and oligodendroglia Sox10::dsRed facilitates patch-clamp recording from oligodendroglial lineage cells
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Affiliation(s)
- Yaoyao Chen
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Sonia Spitzer
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Sylvia Agathou
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Ragnhildur Thora Karadottir
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Austin Smith
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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186
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Miyasaka Y, Uno Y, Yoshimi K, Kunihiro Y, Yoshimura T, Tanaka T, Ishikubo H, Hiraoka Y, Takemoto N, Tanaka T, Ooguchi Y, Skehel P, Aida T, Takeda J, Mashimo T. CLICK: one-step generation of conditional knockout mice. BMC Genomics 2018; 19:318. [PMID: 29720086 PMCID: PMC5930688 DOI: 10.1186/s12864-018-4713-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/23/2018] [Indexed: 02/05/2023] Open
Abstract
Background CRISPR/Cas9 enables the targeting of genes in zygotes; however, efficient approaches to create loxP-flanked (floxed) alleles remain elusive. Results Here, we show that the electroporation of Cas9, two gRNAs, and long single-stranded DNA (lssDNA) into zygotes, termed CLICK (CRISPR with lssDNA inducing conditional knockout alleles), enables the quick generation of floxed alleles in mice and rats. Conclusions The high efficiency of CLICK provides homozygous knock-ins in oocytes carrying tissue-specific Cre, which allows the one-step generation of conditional knockouts in founder (F0) mice. Electronic supplementary material The online version of this article (10.1186/s12864-018-4713-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoshiki Miyasaka
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Yoshihiro Uno
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Kazuto Yoshimi
- Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.,Mouse Genomics Resource Laboratory, National Institute of Genetics, Shizuoka, 411-8540, Japan
| | - Yayoi Kunihiro
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Takuji Yoshimura
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Tomohiro Tanaka
- Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Harumi Ishikubo
- Laboratory of Recombinant Animals, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Chiyoda, Tokyo, 101-0062, Japan
| | - Yuichi Hiraoka
- Laboratory of Recombinant Animals, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Chiyoda, Tokyo, 101-0062, Japan.,Laboratory of Molecular Neuroscience, MRI, TMDU, Tokyo, 113-8510, Japan
| | - Norihiko Takemoto
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | | | | | - Paul Skehel
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Tomomi Aida
- Laboratory of Recombinant Animals, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Chiyoda, Tokyo, 101-0062, Japan.,Laboratory of Molecular Neuroscience, MRI, TMDU, Tokyo, 113-8510, Japan.,Present address: McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Junji Takeda
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Tomoji Mashimo
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan. .,Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
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187
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Kaneko T. Reproductive technologies for the generation and maintenance of valuable animal strains. J Reprod Dev 2018; 64:209-215. [PMID: 29657233 PMCID: PMC6021608 DOI: 10.1262/jrd.2018-035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many types of mutant and genetically engineered strains have been produced in various animal species. Their numbers have dramatically increased in recent years, with new strains being
rapidly produced using genome editing techniques. In the rat, it has been difficult to produce knockout and knock-in strains because the establishment of stem cells has been insufficient.
However, a large number of knockout and knock-in strains can currently be produced using genome editing techniques, including zinc-finger nuclease (ZFN), transcription activator-like
effector nuclease (TALEN), and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system. Microinjection technique has also
contributed widely to the production of various kinds of genome edited animal strains. A novel electroporation method, the “Technique for Animal Knockout system by Electroporation (TAKE)”
method, is a simple and highly efficient tool that has accelerated the production of new strains. Gamete preservation is extremely useful for maintaining large numbers of these valuable
strains as genetic resources in the long term. These reproductive technologies, including microinjection, TAKE method, and gamete preservation, strongly support biomedical research and the
bio-resource banking of animal models. In this review, we introduce the latest reproductive technologies used for the production of genetically engineered animals, especially rats, using
genome editing techniques and the efficient maintenance of valuable strains as genetic resources. These technologies can also be applied to other laboratory animals, including mice, and
domestic and wild animal species.
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Affiliation(s)
- Takehito Kaneko
- Division of Science and Engineering, Graduate School of Arts and Science, Iwate University, Iwate 020-8551, Japan.,Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate 020-8551, Japan.,Soft-Path Science and Engineering Research Center (SPERC), Iwate University, Iwate 020-8551, Japan
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188
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Jang DE, Lee JY, Lee JH, Koo OJ, Bae HS, Jung MH, Bae JH, Hwang WS, Chang YJ, Lee YH, Lee HW, Yeom SC. Multiple sgRNAs with overlapping sequences enhance CRISPR/Cas9-mediated knock-in efficiency. Exp Mol Med 2018; 50:1-9. [PMID: 29622782 PMCID: PMC5938013 DOI: 10.1038/s12276-018-0037-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/05/2017] [Accepted: 12/08/2017] [Indexed: 12/13/2022] Open
Abstract
The CRISPR/Cas9 system is widely applied in genome engineering due to its simplicity and versatility. Although this has revolutionized genome-editing technology, knockin animal generation via homology directed repair (HDR) is not as efficient as nonhomologous end-joining DNA-repair-dependent knockout. Although its double-strand break activity may vary, Cas9 derived from Streptococcus pyogenens allows robust design of single-guide RNAs (sgRNAs) within the target sequence; However, prescreening for different sgRNA activities delays the process of transgenic animal generation. To overcome this limitation, multiple sets of different sgRNAs were examined for their knockin efficiency. We discovered profound advantages associated with single-stranded oligo-donor-mediated HDR processes using overlapping sgRNAs (sharing at least five base pairs of the target sites) as compared with using non-overlapping sgRNAs for knock-in mouse generation. Studies utilizing cell lines revealed shorter sequence deletions near target mutations using overlapping sgRNAs as compared with those observed using non-overlapping sgRNAs, which may favor the HDR process. Using this simple method, we successfully generated several transgenic mouse lines harboring loxP insertions or single-nucleotide substitutions with a highly efficiency of 18-38%. Our results demonstrate a simple and efficient method for generating transgenic animals harboring foreign-sequence knockins or short-nucleotide substitutions by the use of overlapping sgRNAs.
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Affiliation(s)
- Da Eun Jang
- Graduate School of International Agricultural Technology, Seoul National University, 1447 Pyeongchang-Ro, Daewha, Pyeongchang, Kangwon, 25354, Korea
| | - Jae Young Lee
- Toolgen Inc., Gasan Digital-Ro, Geumcheon, Seoul, 08594, Korea
| | - Jae Hoon Lee
- Department of Biochemistry, College of Life Science and Biotechnology, and Yonsei Laboratory Animal Research Center, Yonsei University, Seoul, 03722, Korea
| | - Ok Jae Koo
- Toolgen Inc., Gasan Digital-Ro, Geumcheon, Seoul, 08594, Korea
| | - Hee Sook Bae
- Toolgen Inc., Gasan Digital-Ro, Geumcheon, Seoul, 08594, Korea
| | - Min Hee Jung
- Toolgen Inc., Gasan Digital-Ro, Geumcheon, Seoul, 08594, Korea
| | - Ji Hyun Bae
- Graduate School of International Agricultural Technology, Seoul National University, 1447 Pyeongchang-Ro, Daewha, Pyeongchang, Kangwon, 25354, Korea
| | - Woo Sung Hwang
- Designed Animal and Transplantation Research Institute, Greenbio Research and Technology, Seoul National University, 1447 Pyeongchang-Ro, Daewha, Pyeongchang, Gangwon, 25354, Korea
| | - Yoo Jin Chang
- Graduate School of International Agricultural Technology, Seoul National University, 1447 Pyeongchang-Ro, Daewha, Pyeongchang, Kangwon, 25354, Korea
| | - Yoon Hoo Lee
- Graduate School of International Agricultural Technology, Seoul National University, 1447 Pyeongchang-Ro, Daewha, Pyeongchang, Kangwon, 25354, Korea
| | - Han Woong Lee
- Department of Biochemistry, College of Life Science and Biotechnology, and Yonsei Laboratory Animal Research Center, Yonsei University, Seoul, 03722, Korea.
| | - Su Cheong Yeom
- Graduate School of International Agricultural Technology, Seoul National University, 1447 Pyeongchang-Ro, Daewha, Pyeongchang, Kangwon, 25354, Korea.
- Designed Animal and Transplantation Research Institute, Greenbio Research and Technology, Seoul National University, 1447 Pyeongchang-Ro, Daewha, Pyeongchang, Gangwon, 25354, Korea.
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189
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Kobayashi T, Namba M, Koyano T, Fukushima M, Sato M, Ohtsuka M, Matsuyama M. Successful production of genome-edited rats by the rGONAD method. BMC Biotechnol 2018; 18:19. [PMID: 29606116 PMCID: PMC5879918 DOI: 10.1186/s12896-018-0430-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Recent progress in development of the CRISPR/Cas9 system has been shown to be an efficient gene-editing technology in various organisms. We recently developed a novel method called Genome-editing via Oviductal Nucleic Acids Delivery (GONAD) in mice; a novel in vivo genome editing system that does not require ex vivo handling of embryos, and this technology is newly developed and renamed as "improved GONAD" (i-GONAD). However, this technology has been limited only to mice. Therefore in this study, we challenge to apply this technology to rats. RESULTS Here, we determine the most suitable condition for in vivo gene delivery towards rat preimplantation embryos using tetramethylrhodamine-labelled dextran, termed as Rat improved GONAD (rGONAD). Then, to investigate whether this method is feasible to generate genome-edited rats by delivery of CRISPR/Cas9 components, the tyrosinase (Tyr) gene was used as a target. Some pups showed albino-colored coat, indicating disruption of wild-type Tyr gene allele. Furthermore, we confirm that rGONAD method can be used to introduce genetic changes in rat genome by the ssODN-based knock-in. CONCLUSIONS We first establish the rGONAD method for generating genome-edited rats. We demonstrate high efficiency of the rGONAD method to produce knock-out and knock-in rats, which will facilitate the production of rat genome engineering experiment. The rGONAD method can also be readily applicable in mammals such as guinea pig, hamster, cow, pig, and other mammals.
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Affiliation(s)
- Tomoe Kobayashi
- Division of Molecular Genetics, Shigei Medical Research Institute, 2117 Yamada, Minami-ku, Okayama 701-0202 Japan
| | - Masumi Namba
- Division of Molecular Genetics, Shigei Medical Research Institute, 2117 Yamada, Minami-ku, Okayama 701-0202 Japan
| | - Takayuki Koyano
- Division of Molecular Genetics, Shigei Medical Research Institute, 2117 Yamada, Minami-ku, Okayama 701-0202 Japan
| | - Masaki Fukushima
- Division of Molecular Genetics, Shigei Medical Research Institute, 2117 Yamada, Minami-ku, Okayama 701-0202 Japan
- Shigei Medical Research Hospital, Minami-ku, Okayama 701-0202 Japan
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, Kagoshima, Kagoshima 890-8544 Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa 259-1193 Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa 259-1193 Japan
- The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Makoto Matsuyama
- Division of Molecular Genetics, Shigei Medical Research Institute, 2117 Yamada, Minami-ku, Okayama 701-0202 Japan
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190
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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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191
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Abstract
Knock-in mice are useful for evaluating endogenous gene expressions and functions in vivo. Instead of the conventional gene-targeting method using embryonic stem cells, an exogenous DNA sequence can be inserted into the target locus in the zygote using genome editing technology. In this chapter, I describe the generation of epitope-tagged mice using engineered endonuclease and single-stranded oligodeoxynucleotide through the mouse zygote as an example of how to generate a knock-in mouse by genome editing.
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Affiliation(s)
- Wataru Fujii
- Laboratory of Applied Genetics, Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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192
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Abstract
Tumor suppressor genes play critical roles orchestrating anti-cancer programs that are both context dependent and mechanistically diverse. Beyond canonical tumor suppressive programs that control cell division, cell death, and genome stability, unexpected tumor suppressor gene activities that regulate metabolism, immune surveillance, the epigenetic landscape, and others have recently emerged. This diversity underscores the important roles these genes play in maintaining cellular homeostasis to suppress cancer initiation and progression, but also highlights a tremendous challenge in discerning precise context-specific programs of tumor suppression controlled by a given tumor suppressor. Fortunately, the rapid sophistication of genetically engineered mouse models of cancer has begun to shed light on these context-dependent tumor suppressor activities. By using techniques that not only toggle "off" tumor suppressor genes in nascent tumors, but also facilitate the timely restoration of gene function "back-on again" in disease specific contexts, precise mechanisms of tumor suppression can be revealed in an unbiased manner. This review discusses the development and implementation of genetic systems designed to toggle tumor suppressor genes off and back-on again and their potential to uncover the tumor suppressor's tale.
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Affiliation(s)
- Jonuelle Acosta
- Biomedical Graduate Studies Program in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA
| | - Walter Wang
- Vagelos Scholars Program, School of Arts and Sciences, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA
| | - David M Feldser
- Biomedical Graduate Studies Program in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA. .,Department of Cancer Biology, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA. .,Abramson Family Cancer Research Institute, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA.
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193
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Ahmad G, Amiji M. Use of CRISPR/Cas9 gene-editing tools for developing models in drug discovery. Drug Discov Today 2018; 23:519-533. [DOI: 10.1016/j.drudis.2018.01.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 11/09/2017] [Accepted: 01/04/2018] [Indexed: 12/20/2022]
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194
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Efficient Recreation of t(11;22) EWSR1-FLI1 + in Human Stem Cells Using CRISPR/Cas9. Stem Cell Reports 2018; 8:1408-1420. [PMID: 28494941 PMCID: PMC5425785 DOI: 10.1016/j.stemcr.2017.04.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/12/2017] [Accepted: 04/12/2017] [Indexed: 12/21/2022] Open
Abstract
Efficient methodologies for recreating cancer-associated chromosome translocations are in high demand as tools for investigating how such events initiate cancer. The CRISPR/Cas9 system has been used to reconstruct the genetics of these complex rearrangements at native loci while maintaining the architecture and regulatory elements. However, the CRISPR system remains inefficient in human stem cells. Here, we compared three strategies aimed at enhancing the efficiency of the CRISPR-mediated t(11;22) translocation in human stem cells, including mesenchymal and induced pluripotent stem cells: (1) using end-joining DNA processing factors involved in repair mechanisms, or (2) ssODNs to guide the ligation of the double-strand break ends generated by CRISPR/Cas9; and (3) all-in-one plasmid or ribonucleoprotein complex-based approaches. We report that the generation of targeted t(11;22) is significantly increased by using a combination of ribonucleoprotein complexes and ssODNs. The CRISPR/Cas9-mediated generation of targeted t(11;22) in human stem cells opens up new avenues in modeling Ewing sarcoma.
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195
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Feng W, Liu HK, Kawauchi D. CRISPR-engineered genome editing for the next generation neurological disease modeling. Prog Neuropsychopharmacol Biol Psychiatry 2018; 81:459-467. [PMID: 28536069 DOI: 10.1016/j.pnpbp.2017.05.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/25/2017] [Accepted: 05/19/2017] [Indexed: 12/25/2022]
Abstract
Neurological disorders often occur because of failure of proper brain development and/or appropriate maintenance of neuronal circuits. In order to understand roles of causative factors (e.g. genes, cell types) in disease development, generation of solid animal models has been one of straight-forward approaches. Recent next generation sequencing studies on human patient-derived clinical samples have identified various types of recurrent mutations in individual neurological diseases. While these discoveries have prompted us to evaluate impact of mutated genes on these neurological diseases, a feasible but flexible genome editing tool had remained to be developed. An advance of genome editing technology using the clustered regularly interspaced short palindromic repeats (CRISPR) with the CRISPR-associated protein (Cas) offers us a tremendous potential to create a variety of mutations in the cell, leading to "next generation" disease models carrying disease-associated mutations. We will here review recent progress of CRISPR-based brain disease modeling studies and discuss future requirement to tackle current difficulties in usage of these technologies.
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Affiliation(s)
- Weijun Feng
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Hai-Kun Liu
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Daisuke Kawauchi
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
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196
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Miura H, Quadros RM, Gurumurthy CB, Ohtsuka M. Easi-CRISPR for creating knock-in and conditional knockout mouse models using long ssDNA donors. Nat Protoc 2018; 13:195-215. [PMID: 29266098 PMCID: PMC6058056 DOI: 10.1038/nprot.2017.153] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
CRISPR/Cas9-based genome editing can easily generate knockout mouse models by disrupting the gene sequence, but its efficiency for creating models that require either insertion of exogenous DNA (knock-in) or replacement of genomic segments is very poor. The majority of mouse models used in research involve knock-in (reporters or recombinases) or gene replacement (e.g., conditional knockout alleles containing exons flanked by LoxP sites). A few methods for creating such models have been reported that use double-stranded DNA as donors, but their efficiency is typically 1-10% and therefore not suitable for routine use. We recently demonstrated that long single-stranded DNAs (ssDNAs) serve as very efficient donors, both for insertion and for gene replacement. We call this method efficient additions with ssDNA inserts-CRISPR (Easi-CRISPR) because it is a highly efficient technology (efficiency is typically 30-60% and reaches as high as 100% in some cases). The protocol takes ∼2 months to generate the founder mice.
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Affiliation(s)
- Hiromi Miura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of
Medicine, Tokai University, Kanagawa 259-1193, Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa 259-1193,
Japan
| | - Rolen M. Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical
Center, Omaha, NE, USA
| | - Channabasavaiah B. Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical
Center, Omaha, NE, USA
- Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska
Medical Center, Omaha, NE, USA
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of
Medicine, Tokai University, Kanagawa 259-1193, Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Kanagawa 259-1193,
Japan
- The Institute of Medical Sciences, Tokai University, Kanagawa 259-1193, Japan
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197
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Krieg E, Shih WM. Selective Nascent Polymer Catch-and-Release Enables Scalable Isolation of Multi-Kilobase Single-Stranded DNA. Angew Chem Int Ed Engl 2017; 57:714-718. [PMID: 29210156 DOI: 10.1002/anie.201710469] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 11/06/2022]
Abstract
Scalable methods currently are lacking for isolation of long ssDNA, an important material for numerous biotechnological applications. Conventional biomolecule purification strategies achieve target capture using solid supports, which are limited in scale and susceptible to contamination owing to nonspecific adsorption and desorption on the substrate surface. We herein disclose selective nascent polymer catch and release (SNAPCAR), a method that utilizes the reactivity of growing poly(acrylamide-co-acrylate) chains to capture acrylamide-labeled molecules in free solution. The copolymer acts as a stimuli-responsive anchor that can be precipitated on demand to pull down the target from solution. SNAPCAR enabled scalable isolation of multi-kilobase ssDNA with high purity and 50-70 % yield. The ssDNA products were used to fold various DNA origami. SNAPCAR-produced ssDNA will expand the scope of applications in nanotechnology, gene editing, and DNA library construction.
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Affiliation(s)
- Elisha Krieg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Wyss Institute for Biologically Inspired Engineering at Harvard University, Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - William M Shih
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Wyss Institute for Biologically Inspired Engineering at Harvard University, Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
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198
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Krieg E, Shih WM. Selective Nascent Polymer Catch‐and‐Release Enables Scalable Isolation of Multi‐Kilobase Single‐Stranded DNA. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elisha Krieg
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School, Wyss Institute for Biologically Inspired Engineering at Harvard University Department of Cancer Biology, Dana-Farber Cancer Institute 450 Brookline Ave Boston MA 02215 USA
| | - William M. Shih
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School, Wyss Institute for Biologically Inspired Engineering at Harvard University Department of Cancer Biology, Dana-Farber Cancer Institute 450 Brookline Ave Boston MA 02215 USA
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199
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Lee HJ, Lee KY, Jung KM, Park KJ, Lee KO, Suh JY, Yao Y, Nair V, Han JY. Precise gene editing of chicken Na+/H+ exchange type 1 (chNHE1) confers resistance to avian leukosis virus subgroup J (ALV-J). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:340-349. [PMID: 28899753 DOI: 10.1016/j.dci.2017.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 09/08/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
Avian leukosis virus subgroup J (ALV-J), first isolated in the late 1980s, has caused economic losses to the poultry industry in many countries. As all chicken lines studied to date are susceptible to ALV infection, there is enormous interest in developing resistant chicken lines. The ALV-J receptor, chicken Na+/H+ exchange 1 (chNHE1) and the critical amino acid sequences involved in viral attachment and entry have already been characterized. However, there are no reported attempts to induce resistance to the virus by targeted genome modification of the receptor sequences. In an attempt to induce resistance to ALV-J infection, we used clustered regularly interspaced short palindromic repeats (CRISPR)-associated (CRISPR/Cas9)-based genome editing approaches to modify critical residues of the chNHE1 receptor in chicken cells. The susceptibility of the modified cell lines to ALV-J infection was examined using enhanced green fluorescent protein (EGFP)-expressing marker viruses. We showed that modifying the chNHE1 receptor by artificially generating a premature stop codon induced absolute resistance to viral infection, with mutations of the tryptophan residue at position 38 (Trp38) being very critical. Single-stranded oligodeoxynucleotide (ssODN)-mediated targeted recombination of the Trp38 region revealed that deletions involving the Trp38 residue were most effective in conferring resistance to ALV-J. Moreover, protein structure analysis of the chNHE1 receptor sequence suggested that its intrinsically disordered region undergoes local conformational changes through genetic alteration. Collectively, these results demonstrate that targeted mutations on chNHE1 alter the susceptibility to ALV-J and the technique is expected to contribute to develop disease-resistant chicken lines.
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Affiliation(s)
- Hong Jo Lee
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea.
| | - Kyung Youn Lee
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea.
| | - Kyung Min Jung
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea.
| | - Kyung Je Park
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea.
| | - Ko On Lee
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea.
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea; Institute for Biomedical Sciences, Shinshu University, Nagano, Japan.
| | - Yongxiu Yao
- The Pirbright Institute, Woking, Surrey GU24 0NF, United Kingdom.
| | - Venugopal Nair
- The Pirbright Institute, Woking, Surrey GU24 0NF, United Kingdom.
| | - Jae Yong Han
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea; Institute for Biomedical Sciences, Shinshu University, Nagano, Japan.
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200
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Remy S, Chenouard V, Tesson L, Usal C, Ménoret S, Brusselle L, Heslan JM, Nguyen TH, Bellien J, Merot J, De Cian A, Giovannangeli C, Concordet JP, Anegon I. Generation of gene-edited rats by delivery of CRISPR/Cas9 protein and donor DNA into intact zygotes using electroporation. Sci Rep 2017; 7:16554. [PMID: 29185448 PMCID: PMC5707420 DOI: 10.1038/s41598-017-16328-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/06/2017] [Indexed: 02/05/2023] Open
Abstract
The generation of gene-edited animals using the CRISPRs/Cas9 system is based on microinjection into zygotes which is inefficient, time consuming and demands high technical skills. We report the optimization of an electroporation method for intact rat zygotes using sgRNAs and Cas9 protein in combination or not with ssODNs (~100 nt). This resulted in high frequency of knockouts, between 15 and 50% of analyzed animals. Importantly, using ssODNs as donor template resulted in precise knock-in mutations in 25–100% of analyzed animals, comparable to microinjection. Electroporation of long ssDNA or dsDNA donors successfully used in microinjection in the past did not allow generation of genome-edited animals despite dsDNA visualization within zygotes. Thus, simultaneous electroporation of a large number of intact rat zygotes is a rapid, simple, and efficient method for the generation of a variety of genome-edited rats.
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Affiliation(s)
- Séverine Remy
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France. .,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France. .,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France.
| | - Vanessa Chenouard
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Laurent Tesson
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Claire Usal
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Séverine Ménoret
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Lucas Brusselle
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Jean-Marie Heslan
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France.,Platform GenoCellEdit, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | - Tuan Huan Nguyen
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France.,Platform GenoCellEdit, INSERM UMR 1064-CRTI, F44093, Nantes, France
| | | | - Jean Merot
- Institut du thorax, INSERM UMR 1087, CNRS UMR 6291, F44007, Nantes, France
| | - Anne De Cian
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005, Paris, France
| | - Carine Giovannangeli
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005, Paris, France
| | - Jean-Paul Concordet
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005, Paris, France
| | - Ignacio Anegon
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France. .,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France. .,Platform Transgenic Rats and ImmunoPhenomics, INSERM UMR 1064-CRTI, F44093, Nantes, France.
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