1
|
Clark T, Waller MA, Loo L, Moreno CL, Denes CE, Neely GG. CRISPR activation screens: navigating technologies and applications. Trends Biotechnol 2024:S0167-7799(24)00036-2. [PMID: 38493051 DOI: 10.1016/j.tibtech.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) activation (CRISPRa) has become an integral part of the molecular biology toolkit. CRISPRa genetic screens are an exciting high-throughput means of identifying genes the upregulation of which is sufficient to elicit a given phenotype. Activation machinery is continually under development to achieve greater, more robust, and more consistent activation. In this review, we offer a succinct technological overview of available CRISPRa architectures and a comprehensive summary of pooled CRISPRa screens. Furthermore, we discuss contemporary applications of CRISPRa across broad fields of research, with the aim of presenting a view of exciting emerging applications for CRISPRa screening.
Collapse
Affiliation(s)
- Teleri Clark
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Matthew A Waller
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Lipin Loo
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Cesar L Moreno
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Christopher E Denes
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - G Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia.
| |
Collapse
|
2
|
Matsuzaki S, Sakuma T, Yamamoto T. REMOVER-PITCh: microhomology-assisted long-range gene replacement with highly multiplexed CRISPR-Cas9. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00850-1. [PMID: 38334880 DOI: 10.1007/s11626-024-00850-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024]
Abstract
A variety of CRISPR-Cas9-based gene editing technologies have been developed, including gene insertion and gene replacement, and applied to the study and treatment of diseases. While numerous studies have been conducted to improve the efficiency of gene insertion and to expand the system in various ways, there have been relatively few reports on gene replacement technology; therefore, further improvements are still needed in this context. Here, we developed the REMOVER-PITCh system to establish an efficient long-range gene replacement method and demonstrated its utility at two genomic loci in human cultured cells. REMOVER-PITCh depends on microhomology-assisted gene insertion technology called PITCh with highly multiplexed CRISPR-Cas9. First, we achieved gene replacement of about 20-kb GUSB locus using this system. Second, by applying the previously established knock-in-enhancing platform, the LoAD system, along with REMOVER-PITCh, we achieved the replacement of a longer gene region of about 200 kb at the ARSB locus. Our REMOVER-PITCh system will make it possible to remove and incorporate a variety of sequences from and into the genome, respectively, which will facilitate the generation of various disease and humanized models.
Collapse
Affiliation(s)
- Shu Matsuzaki
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- Drug Discovery Laboratory, Wakunaga Pharmaceutical Co., Ltd., 1624 Shimokotachi, Koda-Cho, Akitakata-Shi, Hiroshima, 739-1195, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| |
Collapse
|
3
|
Bruter AV, Varlamova EA, Okulova YD, Tatarskiy VV, Silaeva YY, Filatov MA. Genetically modified mice as a tool for the study of human diseases. Mol Biol Rep 2024; 51:135. [PMID: 38236499 DOI: 10.1007/s11033-023-09066-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/23/2023] [Indexed: 01/19/2024]
Abstract
Modeling a human disease is an essential part of biomedical research. The recent advances in the field of molecular genetics made it possible to obtain genetically modified animals for the study of various diseases. Not only monogenic disorders but also chromosomal and multifactorial disorders can be mimicked in lab animals due to genetic modification. Even human infectious diseases can be studied in genetically modified animals. An animal model of a disease enables the tracking of its pathogenesis and, more importantly, to test new therapies. In the first part of this paper, we review the most common DNA modification technologies and provide key ideas on specific technology choices according to the task at hand. In the second part, we focus on the application of genetically modified mice in studying human diseases.
Collapse
Affiliation(s)
- Alexandra V Bruter
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334
- Federal State Budgetary Institution "National Medical Research Center of Oncology Named After N.N. Blokhin" of the Ministry of Health of the Russian Federation, Research Institute of Carcinogenesis, Moscow, Russia, 115478
| | - Ekaterina A Varlamova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334
- Federal State Budgetary Institution "National Medical Research Center of Oncology Named After N.N. Blokhin" of the Ministry of Health of the Russian Federation, Research Institute of Carcinogenesis, Moscow, Russia, 115478
| | - Yulia D Okulova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334
| | - Victor V Tatarskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334
| | - Yulia Y Silaeva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334
| | - Maxim A Filatov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, 119334.
| |
Collapse
|
4
|
Liu C, Yue Y, Xue Y, Zhou C, Ma Y. CRISPR-Cas9 assisted non-homologous end joining genome editing system of Halomonas bluephagenesis for large DNA fragment deletion. Microb Cell Fact 2023; 22:211. [PMID: 37838676 PMCID: PMC10576340 DOI: 10.1186/s12934-023-02214-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Halophiles possess several unique properties and have broad biotechnological applications including industrial biotechnology production. Halomonas spp., especially Halomonas bluephagenesis, have been engineered to produce various biopolyesters such as polyhydroxyalkanoates (PHA), some proteins, small molecular compounds, organic acids, and has the potential to become a chassis cell for the next-generation of industrial biotechnology (NGIB) owing to its simple culture, fast growth, contamination-resistant, low production cost, and high production value. An efficient genome editing system is the key for its engineering and application. However, the efficiency of the established CRISPR-Cas-homologous recombination (HR) gene editing tool for large DNA fragments was still relatively low. In this study, we firstly report a CRISPR-Cas9 gene editing system combined with a non-homologous end joining (NHEJ) repair system for efficient large DNA fragment deletion in Halomonas bluephagenesis. RESULTS Three different NHEJ repair systems were selected and functionally identified in Halomonas bluephagenesis TD01. The NHEJ system from M. tuberculosis H37Rv (Mt-NHEJ) can functionally work in H. bluephagenesis TD01, resulting in base deletion of different lengths for different genes and some random base insertions. Factors affecting knockout efficiencies, such as the number and position of sgRNAs on the DNA double-strands, the Cas9 protein promoter, and the interaction between the HR and the NHEJ repair system, were further investigated. Finally, the optimized CRISPR-Cas9-NHEJ editing system was able to delete DNA fragments up to 50 kb rapidly with high efficiency of 31.3%, when three sgRNAs on the Crick/Watson/Watson DNA double-strands and the arabinose-induced promoter Para for Cas9 were used, along with the background expression of the HR repair system. CONCLUSIONS This was the first report of CRISPR-Cas9 gene editing system combined with a non-homologous end joining (NHEJ) repair system for efficient large DNA fragment deletion in Halomonas spp. These results not only suggest that this editing system is a powerful genome engineering tool for constructing chassis cells in Halomonas, but also extend the application of the NHEJ repair system.
Collapse
Affiliation(s)
- Chunyan Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaxin Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cheng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China.
- Beijing Key Laboratory for Utilization of Biomass Wastes, Beijing, 100023, China.
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
5
|
Sugiyama Y, Harada T, Kamei Y, Yasuda T, Mashimo T, Nishikimi A, Maruyama M. A senolytic immunotoxin eliminates p16 INK4a-positive T cells and ameliorates age-associated phenotypes of CD4 + T cells in a surface marker knock-in mouse. Exp Gerontol 2023; 174:112130. [PMID: 36822486 DOI: 10.1016/j.exger.2023.112130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/29/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
Senescent cells were recently shown to play a role in aging-related malfunctions and pathologies. This consensus has been facilitated by evidence from senolytic model mice capable of eliminating senescent cells in tissues using well-characterized senescent markers, such as p16INK4a (hereafter p16). However, since the incomplete or artificial gene expression regulatory regions of manipulated marker genes affect their cognate expression, it currently remains unclear whether these models accurately reflect physiological senescence. We herein describe a novel approach to eliminate p16-expressing cells from mice at any given point in time, generating a new type of knock-in model, p16hCD2 mice and a toxin-conjugated anti-human CD2 antibody (hCD2-SAP) as an inducer. p16hCD2 mice possess an intact Cdkn2a locus that includes a p16 coding region and human CD2 (hCD2) expression unit. We confirmed cognate p16-associated hCD2 expression in mouse embryonic fibroblasts (MEFs) and in several tissues, such as the spleen, liver, and skin. We detected chronological increases in the hCD2-positive population in T lymphocytes that occurred in a p16-dependent manner, which reflected physiological aging. We then confirmed the high sensitivity of hCD2-SAP to hCD2 and validated its efficacy to remove p16-positive cells, particularly in T lymphocytes. The multiple administration of hCD2-SAP for a prolonged p16-positive cell deficiency partially restored aging-related phenotypes in T lymphocytes, such as the contraction of the CD4+ naïve population and expansion of senescence-associated T cells. Our novel approach of targeting p16-positive senescent cells will provide novel insights into the mechanisms underlying physiological aging in vivo.
Collapse
Affiliation(s)
- Yuma Sugiyama
- Department of Inflammation and Immunosenescence, Geroscience Research Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Tanenobu Harada
- Department of Inflammation and Immunosenescence, Geroscience Research Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Yuka Kamei
- Department of Inflammation and Immunosenescence, Geroscience Research Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Tomoharu Yasuda
- Department of Immunology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Tomoji Mashimo
- Laboratory Animal Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Akihiko Nishikimi
- Biosafety Division, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan.
| | - Mitsuo Maruyama
- Department of Inflammation and Immunosenescence, Geroscience Research Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan; Department of Aging Research, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| |
Collapse
|
6
|
Matsushita N, Kato S, Nishizawa K, Sugawara M, Takeuchi K, Miyasaka Y, Mashimo T, Kobayashi K. Highly selective transgene expression through the flip-excision switch system by using a unilateral spacer sequence. CELL REPORTS METHODS 2023; 3:100393. [PMID: 36936079 PMCID: PMC10014282 DOI: 10.1016/j.crmeth.2022.100393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 11/09/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023]
Abstract
The flip-excision switch (FLEX) system with an adeno-associated viral (AAV) vector allows expression of transgenes in specific cell populations having Cre recombinase. A significant issue with this system is non-specific expression of transgenes in tissues after vector injection. We show here that Cre-independent recombination events in the AAV genome carrying the FLEX sequence occur mainly during the production of viral vectors in packaging cells, which results in transgene expression in off-target populations. Introduction of a relatively longer nucleotide sequence between two recognition sites at the unilateral side of the transgene cassette, termed a unilateral spacer sequence (USS), is useful to suppress the recombination in the viral genome, leading to the protection of non-specific transgene expression with enhanced gene expression selectivity. Our FLEX/USS system offers a powerful strategy for highly specific Cre-dependent transgene expression, aiming at various applications for structural and functional analyses of target cell populations.
Collapse
Affiliation(s)
- Natsuki Matsushita
- Division of Laboratory Animal Research, Aichi Medical University School of Medicine, Nagakute, Aichi 480-1195, Japan
| | - Shigeki Kato
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kayo Nishizawa
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Masateru Sugawara
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kosei Takeuchi
- Department of Medical Cell Biology, Aichi Medical University School of Medicine, Nagakute, Aichi 480-1195, Japan
| | - Yoshiki Miyasaka
- Laboratory of Reproductive Engineering, Institute of Experimental Animal Sciences, Osaka University Medical School, Suita 565-0871, Japan
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuto Kobayashi
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| |
Collapse
|
7
|
A novel technique for large-fragment knock-in animal production without ex vivo handling of zygotes. Sci Rep 2023; 13:2245. [PMID: 36755180 PMCID: PMC9908863 DOI: 10.1038/s41598-023-29468-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
CRISPR/Cas-based genome editing has dramatically improved genetic modification technology. In situ electroporation called genome editing via oviductal nucleic acid delivery (GONAD), which eliminates the need for ex vivo embryo handling, is technically the simplest method for gene transfer and can be performed in laboratories without developmental engineering expertise including micromanipulation techniques. However, the use of this method remains challenging in the case of large-fragment knock-in, such as gene expression cassettes. Adeno-associated viruses (AAV) act as donor DNA for homologous recombination in infected cells, including rodent embryos. In this study, we demonstrated simultaneous electroporation of AAV donors and CRISPR/Cas9 components into embryos to create knock-in animals, and successfully generated knock-in rats carrying a gene cassette with a length of 3.0 kb using a small number of animals and in situ electroporation. These findings indicate that this technique is an efficient high-throughput strategy for producing genetically modified rodents and may be applicable to other animal species.
Collapse
|
8
|
Shakirova A, Karpov T, Komarova Y, Lepik K. In search of an ideal template for therapeutic genome editing: A review of current developments for structure optimization. Front Genome Ed 2023; 5:1068637. [PMID: 36911237 PMCID: PMC9992834 DOI: 10.3389/fgeed.2023.1068637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
Gene therapy is a fast developing field of medicine with hundreds of ongoing early-stage clinical trials and numerous preclinical studies. Genome editing (GE) now is an increasingly important technology for achieving stable therapeutic effect in gene correction, with hematopoietic cells representing a key target cell population for developing novel treatments for a number of hereditary diseases, infections and cancer. By introducing a double strand break (DSB) in the defined locus of genomic DNA, GE tools allow to knockout the desired gene or to knock-in the therapeutic gene if provided with an appropriate repair template. Currently, the efficiency of methods for GE-mediated knock-in is limited. Significant efforts were focused on improving the parameters and interaction of GE nuclease proteins. However, emerging data suggests that optimal characteristics of repair templates may play an important role in the knock-in mechanisms. While viral vectors with notable example of AAVs as a donor template carrier remain the mainstay in many preclinical trials, non-viral templates, including plasmid and linear dsDNA, long ssDNA templates, single and double-stranded ODNs, represent a promising alternative. Furthermore, tuning of editing conditions for the chosen template as well as its structure, length, sequence optimization, homology arm (HA) modifications may have paramount importance for achieving highly efficient knock-in with favorable safety profile. This review outlines the current developments in optimization of templates for the GE mediated therapeutic gene correction.
Collapse
Affiliation(s)
- Alena Shakirova
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| | - Timofey Karpov
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia.,Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Yaroslava Komarova
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| | - Kirill Lepik
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| |
Collapse
|
9
|
Xing D, Li S, Shang M, Wang W, Zhang Q, Wang J, Hasin T, Hettiarachchi D, Alston V, Bern L, Parrales AP, Lu C, Coogan M, Johnson A, Qin Z, Su B, Dunham R. A New Strategy for Increasing Knock-in Efficiency: Multiple Elongase and Desaturase Transgenes Knock-in by Targeting Long Repeated Sequences. ACS Synth Biol 2022; 11:4210-4219. [PMID: 36332126 DOI: 10.1021/acssynbio.2c00252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CRISPR/Cas9-mediated knock-in (KI) has a wide application in gene therapy, gene function study, and transgenic breeding programs. Unlike gene therapy, which requires accurate KI to correct gene mutation, transgenic breeding programs can accept robust KI as long as integration does not interrupt normal gene functions and result in any negative pleiotropic effects. High KI efficiency is required to reduce the breeding cost and shorten the breeding period, especially in transferring multiple foreign genes to a single individual. To elevate the KI efficacy and achieve multiple gene KIs simultaneously, we introduced a new strategy that enables transgene integration into numerous sites of the genome by targeting long repeated sequences (LRSs). Using this simple strategy, for the first time we successfully generated transgenic fish carrying the masu salmon (Oncorhynchus masou) elovl2 gene and rabbitfish (Siganus canaliculatus) Δ4 fad and Δ6 fad genes, and achieved robust target KI of elovl2 and Δ6 fad genes at multiple sites of LRS1 and LRS3, respectively, in the initial generation. This demonstrated that donor plasmid homology arms, which were nearly identical but not completely the same as the genome sequence, still led to on-target KI. Although the target KI efficiencies at LRS1, LRS2, and LRS3 sites were still relatively low in the current study, it is very promising that 100% KI efficiency in the future could be realized and perfected by selection of better LRSs and optimization of sgRNAs.
Collapse
Affiliation(s)
- De Xing
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Shangjia Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Wenwen Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Qin Zhang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Jinhai Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Tasnuba Hasin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Darshika Hettiarachchi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Veronica Alston
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Logan Bern
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Abel Paladines Parrales
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Cuiyu Lu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Michael Coogan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Andrew Johnson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao266003, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| |
Collapse
|
10
|
Ozawa M, Taguchi J, Katsuma K, Ishikawa-Yamauchi Y, Kikuchi M, Sakamoto R, Yamada Y, Ikawa M. Efficient simultaneous double DNA knock-in in murine embryonic stem cells by CRISPR/Cas9 ribonucleoprotein-mediated circular plasmid targeting for generating gene-manipulated mice. Sci Rep 2022; 12:21558. [PMID: 36513736 PMCID: PMC9748034 DOI: 10.1038/s41598-022-26107-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Gene targeting of embryonic stem (ES) cells followed by chimera production has been conventionally used for developing gene-manipulated mice. Although direct knock-in (KI) using murine zygote via CRISPR/Cas9-mediated genome editing has been reported, ES cell targeting still has merits, e.g., high throughput work can be performed in vitro. In this study, we first compared the KI efficiency of mouse ES cells with CRISPR/Cas9 expression vector and ribonucleoprotein (RNP), and confirmed that KI efficiency was significantly increased by using RNP. Using CRISPR/Cas9 RNP and circular plasmid with homologous arms as a targeting vector, knock-in within ES cell clones could be obtained efficiently without drug selection, thus potentially shortening the vector construction or cell culture period. Moreover, by incorporating a drug-resistant cassette into the targeting vectors, double DNA KI can be simultaneously achieved at high efficiency by a single electroporation. This technique will help to facilitate the production of genetically modified mouse models that are fundamental for exploring topics related to human and mammalian biology.
Collapse
Affiliation(s)
- Manabu Ozawa
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Jumpei Taguchi
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Kento Katsuma
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Yu Ishikawa-Yamauchi
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Mio Kikuchi
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Reiko Sakamoto
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Yasuhiro Yamada
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Masahito Ikawa
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan ,grid.136593.b0000 0004 0373 3971Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan
| |
Collapse
|
11
|
Yoshida M, Saito T, Takayanagi Y, Totsuka Y, Onaka T. Necessity of integrated genomic analysis to establish a designed knock-in mouse from CRISPR-Cas9-induced mutants. Sci Rep 2022; 12:20390. [PMID: 36437283 PMCID: PMC9701781 DOI: 10.1038/s41598-022-24810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The CRISPR-Cas9 method for generation of knock-in mutations in rodent embryos yields many F0 generation candidates that may have the designed mutations. The first task for selection of promising F0 generations is to analyze genomic DNA which likely contains a mixture of designed and unexpected mutations. In our study, while generating Prlhr-Venus knock-in reporter mice, we found that genomic rearrangements near the targeted knock-in allele, tandem multicopies at a target allele locus, and mosaic genotypes for two different knock-in alleles occurred in addition to the designed knock-in mutation in the F0 generation. Conventional PCR and genomic sequencing were not able to detect mosaicism nor discriminate between the designed one-copy knock-in mutant and a multicopy-inserted mutant. However, by using a combination of Southern blotting and the next-generation sequencing-based RAISING method, these mutants were successfully detected in the F0 generation. In the F1 and F2 generations, droplet digital PCR assisted in establishing the strain, although a multicopy was falsely detected as one copy by analysis of the F0 generation. Thus, the combination of these methods allowed us to select promising F0 generations and facilitated establishment of the designed strain. We emphasize that focusing only on positive evidence of knock-in can lead to erroneous selection of undesirable strains.
Collapse
Affiliation(s)
- Masahide Yoshida
- grid.410804.90000000123090000Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Tomoko Saito
- Institute of Immunology Co., Ltd., 1198-4 Iwazo, Utsunomiya, Tochigi 321-0973 Japan
| | - Yuki Takayanagi
- grid.410804.90000000123090000Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Yoshikazu Totsuka
- Institute of Immunology Co., Ltd., 1198-4 Iwazo, Utsunomiya, Tochigi 321-0973 Japan
| | - Tatsushi Onaka
- grid.410804.90000000123090000Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| |
Collapse
|
12
|
Catecholaminergic cell type-specific expression of Cre recombinase in knock-in transgenic rats generated by the Combi-CRISPR technology. J Neurosci Methods 2022; 381:109707. [PMID: 36089167 DOI: 10.1016/j.jneumeth.2022.109707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Cell groups containing catecholamines provide a useful model to study the molecular and cellular mechanisms underlying the morphogenesis, physiology, and pathology of the central nervous system. For this purpose, it is necessary to establish a system to induce catecholaminergic group-specific expression of Cre recombinase. Recently, we introduced a gene cassette encoding 2A peptide fused to Cre recombinase into the site between the C-terminus and translational termination codons of the rat tyrosine hydroxylase (TH) open reading frame by the Combi-CRISPR technology, which is a genomic editing method to enable an efficient knock-in (KI) of long DNA sequence into a target site. However, the expression patterns of the transgene and its function as well as the effect of the mutation on the biochemical and behavioral phenotypes in the KI strains have not been characterized yet. NEW METHOD We aimed to evaluate the usefulness of TH-Cre KI rats as an experimental model for investigating the structure and function of catecholaminergic neurons in the brain. RESULTS We detected cell type-specific expression of Cre recombinase and site-specific recombination activity in the representative catecholaminergic groups in the TH-Cre KI rat strains. In addition, we measured TH protein levels and catecholamine accumulation in the brain regions, as well as motor, reward-related, and anxiety-like behaviors, indicating that catecholamine metabolism and general behavior are apparently normal in these KI rats. CONCLUSIONS TH-Cre KI rat strains produced by the Combi-CRISPR system offer a beneficial model to study the molecular and cellular mechanics for the morphogenesis, physiology, and pathology of catecholamine-containing neurons in the brain.
Collapse
|
13
|
Tanaka M, Yokoyama K, Hayashi H, Isaki S, Kitatani K, Wang T, Kawata H, Matsuzawa H, Gurumurthy CB, Miura H, Ohtsuka M. CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice. Genome Biol 2022; 23:228. [PMID: 36284311 PMCID: PMC9594901 DOI: 10.1186/s13059-022-02779-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/30/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR tools can generate knockout and knock-in animal models easily, but the models can contain off-target genomic lesions or random insertions of donor DNAs. Simpler methods to identify off-target lesions and random insertions, using tail or earpiece DNA, are unavailable. We develop CRISPR-KRISPR (CRISPR-Knock-ins and Random Inserts Searching PRotocol), a method to identify both off-target lesions and random insertions. CRISPR-KRISPR uses as little as 3.4 μg of genomic DNA; thus, it can be easily incorporated as an additional step to genotype founder animals for further breeding.
Collapse
Affiliation(s)
- Masayuki Tanaka
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Keiko Yokoyama
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hideki Hayashi
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Sanae Isaki
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Kanae Kitatani
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Ting Wang
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hisako Kawata
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hideyuki Matsuzawa
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Channabasavaiah B. Gurumurthy
- grid.266813.80000 0001 0666 4105Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE USA ,grid.266813.80000 0001 0666 4105Genome Editing and Education Center Nebraska (GEEC-Nebraska), College of Medicine, University of Nebraska Medical Center, Omaha, NE USA ,grid.266813.80000 0001 0666 4105Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE USA
| | - Hiromi Miura
- grid.265061.60000 0001 1516 6626Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Masato Ohtsuka
- grid.265061.60000 0001 1516 6626Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa 259-1193 Japan ,grid.265061.60000 0001 1516 6626The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193 Japan
| |
Collapse
|
14
|
Targeted-Deletion of a Tiny Sequence via Prime Editing to Restore SMN Expression. Int J Mol Sci 2022; 23:ijms23147941. [PMID: 35887289 PMCID: PMC9317564 DOI: 10.3390/ijms23147941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/13/2022] [Accepted: 07/17/2022] [Indexed: 01/27/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a devastating autosomal recessive motor neuron disease associated with mutations in the survival motor neuron 1 (SMN1) gene, the leading genetic cause of infant mortality. A nearly identical copy gene (SMN2) is retained in almost all patients with SMA. However, SMN2 fails to prevent disease development because of its alternative splicing, leading to a lack of exon 7 in the majority of SMN2 transcripts and yielding an unstable truncated protein. Several splicing regulatory elements, including intronic splicing silencer-N1 (ISS-N1) of SMN2 have been described. In this study, targeted-deletion of ISS-N1 was achieved using prime editing (PE) in SMA patient-specific induced pluripotent stem cells (SMA-iPSCs) with a high efficiency of 7/24. FL-SMN expression was restored in the targeted-deletion iPS clones and their derived motor neurons (iMNs). Notably, the apoptosis of the iMNs, caused by the loss of SMN protein that leads to the hyperactivity of endoplasmic reticulum (ER) stress, was alleviated in targeted-deletion iPSCs derived-iMNs. Thus, this is the first study to demonstrate that the targeted-deletion of ISS-N1 via PE for restoring FL-SMN expression holds therapeutic promise for SMA.
Collapse
|
15
|
Volodina OV, Smirnikhina SA. The Choice of a Donor Molecule in Genome Editing Experiments in Animal Cells. Mol Biol 2022. [DOI: 10.1134/s002689332203013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Feng S, Wang Z, Li A, Xie X, Liu J, Li S, Li Y, Wang B, Hu L, Yang L, Guo T. Strategies for High-Efficiency Mutation Using the CRISPR/Cas System. Front Cell Dev Biol 2022; 9:803252. [PMID: 35198566 PMCID: PMC8860194 DOI: 10.3389/fcell.2021.803252] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/22/2021] [Indexed: 12/15/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated systems have revolutionized traditional gene-editing tools and are a significant tool for ameliorating gene defects. Characterized by high target specificity, extraordinary efficiency, and cost-effectiveness, CRISPR/Cas systems have displayed tremendous potential for genetic manipulation in almost any organism and cell type. Despite their numerous advantages, however, CRISPR/Cas systems have some inherent limitations, such as off-target effects, unsatisfactory efficiency of delivery, and unwanted adverse effects, thereby resulting in a desire to explore approaches to address these issues. Strategies for improving the efficiency of CRISPR/Cas-induced mutations, such as reducing off-target effects, improving the design and modification of sgRNA, optimizing the editing time and the temperature, choice of delivery system, and enrichment of sgRNA, are comprehensively described in this review. Additionally, several newly emerging approaches, including the use of Cas variants, anti-CRISPR proteins, and mutant enrichment, are discussed in detail. Furthermore, the authors provide a deep analysis of the current challenges in the utilization of CRISPR/Cas systems and the future applications of CRISPR/Cas systems in various scenarios. This review not only serves as a reference for improving the maturity of CRISPR/Cas systems but also supplies practical guidance for expanding the applicability of this technology.
Collapse
Affiliation(s)
- Shuying Feng
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zilong Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Aifang Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xin Xie
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Junjie Liu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Shuxuan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yalan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Baiyan Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lina Hu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lianhe Yang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Tao Guo
- Department of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| |
Collapse
|
17
|
Sato M, Nakamura S, Inada E, Takabayashi S. Recent Advances in the Production of Genome-Edited Rats. Int J Mol Sci 2022; 23:ijms23052548. [PMID: 35269691 PMCID: PMC8910656 DOI: 10.3390/ijms23052548] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 12/14/2022] Open
Abstract
The rat is an important animal model for understanding gene function and developing human disease models. Knocking out a gene function in rats was difficult until recently, when a series of genome editing (GE) technologies, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the type II bacterial clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated Cas9 (CRISPR/Cas9) systems were successfully applied for gene modification (as exemplified by gene-specific knockout and knock-in) in the endogenous target genes of various organisms including rats. Owing to its simple application for gene modification and its ease of use, the CRISPR/Cas9 system is now commonly used worldwide. The most important aspect of this process is the selection of the method used to deliver GE components to rat embryos. In earlier stages, the microinjection (MI) of GE components into the cytoplasm and/or nuclei of a zygote was frequently employed. However, this method is associated with the use of an expensive manipulator system, the skills required to operate it, and the egg transfer (ET) of MI-treated embryos to recipient females for further development. In vitro electroporation (EP) of zygotes is next recognized as a simple and rapid method to introduce GE components to produce GE animals. Furthermore, in vitro transduction of rat embryos with adeno-associated viruses is potentially effective for obtaining GE rats. However, these two approaches also require ET. The use of gene-engineered embryonic stem cells or spermatogonial stem cells appears to be of interest to obtain GE rats; however, the procedure itself is difficult and laborious. Genome-editing via oviductal nucleic acids delivery (GONAD) (or improved GONAD (i-GONAD)) is a novel method allowing for the in situ production of GE zygotes existing within the oviductal lumen. This can be performed by the simple intraoviductal injection of GE components and subsequent in vivo EP toward the injected oviducts and does not require ET. In this review, we describe the development of various approaches for producing GE rats together with an assessment of their technical advantages and limitations, and present new GE-related technologies and current achievements using those rats in relation to human diseases.
Collapse
Affiliation(s)
- Masahiro Sato
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo 157-8535, Japan
- Correspondence: (M.S.); (S.T.); Tel.: +81-3-3416-0181 (M.S.); +81-53-435-2001 (S.T.)
| | - Shingo Nakamura
- Division of Biomedical Engineering, National Defense Medical College Research Institute, Saitama 359-8513, Japan;
| | - Emi Inada
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan;
| | - Shuji Takabayashi
- Laboratory Animal Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
- Correspondence: (M.S.); (S.T.); Tel.: +81-3-3416-0181 (M.S.); +81-53-435-2001 (S.T.)
| |
Collapse
|
18
|
Wang S, Li Y, Zhong L, Wu K, Zhang R, Kang T, Wu S, Wu Y. Efficient gene editing through an intronic selection marker in cells. Cell Mol Life Sci 2022; 79:111. [PMID: 35098362 PMCID: PMC8801403 DOI: 10.1007/s00018-022-04152-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Gene editing technology has provided researchers with the ability to modify genome sequences in almost all eukaryotes. Gene-edited cell lines are being used with increasing frequency in both bench research and targeted therapy. However, despite the great importance and universality of gene editing, the efficiency of homology-directed DNA repair (HDR) is too low, and base editors (BEs) cannot accomplish desired indel editing tasks. RESULTS AND DISCUSSION Our group has improved HDR gene editing technology to indicate DNA variation with an independent selection marker using an HDR strategy, which we named Gene Editing through an Intronic Selection marker (GEIS). GEIS uses a simple process to avoid nonhomologous end joining (NHEJ)-mediated false-positive effects and achieves a DsRed positive rate as high as 87.5% after two rounds of fluorescence-activated cell sorter (FACS) selection without disturbing endogenous gene splicing and expression. We re-examined the correlation of the conversion tract and efficiency, and our data suggest that GEIS has the potential to edit approximately 97% of gene editing targets in human and mouse cells. The results of further comprehensive analysis suggest that the strategy may be useful for introducing multiple DNA variations in cells.
Collapse
Affiliation(s)
- Shang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
| | - Yuqing Li
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
- Teaching Center of Shenzhen Luohu Hospital, Shantou University Medical College, Shantou, 515000, China
| | - Li Zhong
- Center of Digestive Diseases, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, China
| | - Kai Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Song Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China.
- Teaching Center of Shenzhen Luohu Hospital, Shantou University Medical College, Shantou, 515000, China.
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen, 518000, China.
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| |
Collapse
|
19
|
Liu C, Xu X, Koivisto O, Zhou W, Jacquemet G, Rosenholm JM, Zhang H. Improving the knock-in efficiency of the MOF-encapsulated CRISPR/Cas9 system through controllable embedding structures. NANOSCALE 2021; 13:16525-16532. [PMID: 34596650 DOI: 10.1039/d1nr02872c] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Appropriate tuning of robust artificial coatings can not only enhance intracellular delivery but also preserve the biological functions of genetic molecules in gene based therapies. Here, we report a strategy to synthesize controllable nanostructures in situ by encapsulating CRISPR/Cas9 plasmids into metal-organic frameworks (MOFs) via biomimetic mineralization. The structure-functionality relationship studies indicate that MOF-coated nanostructures dramatically impact the biological features of the contained plasmids through different embedding structures. The plasmids are homogeneously distributed within the heterogeneous nanoarchitecture and protected from enzymatic degradation. In addition, the plasmid-MOF structure exhibits excellent loading capability, pH-responsive release, and affinity for plasmid binding. Through in vitro assays it was found that the superior MOF vector can greatly enhance cellular endocytosis and endo/lysosomal escape of sheltered plasmids, resulting in successful knock-in of GFP-tagged paxillin genomic sequences in cancer cell lines with high transfection potency compared to our previous studies. Thus, the development of new cost-effective approaches for MOF-based intracellular delivery systems offers an attractive option for overcoming the physiological barriers to CRISPR/Cas9 delivery, which shows great potential for investigating paxillin-associated focal adhesions and signal regulation.
Collapse
Affiliation(s)
- Chang Liu
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, Turku 20520, Finland.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Xiaoyu Xu
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, Turku 20520, Finland.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Oliver Koivisto
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, Turku 20520, Finland.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
| | - Wenhui Zhou
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, Turku 20520, Finland.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Southern Medical University Affiliated Fengxian Hospital, Shanghai, 201499, China
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Faculty of Science and Engineering, Cell biology, Åbo Akademi University, FI-20520 Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Jessica M Rosenholm
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, Turku 20520, Finland.
| | - Hongbo Zhang
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, Turku 20520, Finland.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, P. R. China
| |
Collapse
|
20
|
Gurumurthy CB, Saunders TL, Ohtsuka M. Designing and generating a mouse model: frequently asked questions. J Biomed Res 2021; 35:76-90. [PMID: 33797414 PMCID: PMC8038528 DOI: 10.7555/jbr.35.20200197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genetically engineered mouse (GEM) models are commonly used in biomedical research. Generating GEMs involve complex set of experimental procedures requiring sophisticated equipment and highly skilled technical staff. Because of these reasons, most research institutes set up centralized core facilities where custom GEMs are created for research groups. Researchers, on the other hand, when they begin thinking about generating GEMs for their research, several questions arise in their minds. For example, what type of model(s) would be best useful for my research, how do I design them, what are the latest technologies and tools available for developing my model(s), and finally how to breed GEMs in my research. As there are several considerations and options in mouse designs, and as it is an expensive and time-consuming endeavor, careful planning upfront can ensure the highest chance of success. In this article, we provide brief answers to several frequently asked questions that arise when researchers begin thinking about generating mouse model(s) for their work.
Collapse
Affiliation(s)
- Channabasavaiah B Gurumurthy
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA.,Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
| | - Thomas L Saunders
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - 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.,The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan
| |
Collapse
|
21
|
Gurumurthy CB, Quadros RM, Richardson GP, Poluektova LY, Mansour SL, Ohtsuka M. Genetically modified mouse models to help fight COVID-19. Nat Protoc 2020; 15:3777-3787. [PMID: 33106680 PMCID: PMC7704938 DOI: 10.1038/s41596-020-00403-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023]
Abstract
The research community is in a race to understand the molecular mechanisms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, to repurpose currently available antiviral drugs and to develop new therapies and vaccines against coronavirus disease 2019 (COVID-19). One major challenge in achieving these goals is the paucity of suitable preclinical animal models. Mice constitute ~70% of all the laboratory animal species used in biomedical research. Unfortunately, SARS-CoV-2 infects mice only if they have been genetically modified to express human ACE2. The inherent resistance of wild-type mice to SARS-CoV-2, combined with a wealth of genetic tools that are available only for modifying mice, offers a unique opportunity to create a versatile set of genetically engineered mouse models useful for COVID-19 research. We propose three broad categories of these models and more than two dozen designs that may be useful for SARS-CoV-2 research and for fighting COVID-19.
Collapse
Affiliation(s)
- Channabasavaiah B Gurumurthy
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.
- Mouse Genome Engineering Core Facility, Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Larisa Y Poluektova
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Suzanne L Mansour
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Masato Ohtsuka
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan.
- The Institute of Medical Sciences, Tokai University, Isehara, Japan.
| |
Collapse
|