1
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Gim GM, Jang G. Outlook on genome editing application to cattle. J Vet Sci 2024; 25:e10. [PMID: 38311323 PMCID: PMC10839183 DOI: 10.4142/jvs.23133] [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: 05/15/2023] [Revised: 08/04/2023] [Accepted: 08/20/2023] [Indexed: 02/07/2024] Open
Abstract
In livestock industry, there is growing interest in methods to increase the production efficiency of livestock to address food shortages, given the increasing global population. With the advancements in gene engineering technology, it is a valuable tool and has been intensively utilized in research specifically focused on human disease. In historically, this technology has been used with livestock to create human disease models or to produce recombinant proteins from their byproducts. However, in recent years, utilizing gene editing technology, cattle with identified genes related to productivity can be edited, thereby enhancing productivity in response to climate change or specific disease instead of producing recombinant proteins. Furthermore, with the advancement in the efficiency of gene editing, it has become possible to edit multiple genes simultaneously. This cattle breed improvement has been achieved by discovering the genes through the comprehensive analysis of the entire genome of cattle. The cattle industry has been able to address gene bottlenecks that were previously impossible through conventional breeding systems. This review concludes that gene editing is necessary to expand the cattle industry, improving productivity in the future. Additionally, the enhancement of cattle through gene editing is expected to contribute to addressing environmental challenges associated with the cattle industry. Further research and development in gene editing, coupled with genomic analysis technologies, will significantly contribute to solving issues that conventional breeding systems have not been able to address.
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Affiliation(s)
| | - Goo Jang
- LARTBio Inco, Seoul 06221, Korea
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul 08826, Korea
- Comparative medicine Disease Research Center, Seoul National University, Seoul 08826, Korea
- Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia.
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2
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Yum SY, Choi W, Kim S, Jang G, Koo O. Identification AAVS1-like locus from the porcine genome and site-specific integration of recombinase-mediated cassette exchange using CRISPR/Cas9. Anim Biotechnol 2023; 34:4730-4735. [PMID: 36905152 DOI: 10.1080/10495398.2023.2187408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Gene integration at site-specific loci is a critical approach for understanding the function of a gene in cells or animals. The AAVS1 locus is a well-known safe harbor for human and mouse studies. In this study, we found an AAVS1-like sequence (pAAVS1) in the porcine genome using the Genome Browser and designed TALEN and CRISPR/Cas9 to target the pAAVS1. The efficiency of CRISPR/Cas9 in porcine cells was superior to that of TALEN. We added a loxP-lox2272 sequences to the pAAVS1 targeting donor vector containing GFP for further exchange of various transgenes via recombinase-mediated cassette exchange (RMCE). The donor vector and CRISPR/Cas9 components were transfected into porcine fibroblasts. Targeted cells of CRISPR/Cas9-mediated homologous recombination were identified by antibiotic selection. Gene knock-in was confirmed by PCR. To induce RMCE, another donor vector containing the loxP-lox2272 and inducible Cre recombinase was cloned. The Cre-donor vector was transfected into the pAAVS1 targeted cell line, and RMCE was induced by adding doxycycline to the culture medium. RMCE in porcine fibroblasts was confirmed using PCR. In conclusion, gene targeting at the pAAVS1 and RMCE in porcine fibroblasts was successful. This technology will be useful for future porcine transgenesis studies and the generation of stable transgenic pigs.
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Affiliation(s)
- Soo-Young Yum
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul, Republic of Korea
- LARTBio Incorp, Seoul, Republic of Korea
| | - Woojae Choi
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | | | - Goo Jang
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul, Republic of Korea
- LARTBio Incorp, Seoul, Republic of Korea
- BK21 Plus program, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- Institute of Green Bio Science Technology, Seoul National University, Pyeongchang-gun, Republic of Korea
- Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Okjae Koo
- ToolGen, Inc, Seoul, South Korea
- nSAGE Inc., Incheon, South Korea
- SeaWith Inc., Daegu, South Korea
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3
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Kheirandish MH, Rahmani B, Zarei Jaliani H, Barkhordari F, Mazlomi MA, Davami F. Efficient site-specific integration in CHO-K1 cells using CRISPR/Cas9-modified donors. Mol Biol Rep 2023:10.1007/s11033-023-08529-8. [PMID: 37244887 DOI: 10.1007/s11033-023-08529-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Conventional methods applied to develop recombinant CHO (rCHO) cell line as a predominant host for mammalian protein expression are limited to random integration approaches, which can prolong the process of getting the desired clones for months. CRISPR/Cas9 could be an alternative by mediating site-specific integration into transcriptionally active hot spots, promoting homogenous clones, and shortening the clonal selection process. However, applying this approach for the rCHO cell line development depends on an acceptable integration rate and robust sites for the sustained expression. METHODS AND RESULTS In this study, we aimed at improving the rate of GFP reporter integration to the Chromosome 3 (Chr3) pseudo-attP site of the CHO-K1 genome via two strategies; these include the PCR-based donor linearization and increasing local concentration of donor in the vicinity of DSB site by applying the monomeric streptavidin (mSA)-biotin tethering approach. According to the results, compared to the conventional CRISPR-mediated targeting, donor linearization and tethering methods exhibited 1.6- and 2.4-fold improvement in knock-in efficiency; among on-target clones, 84% and 73% were determined to be single copy by the quantitative PCR, respectively. Finally, to evaluate the expression level of the targeted integration, the expression cassette of hrsACE2 as a secretory protein was targeted to the Chr3 pseudo-attP site by applying the established tethering method. The generated cell pool reached 2-fold productivity, as compared to the random integration cell line. CONCLUSION Our study suggested reliable strategies for enhancing the CRISPR-mediated integration, introducing Chr3 pseudo-attP site as a potential candidate for the sustained transgene expression, which might be applied to promote the rCHO cell line development.
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Affiliation(s)
- Mohammad Hassan Kheirandish
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behnaz Rahmani
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Hossein Zarei Jaliani
- Department of Medical Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Mohammad Ali Mazlomi
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Fatemeh Davami
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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4
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Amiri S, Adibzadeh S, Ghanbari S, Rahmani B, Kheirandish MH, Farokhi-Fard A, Dastjerdeh MS, Davami F. CRISPR-interceded CHO cell line development approaches. Biotechnol Bioeng 2023; 120:865-902. [PMID: 36597180 DOI: 10.1002/bit.28329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/28/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
For industrial production of recombinant protein biopharmaceuticals, Chinese hamster ovary (CHO) cells represent the most widely adopted host cell system, owing to their capacity to produce high-quality biologics with human-like posttranslational modifications. As opposed to random integration, targeted genome editing in genomic safe harbor sites has offered CHO cell line engineering a new perspective, ensuring production consistency in long-term culture and high biotherapeutic expression levels. Corresponding the remarkable advancements in knowledge of CRISPR-Cas systems, the use of CRISPR-Cas technology along with the donor design strategies has been pushed into increasing novel scenarios in cell line engineering, allowing scientists to modify mammalian genomes such as CHO cell line quickly, readily, and efficiently. Depending on the strategies and production requirements, the gene of interest can also be incorporated at single or multiple loci. This review will give a gist of all the most fundamental recent advancements in CHO cell line development, such as different cell line engineering approaches along with donor design strategies for targeted integration of the desired construct into genomic hot spots, which could ultimately lead to the fast-track product development process with consistent, improved product yield and quality.
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Affiliation(s)
- Shahin Amiri
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Setare Adibzadeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Samaneh Ghanbari
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behnaz Rahmani
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad H Kheirandish
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies, Tehran University of Medical Sciences, Tehran, Iran
| | - Aref Farokhi-Fard
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mansoureh S Dastjerdeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Davami
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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5
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Kashyap D, Jakhmola S, Tiwari D, Kumar R, Moorthy NSHN, Elangovan M, Brás NF, Jha HC. Plant derived active compounds as potential anti SARS-CoV-2 agents: an in-silico study. J Biomol Struct Dyn 2022; 40:10629-10650. [PMID: 34225565 DOI: 10.1080/07391102.2021.1947384] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Plants are a valued potential source of drugs for a variety of diseases and are often considered less toxic to humans. We investigated antiviral compounds that may potentially target SARS-CoV-2 antigenic spike (S) and host proteins; angiotensin-converting enzyme2 (ACE2), and transmembrane serine protease2 (TMPRSS2). We scrutinized 36 phytochemicals from 15 Indian medicinal plants known to be effective against RNA viruses via molecular docking. Besides, the TMPRSS2 structure was modeled and validated using the SWISS-MODEL. Docking was performed using Autodock Vina and 4.2 followed by visualization of the docking poses on Pymol version 2.4.0 and Discovery Studio Visualizer. Molecular docking showed that 12 out of 36 active compounds interacted efficiently with S, ACE2, and TMPRSS2 proteins. The ADMET profile generated using the swissADME and pkCSM server revealed that these compounds were possessed druggable properties. The Amber 12 simulation package was used to carry out energy minimizations and molecular dynamics (MD) simulations. The total simulation time for both S protein: WFA and S protein: WND complexes was 300 ns (100 ns per replica). A total of 120 structures were extracted from the last 60 ns of each MD simulation for further analysis. MM-PBSA and MM-GBSA were employed to assess the binding energy of each ligand and the receptor-binding domain of the viral S-protein. The methods suggested that WND and WFA showed thermodynamically favorable binding energies, and the S protein had a higher affinity with WND. Interestingly, Leu455 hotspot residue in the S protein, also predicted to participate in binding with ACE2, was engaged by WND and WFA. HighlightsPlants' natural active compounds may aid in the development of COVID-19 therapeutics.MD simulation study revealed stable binding of withanolide D and withaferin A with spike proteinWithanolide D and withaferin A could be effective against SARS-CoV-2 spike protein.Discovery of druggable agents that have less or lack of binding affinity with ACE2 to avoid the organs associated with comorbidities.According to ADMET selected phytochemicals may be used as druggable compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Shweta Jakhmola
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Deeksha Tiwari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Rajesh Kumar
- Department of Physics, Indian Institute of Technology Indore, Indore, India
| | | | | | - Natércia F Brás
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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6
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Stewart ZA. Xenotransplantation: The Contribution of CRISPR/Cas9 Gene Editing Technology. CURRENT TRANSPLANTATION REPORTS 2022. [DOI: 10.1007/s40472-022-00380-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Simone BW, Lee HB, Daby CL, Ata H, Restrepo-Castillo S, Martínez-Gálvez G, Kar B, Gendron WA, Clark KJ, Ekker SC. Chimeric RNA: DNA TracrRNA Improves Homology-Directed Repair In Vitro and In Vivo. CRISPR J 2022; 5:40-52. [PMID: 34935462 PMCID: PMC8892967 DOI: 10.1089/crispr.2021.0087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nearly 90% of human pathogenic mutations are caused by small genetic variations, and methods to correct these errors efficiently are critically important. One way to make small DNA changes is providing a single-stranded oligo deoxynucleotide (ssODN) containing an alteration coupled with a targeted double-strand break (DSB) at the target locus in the genome. Coupling an ssODN donor with a CRISPR-Cas9-mediated DSB is one of the most streamlined approaches to introduce small changes. However, in many systems, this approach is inefficient and introduces imprecise repair at the genetic junctions. We herein report a technology that uses spatiotemporal localization of an ssODN with CRISPR-Cas9 to improve gene alteration. We show that by fusing an ssODN template to the trans-activating RNA (tracrRNA), we recover precise genetic alterations, with increased integration and precision in vitro and in vivo. Finally, we show that this technology can be used to enhance gene conversion with other gene editing tools such as transcription activator like effector nucleases.
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Affiliation(s)
- Brandon W. Simone
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Han B. Lee
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Camden L. Daby
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Hirotaka Ata
- Department of Clinical and Translational Sciences, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Santiago Restrepo-Castillo
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Gabriel Martínez-Gálvez
- Mayo Clinic Graduate School of Biomedical Sciences, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - William A.C. Gendron
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
- Address correspondence to: Stephen C. Ekker, PhD, Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA,
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8
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Papasavva PL, Patsali P, Loucari CC, Kurita R, Nakamura Y, Kleanthous M, Lederer CW. CRISPR Editing Enables Consequential Tag-Activated MicroRNA-Mediated Endogene Deactivation. Int J Mol Sci 2022; 23:1082. [PMID: 35163006 PMCID: PMC8834719 DOI: 10.3390/ijms23031082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Molecular therapies and functional studies greatly benefit from spatial and temporal precision of genetic intervention. We therefore conceived and explored tag-activated microRNA (miRNA)-mediated endogene deactivation (TAMED) as a research tool and potential lineage-specific therapy. For proof of principle, we aimed to deactivate γ-globin repressor BCL11A in erythroid cells by tagging the 3' untranslated region (UTR) of BCL11A with miRNA recognition sites (MRSs) for the abundant erythromiR miR-451a. To this end, we employed nucleofection of CRISPR/Cas9 ribonucleoprotein (RNP) particles alongside double- or single-stranded oligodeoxynucleotides for, respectively, non-homologous-end-joining (NHEJ)- or homology-directed-repair (HDR)-mediated MRS insertion. NHEJ-based tagging was imprecise and inefficient (≤6%) and uniformly produced knock-in- and indel-containing MRS tags, whereas HDR-based tagging was more efficient (≤18%), but toxic for longer donors encoding concatenated and thus potentially more efficient MRS tags. Isolation of clones for robust HEK293T cells tagged with a homozygous quadruple MRS resulted in 25% spontaneous reduction in BCL11A and up to 36% reduction after transfection with an miR-451a mimic. Isolation of clones for human umbilical cord blood-derived erythroid progenitor-2 (HUDEP-2) cells tagged with single or double MRS allowed detection of albeit weak γ-globin induction. Our study demonstrates suitability of TAMED for physiologically relevant modulation of gene expression and its unsuitability for therapeutic application in its current form.
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Affiliation(s)
- Panayiota L. Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Constantinos C. Loucari
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Koto-ku, Tokyo 135-8521, Japan;
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan;
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
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9
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Arnesen JA, Hoof JB, Kildegaard HF, Borodina I. Genome Editing of Eukarya. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Lu H, Liu J, Feng T, Guo Z, Yin Y, Gao F, Cao G, Du X, Wu S. A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor. Genome Res 2021; 31:900-909. [PMID: 33795333 PMCID: PMC8092013 DOI: 10.1101/gr.271312.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Targeted mutagenesis in model organisms is key for gene functional annotation and biomedical research. Despite technological advances in gene editing by the CRISPR-Cas9 systems, rapid and efficient introduction of site-directed mutations remains a challenge in large animal models. Here, we developed a robust and flexible insertional mutagenesis strategy, homology-independent targeted trapping (HIT-trapping), which is generic and can efficiently target-trap an endogenous gene of interest independent of homology arm and embryonic stem cells. Further optimization and equipping the HIT-trap donor with a site-specific DNA inversion mechanism enabled one-step generation of reversible and conditional alleles in a single experiment. As a proof of concept, we successfully created mutant alleles for 21 disease-related genes in primary porcine fibroblasts with an average knock-in frequency of 53.2%, a great improvement over previous approaches. The versatile HIT-trapping strategy presented here is expected to simplify the targeted generation of mutant alleles and facilitate large-scale mutagenesis in large mammals such as pigs.
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Affiliation(s)
- Hengxing Lu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jun Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tao Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610200, China
| | - Zihang Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yunjun Yin
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fei Gao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Gengsheng Cao
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Science, Henan University, Kaifeng 475004, China
| | - Xuguang Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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11
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Danner E, Lebedin M, de la Rosa K, Kühn R. A homology independent sequence replacement strategy in human cells using a CRISPR nuclease. Open Biol 2021; 11:200283. [PMID: 33499763 PMCID: PMC7881171 DOI: 10.1098/rsob.200283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Precision genomic alterations largely rely on homology directed repair (HDR), but targeting without homology using the non-homologous end-joining (NHEJ) pathway has gained attention as a promising alternative. Previous studies demonstrated precise insertions formed by the ligation of donor DNA into a targeted genomic double-strand break in both dividing and non-dividing cells. Here, we demonstrate the use of NHEJ repair to replace genomic segments with donor sequences; we name this method 'Replace' editing (Rational end-joining protocol delivering a targeted sequence exchange). Using CRISPR/Cas9, we create two genomic breaks and ligate a donor sequence in-between. This exchange of a genomic for a donor sequence uses neither microhomology nor homology arms. We target four loci in cell lines and show successful exchange of exons in 16-54% of human cells. Using linear amplification methods and deep sequencing, we quantify the diversity of outcomes following Replace editing and profile the ligated interfaces. The ability to replace exons or other genomic sequences in cells not efficiently modified by HDR holds promise for both basic research and medicine.
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Affiliation(s)
- Eric Danner
- Max Delbrück Center for Molecular Medicine of the Helmholtz Association, Berlin, Germany
| | | | | | - Ralf Kühn
- Max Delbrück Center for Molecular Medicine of the Helmholtz Association, Berlin, Germany
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12
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Shin SW, Lee JS. CHO Cell Line Development and Engineering via Site-specific Integration: Challenges and Opportunities. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0093-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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13
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Thakur VS, Welford SM. Generation of a conditional mutant knock-in under the control of the natural promoter using CRISPR-Cas9 and Cre-Lox systems. PLoS One 2020; 15:e0240256. [PMID: 33007045 PMCID: PMC7531807 DOI: 10.1371/journal.pone.0240256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/22/2020] [Indexed: 01/04/2023] Open
Abstract
Modulation of gene activity by creating mutations has contributed significantly to the understanding of protein functions. Oftentimes, however, mutational analyses use overexpression studies, in which proteins are taken out of their normal contexts and stoichiometries. In the present work, we sought to develop an approach to simultaneously use the CRISPR/Cas9 and Cre-Lox techniques to modify the endogenous SAT1 gene to introduce mutant forms of the protein while still under the control of its natural gene promoter. We cloned the C-terminal portion of wild type (WT) SAT1, through the transcriptional stop elements, and flanked by LoxP sites in front of an identical version of SAT1 containing point mutations in critical binding sites. The construct was inserted into the endogenous SAT1 locus by Non-Homologous End Joining (NHEJ) after a CRISPR/Cas9 induced DNA double strand break. After validating that normal function of SAT1 was not altered by the insertional event, we were then able to assess the impact of point mutations by introduction of Cre recombinase. The system thus enables generation of cells in which endogenous WT SAT1 can be conditionally modified, and allow investigation of the functional consequences of site specific mutations in the context of the normal promoter and chromatin regulation.
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Affiliation(s)
- Vijay S. Thakur
- Department of Radiation Oncology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Scott M. Welford
- Department of Radiation Oncology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- * E-mail:
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14
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Tasan I, Su CJ, Enghiad B, Zhang M, Mishra S, Zhao H. Two-Color Imaging of Nonrepetitive Endogenous Loci in Human Cells. ACS Synth Biol 2020; 9:2502-2514. [PMID: 32822529 DOI: 10.1021/acssynbio.0c00295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tools for live cell imaging of multiple nonrepetitive genomic loci in mammalian cells are necessary to study chromatin dynamics. Here, we report a new system based on two chromosomally integrated orthogonal irregular repeat arrays and particularly a new general strategy to construct irregular repeat arrays. Briefly, we utilized a "bridge oligonucleotide-mediated ligation" protocol to assemble 8-mer repeats de novo which were then combined into a final 96-mer repeat array using Golden Gate cloning. This strategy was used for assembling a new mutant TetO irregular repeat array, which worked orthogonally to the wild type TetO repeat. Single copy integration of the new repeat array did not cause replication deficiencies at the tagged locus. Moreover, the mutant TetO irregular repeat could also be visualized by CRISPR imaging. Our new irregular repeat assembly method demonstrates a generally applicable strategy that can be used for assembling additional orthogonal repeat arrays for imaging genomic loci and irregular repeats to visualize RNA or proteins via signal amplification.
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Affiliation(s)
- Ipek Tasan
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Christina Jean Su
- Department of Molecular and Cellular Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Behnam Enghiad
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Meng Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Shekhar Mishra
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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15
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Fueller J, Herbst K, Meurer M, Gubicza K, Kurtulmus B, Knopf JD, Kirrmaier D, Buchmuller BC, Pereira G, Lemberg MK, Knop M. CRISPR-Cas12a-assisted PCR tagging of mammalian genes. J Cell Biol 2020; 219:e201910210. [PMID: 32406907 PMCID: PMC7265327 DOI: 10.1083/jcb.201910210] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/10/2020] [Accepted: 03/26/2020] [Indexed: 12/20/2022] Open
Abstract
Here we describe a time-efficient strategy for endogenous C-terminal gene tagging in mammalian tissue culture cells. An online platform is used to design two long gene-specific oligonucleotides for PCR with generic template cassettes to create linear dsDNA donors, termed PCR cassettes. PCR cassettes encode the tag (e.g., GFP), a Cas12a CRISPR RNA for cleavage of the target locus, and short homology arms for directed integration via homologous recombination. The integrated tag is coupled to a generic terminator shielding the tagged gene from the co-inserted auxiliary sequences. Co-transfection of PCR cassettes with a Cas12a-encoding plasmid leads to robust endogenous expression of tagged genes, with tagging efficiency of up to 20% without selection, and up to 60% when selection markers are used. We used target-enrichment sequencing to investigate all potential sources of artifacts. Our work outlines a quick strategy particularly suitable for exploratory studies using endogenous expression of fluorescent protein-tagged genes.
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Affiliation(s)
- Julia Fueller
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Konrad Herbst
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Matthias Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Krisztina Gubicza
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Bahtiyar Kurtulmus
- Center for Organismal Studies, University of Heidelberg and DKFZ, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia D. Knopf
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Daniel Kirrmaier
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
- Cell Morphogenesis and Signal Transduction, DKFZ-ZMBH Alliance and DKFZ, Heidelberg, Germany
| | - Benjamin C. Buchmuller
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Gislene Pereira
- Center for Organismal Studies, University of Heidelberg and DKFZ, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marius K. Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
- Cell Morphogenesis and Signal Transduction, DKFZ-ZMBH Alliance and DKFZ, Heidelberg, Germany
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16
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Live cell imaging and proteomic profiling of endogenous NEAT1 lncRNA by CRISPR/Cas9-mediated knock-in. Protein Cell 2020; 11:641-660. [PMID: 32458346 PMCID: PMC7452982 DOI: 10.1007/s13238-020-00706-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, long noncoding RNAs (lncRNAs) form complexes with proteins to execute various biological functions such as gene transcription, RNA processing and other signaling activities. However, methods to track endogenous lncRNA dynamics in live cells and screen for lncRNA interacting proteins are limited. Here, we report the development of CERTIS (CRISPR-mediated Endogenous lncRNA Tracking and Immunoprecipitation System) to visualize and isolate endogenous lncRNA, by precisely inserting a 24-repeat MS2 tag into the distal end of lncRNA locus through the CRISPR/Cas9 technology. In this study, we show that CERTIS effectively labeled the paraspeckle lncRNA NEAT1 without disturbing its physiological properties and could monitor the endogenous expression variation of NEAT1. In addition, CERTIS displayed superior performance on both short- and long-term tracking of NEAT1 dynamics in live cells. We found that NEAT1 and paraspeckles were sensitive to topoisomerase I specific inhibitors. Moreover, RNA Immunoprecipitation (RIP) of the MS2-tagged NEAT1 lncRNA successfully revealed several new protein components of paraspeckle. Our results support CERTIS as a tool suitable to track both spatial and temporal lncRNA regulation in live cells as well as study the lncRNA-protein interactomes.
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17
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Atkins PA, Voytas DF. Overcoming bottlenecks in plant gene editing. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:79-84. [PMID: 32143167 DOI: 10.1016/j.pbi.2020.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/30/2019] [Accepted: 01/22/2020] [Indexed: 05/06/2023]
Abstract
Agriculture has reached a technological inflection point. The development of novel gene editing tools and methods for their delivery to plant cells promises to increase genome malleability and transform plant biology. Whereas gene editing is capable of making a myriad of DNA sequence modifications, its widespread adoption has been hindered by a number of factors, particularly inefficiencies in creating precise DNA sequence modifications and ineffective methods for delivering gene editing reagents to plant cells. Here, we briefly overview the principles of plant genome editing and highlight a subset of the most recent advances that promise to overcome current limitations.
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Affiliation(s)
- Paul Ap Atkins
- Center for Genome Engineering, Center for Precision Plant Genomics and Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
| | - Daniel F Voytas
- Center for Genome Engineering, Center for Precision Plant Genomics and Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA.
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18
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is a precise genome manipulating tool that can produce targeted gene mutations in various cells and organisms. Although CRISPR/Cas9 can efficiently generate gene knockout, the gene knock-in (KI) efficiency mediated by homology-directed repair remains low, especially for large fragment integration. In this study, we established an efficient method for the CRISPR/Cas9-mediated integration of large transgene cassette, which carries salivary gland-expressed multiple digestion enzymes (≈ 20 kbp) in CEP112 locus in pig fetal fibroblasts (PFFs). Our results showed that using an optimal homology donor with a short and a long arm yielded the best CRISPR/Cas9-mediated KI efficiency in CEP112 locus, and the targeting efficiency in CEP112 locus was higher than in ROSA26 locus. The CEP112 KI cell lines were used as nuclear donors for somatic cell nuclear transfer to create genetically modified pigs. We found that KI pig (705) successfully expressed three microbial enzymes (β-glucanase, xylanase, and phytase) in salivary gland. This finding suggested that the CEP112 locus supports exogenous gene expression by a tissue-specific promoter. In summary, we successfully targeted CEP112 locus in pigs by using our optimal homology arm system and established a modified pig model for foreign digestion enzyme expression in the saliva.
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19
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Abstract
Recent advances in genome engineering are revolutionizing crop research and plant breeding. The ability to make specific modifications to a plant's genetic material creates opportunities for rapid development of elite cultivars with desired traits. The plant genome can be altered in several ways, including targeted introduction of nucleotide changes, deleting DNA segments, introducing exogenous DNA fragments and epigenetic modifications. Targeted changes are mediated by sequence specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspersed short palindromic repeats)-Cas (CRISPR associated protein) systems. Recent advances in engineering chimeric Cas nucleases fused to base editing enzymes permit for even greater precision in base editing and control over gene expression. In addition to gene editing technologies, improvement in delivery systems of exogenous DNA into plant cells have increased the rate of successful gene editing events. Regeneration of fertile plants containing the desired edits remains challenging; however, manipulation of embryogenesis-related genes such as BABY BOOM (BBM) has been shown to facilitate regeneration through tissue culture, often a major hurdle in recalcitrant cultivars. Epigenome reprogramming for improved crop performance is another possibility for future breeders, with recent studies on MutS HOMOLOG 1 (MSH1) demonstrating epigenetic-dependent hybrid vigor in several crops. While these technologies offer plant breeders new tools in creating high yielding, better adapted crop varieties, constantly evolving government policy regarding the cultivation of plants containing transgenes may impede the widespread adoption of some of these techniques. This chapter summarizes advances in genome editing tools and discusses the future of these techniques for crop improvement.
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Affiliation(s)
- Andriy Bilichak
- Morden Research and Development Center, Agriculture and Agri-Food Canada, Morden, MB, Canada.
| | - Daniel Gaudet
- The University of Lethbridge, Lethbridge, AB, Canada
| | - John Laurie
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
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20
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Schweickert PG, Cheng Z. Application of Genetic Engineering in Biotherapeutics Development. J Pharm Innov 2019. [DOI: 10.1007/s12247-019-09411-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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21
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Bukhari H, Müller T. Endogenous Fluorescence Tagging by CRISPR. Trends Cell Biol 2019; 29:912-928. [PMID: 31522960 DOI: 10.1016/j.tcb.2019.08.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 01/01/2023]
Abstract
Fluorescent proteins have revolutionized biomedical research as they are easy to use for protein tagging, cope without fixation or permeabilization, and thus, enable live cell imaging in various models. Current methods allow easy and quick integration of fluorescent markers to endogenous genes of interest. In this review, we introduce the three central methods, zinc finger nucleases (ZFNs), transcription activator-like effectors (TALENs), and CRISPR, that have been widely used to manipulate cells or organisms. Focusing on CRISPR technology, we give an overview on homology-directed repair (HDR)-, microhomology-mediated end joining (MMEJ)-, and nonhomologous end joining (NHEJ)-based strategies for the knock-in of markers, figure out recent developments of the technique for highly efficient knock-in, and demonstrate pros and cons. We highlight the unique aspects of fluorescent protein knock-ins and pinpoint specific improvements and perspectives, like the combination of editing with stem cell derived organoid development.
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Affiliation(s)
- Hassan Bukhari
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Molecular Biochemistry, Cell Signalling, Ruhr-University Bochum, Bochum, Germany
| | - Thorsten Müller
- Department of Molecular Biochemistry, Cell Signalling, Ruhr-University Bochum, Bochum, Germany; Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich 80336, Germany.
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22
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Bosshard S, Duroy PO, Mermod N. A role for alternative end-joining factors in homologous recombination and genome editing in Chinese hamster ovary cells. DNA Repair (Amst) 2019; 82:102691. [PMID: 31476574 DOI: 10.1016/j.dnarep.2019.102691] [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: 03/01/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022]
Abstract
CRISPR technologies greatly foster genome editing in mammalian cells through site-directed DNA double strand breaks (DSBs). However, precise editing outcomes, as mediated by homologous recombination (HR) repair, are typically infrequent and outnumbered by undesired genome alterations. By using knockdown and overexpression studies in Chinese hamster ovary (CHO) cells as well as characterizing repaired DNA junctions, we found that efficient HR-mediated genome editing depends on alternative end-joining (alt-EJ) DNA repair activities, a family of incompletely characterized DNA repair pathways traditionally considered to oppose HR. This dependency was influenced by the CRISPR nuclease type and the DSB-to-mutation distance, but not by the DNA sequence surrounding the DSBs or reporter cell line. We also identified elevated Mre11 and Pari, and low Rad51 expression levels as the most rate-limiting factors for HR in CHO cells. Counteracting these three bottlenecks improved precise genome editing by up to 75%. Altogether, our study provides novel insights into the complex interplay of alt-EJ and HR repair pathways, highlighting their relevance for developing improved genome editing strategies.
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Affiliation(s)
- Sandra Bosshard
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Pierre-Olivier Duroy
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Mermod
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
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23
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Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M, HamediRad M, Wang Y, Genova J, Ma J, Belmont AS, Zhao H. CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. Nucleic Acids Res 2019; 46:e100. [PMID: 29912475 PMCID: PMC6158506 DOI: 10.1093/nar/gky501] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 06/13/2018] [Indexed: 12/30/2022] Open
Abstract
Nuclear organization has an important role in determining genome function; however, it is not clear how spatiotemporal organization of the genome relates to functionality. To elucidate this relationship, a method for tracking any locus of interest is desirable. Recently clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or transcription activator-like effectors were adapted for imaging endogenous loci; however, they are mostly limited to visualization of repetitive regions. Here, we report an efficient and scalable method named SHACKTeR (Short Homology and CRISPR/Cas9-mediated Knock-in of a TetO Repeat) for live cell imaging of specific chromosomal regions without the need for a pre-existing repetitive sequence. SHACKTeR requires only two modifications to the genome: CRISPR/Cas9-mediated knock-in of an optimized TetO repeat and its visualization by TetR-EGFP expression. Our simplified knock-in protocol, utilizing short homology arms integrated by polymerase chain reaction, was successful at labeling 10 different loci in HCT116 cells. We also showed the feasibility of knock-in into lamina-associated, heterochromatin regions, demonstrating that these regions prefer non-homologous end joining for knock-in. Using SHACKTeR, we were able to observe DNA replication at a specific locus by long-term live cell imaging. We anticipate the general applicability and scalability of our method will enhance causative analyses between gene function and compartmentalization in a high-throughput manner.
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Affiliation(s)
- Ipek Tasan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gabriela Sustackova
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Liguo Zhang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jiah Kim
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mohammad HamediRad
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Justin Genova
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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24
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Miller JC, Patil DP, Xia DF, Paine CB, Fauser F, Richards HW, Shivak DA, Bendaña YR, Hinkley SJ, Scarlott NA, Lam SC, Reik A, Zhou Y, Paschon DE, Li P, Wangzor T, Lee G, Zhang L, Rebar EJ. Enhancing gene editing specificity by attenuating DNA cleavage kinetics. Nat Biotechnol 2019; 37:945-952. [PMID: 31359006 DOI: 10.1038/s41587-019-0186-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/11/2019] [Indexed: 12/22/2022]
Abstract
Engineered nucleases have gained broad appeal for their ability to mediate highly efficient genome editing. However the specificity of these reagents remains a concern, especially for therapeutic applications, given the potential mutagenic consequences of off-target cleavage. Here we have developed an approach for improving the specificity of zinc finger nucleases (ZFNs) that engineers the FokI catalytic domain with the aim of slowing cleavage, which should selectively reduce activity at low-affinity off-target sites. For three ZFN pairs, we engineered single-residue substitutions in the FokI domain that preserved full on-target activity but showed a reduction in off-target indels of up to 3,000-fold. By combining this approach with substitutions that reduced the affinity of zinc fingers, we developed ZFNs specific for the TRAC locus that mediated 98% knockout in T cells with no detectable off-target activity at an assay background of ~0.01%. We anticipate that this approach, and the FokI variants we report, will enable routine generation of nucleases for gene editing with no detectable off-target activity.
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Affiliation(s)
| | | | - Danny F Xia
- Sangamo Therapeutics, Inc., Richmond, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Patrick Li
- Sangamo Therapeutics, Inc., Richmond, CA, USA
| | | | - Gary Lee
- Sangamo Therapeutics, Inc., Richmond, CA, USA
| | - Lei Zhang
- Sangamo Therapeutics, Inc., Richmond, CA, USA
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25
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Harmsen T, Klaasen S, van de Vrugt H, Te Riele H. DNA mismatch repair and oligonucleotide end-protection promote base-pair substitution distal from a CRISPR/Cas9-induced DNA break. Nucleic Acids Res 2019; 46:2945-2955. [PMID: 29447381 PMCID: PMC5888797 DOI: 10.1093/nar/gky076] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/25/2018] [Indexed: 12/14/2022] Open
Abstract
Single-stranded oligodeoxyribonucleotide (ssODN)-mediated repair of CRISPR/Cas9-induced DNA double-strand breaks (DSB) can effectively be used to introduce small genomic alterations in a defined locus. Here, we reveal DNA mismatch repair (MMR) activity is crucial for efficient nucleotide substitution distal from the Cas9-induced DNA break when the substitution is instructed by the 3' half of the ssODN. Furthermore, protecting the ssODN 3' end with phosphorothioate linkages enhances MMR-dependent gene editing events. Our findings can be exploited to optimize efficiencies of nucleotide substitutions distal from the DSB and imply that oligonucleotide-mediated gene editing is effectuated by templated break repair.
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Affiliation(s)
- Tim Harmsen
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Sjoerd Klaasen
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Henri van de Vrugt
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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26
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Spiegel A, Bachmann M, Jurado Jiménez G, Sarov M. CRISPR/Cas9-based knockout pipeline for reverse genetics in mammalian cell culture. Methods 2019; 164-165:49-58. [PMID: 31051255 DOI: 10.1016/j.ymeth.2019.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/04/2019] [Accepted: 04/24/2019] [Indexed: 12/14/2022] Open
Abstract
We present a straightforward protocol for reverse genetics in cultured mammalian cells, using CRISPR/Cas9-mediated homology-dependent repair (HDR) based insertion of a protein trap cassette, resulting in a termination of the endogenous gene expression. Complete loss of function can be achieved with monoallelic trap cassette insertion, as the second allele is frequently disrupted by an error-prone non-homologous end joining (NHEJ) mechanism. The method should be applicable to any expressed gene in most cell lines, including those with low HDR efficiency, as the knockout alleles can be directly selected for.
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Affiliation(s)
- Aleksandra Spiegel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Mandy Bachmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Gabriel Jurado Jiménez
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
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27
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Bonawitz ND, Ainley WM, Itaya A, Chennareddy SR, Cicak T, Effinger K, Jiang K, Mall TK, Marri PR, Samuel JP, Sardesai N, Simpson M, Folkerts O, Sarria R, Webb SR, Gonzalez DO, Simmonds DH, Pareddy DR. Zinc finger nuclease-mediated targeting of multiple transgenes to an endogenous soybean genomic locus via non-homologous end joining. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:750-761. [PMID: 30220095 PMCID: PMC6419576 DOI: 10.1111/pbi.13012] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/29/2018] [Accepted: 09/10/2018] [Indexed: 05/03/2023]
Abstract
Emerging genome editing technologies hold great promise for the improvement of agricultural crops. Several related genome editing methods currently in development utilize engineered, sequence-specific endonucleases to generate DNA double strand breaks (DSBs) at user-specified genomic loci. These DSBs subsequently result in small insertions/deletions (indels), base substitutions or incorporation of exogenous donor sequences at the target site, depending on the application. Targeted mutagenesis in soybean (Glycine max) via non-homologous end joining (NHEJ)-mediated repair of such DSBs has been previously demonstrated with multiple nucleases, as has homology-directed repair (HDR)-mediated integration of a single transgene into target endogenous soybean loci using CRISPR/Cas9. Here we report targeted integration of multiple transgenes into a single soybean locus using a zinc finger nuclease (ZFN). First, we demonstrate targeted integration of biolistically delivered DNA via either HDR or NHEJ to the FATTY ACID DESATURASE 2-1a (FAD2-1a) locus of embryogenic cells in tissue culture. We then describe ZFN- and NHEJ-mediated, targeted integration of two different multigene donors to the FAD2-1a locus of immature embryos. The largest donor delivered was 16.2 kb, carried four transgenes, and was successfully transmitted to T1 progeny of mature targeted plants obtained via somatic embryogenesis. The insertions in most plants with a targeted, 7.1 kb, NHEJ-integrated donor were perfect or near-perfect, demonstrating that NHEJ is a viable alternative to HDR for gene targeting in soybean. Taken together, these results show that ZFNs can be used to generate fertile transgenic soybean plants with NHEJ-mediated targeted insertions of multigene donors at an endogenous genomic locus.
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Affiliation(s)
| | | | - Asuka Itaya
- Agriculture and Agri‐Food CanadaOttawaONCanada
| | | | | | | | - Ke Jiang
- Dow AgroSciences LLCIndianapolisINUSA
- Present address:
Genus IntelliGen TechnologiesWindsorWIUSA
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Porter SN, Levine RM, Pruett-Miller SM. A Practical Guide to Genome Editing Using Targeted Nuclease Technologies. Compr Physiol 2019; 9:665-714. [PMID: 30873595 DOI: 10.1002/cphy.c180022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome engineering using programmable nucleases is a rapidly evolving technique that enables precise genetic manipulations within complex genomes. Although this technology first surfaced with the creation of meganucleases, zinc finger nucleases, and transcription activator-like effector nucleases, CRISPR-Cas9 has been the most widely adopted platform because of its ease of use. This comprehensive review presents a basic overview of genome engineering and discusses the major technological advances in the field. In addition to nucleases, we discuss CRISPR-derived base editors and epigenetic modifiers. We also delve into practical applications of these tools, including creating custom-edited cell and animal models as well as performing genetic screens. Finally, we discuss the potential for therapeutic applications and ethical considerations related to employing this technology in humans. © 2019 American Physiological Society. Compr Physiol 9:665-714, 2019.
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Affiliation(s)
- Shaina N Porter
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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29
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Loureiro A, da Silva GJ. CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool. Antibiotics (Basel) 2019; 8:E18. [PMID: 30823430 PMCID: PMC6466564 DOI: 10.3390/antibiotics8010018] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/14/2019] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages are pervasive viruses that infect bacteria, relying on their genetic machinery to replicate. In order to protect themselves from this kind of invader, bacteria developed an ingenious adaptive defence system, clustered regularly interspaced short palindromic repeats (CRISPR). Researchers soon realised that a specific type of CRISPR system, CRISPR-Cas9, could be modified into a simple and efficient genetic engineering technology, with several improvements over currently used systems. This discovery set in motion a revolution in genetics, with new and improved CRISPR systems being used in plenty of in vitro and in vivo experiments in recent years. This review illustrates the mechanisms behind CRISPR-Cas systems as a means of bacterial immunity against phage invasion and how these systems were engineered to originate new genetic manipulation tools. Newfound CRISPR-Cas technologies and the up-and-coming applications of these systems on healthcare and other fields of science are also discussed.
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Affiliation(s)
- Alexandre Loureiro
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Health Sciences Campus, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal.
| | - Gabriela Jorge da Silva
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Health Sciences Campus, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal.
- Center for Neurosciences Cell Biology, University of Coimbra, 3000-548 Coimbra, Portugal.
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30
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Zhao J, Song Y, Liu D. Clinical trials of dual-target CAR T cells, donor-derived CAR T cells, and universal CAR T cells for acute lymphoid leukemia. J Hematol Oncol 2019; 12:17. [PMID: 30764841 PMCID: PMC6376657 DOI: 10.1186/s13045-019-0705-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/07/2019] [Indexed: 02/08/2023] Open
Abstract
The current treatment for pediatric acute lymphoblastic leukemia (ALL) is highly successful with high cure rate. However, the treatment of adult ALL remains a challenge, particularly for refractory and/or relapsed (R/R) ALL. The advent of new targeted agents, blinatumomab, inotuzumab ozogamycin, and chimeric antigen receptor (CAR) T cells, are changing the treatment paradigm for ALL. Tisagenlecleucel (kymriah, Novartis) is an autologous CD19-targeted CAR T cell product approved for treatment of R/R B cell ALL and lymphoma. In an attempt to reduce the relapse rate and treat those relapsed patients with antigen loss, donor-derived CAR T cells and CD19/CD22 dual-target CAR T cells are in clinical trials. Gene-edited “off-the-shelf” universal CAR T cells are also undergoing active clinical development. This review summarized new clinical trials and latest updates at the 2018 ASH Annual Meeting on CAR T therapy for ALL with a focus on dual-target CAR T and universal CAR T cell trials.
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Affiliation(s)
- Juanjuan Zhao
- The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008, China
| | - Yongping Song
- The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008, China
| | - Delong Liu
- The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, 127 Dongming Road, Zhengzhou, 450008, China.
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31
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Gridina ММ. Improvement of the knock-in effciency in the genome of human induced pluripotent stem cells using the CRISPR/Cas9 system. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj18.446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human induced pluripotent stem (hiPS) cells are a powerful tool for biomedical research. The ability to create patient-specifc pluripotent cells and their subsequent differentiation into any somatic cell type makes hiPS cells a valuable object for creating in vitro models of human diseases, screening drugs and a future source of cells for regenerative medicine. To realize entirely a potential of hiPScells, effective and precise methods for their genome editing are needed. The CRISPR/Cas9 system is the most widely used method for introducing site-specifc double-stranded breaks into DNA. It allows genes of interest to be knocked out with high efciency. However, knock-in into the target site of the genome is a much more difcult task. Moreover, many researchers have noted a low efciency of introducing target constructs into the hiPS cells’ genome. In this review, I attempt to describe the currently known information regarding the matter of increasing efciency of targeted insertions into hiPS cells’ genome. Here I will describe the most effective strategies for designing the donor template for homology-directed repair, methods to manipulate the double-strand break repair pathways introduced by a nuclease, including control of CRISPR/Cas9 delivery time. A low survival rate of hiPS cells following genome editing experiments is another difculty on the way towards successful knock-in, and here several highly effective approaches addressing it are proposed. Finally, I describe the most promising strategies, one-step reprogramming and genome editing, which allows gene-modifed integration-free hiPS cells to be efciently generated directly from somatic cells.
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32
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Abstract
The emergence of CRISPR/Cas9 system as a precise and affordable method for genome editing has prompted its rapid adoption for the targeted integration of transgenes in Chinese hamster ovary (CHO) cells. Targeted gene integration allows the generation of stable cell lines with a controlled and predictable behavior, which is an important feature for the rational design of cell factories aimed at the large-scale production of recombinant proteins. Here we present the protocol for CRISPR/Cas9-mediated integration of a gene expression cassette into a specific genomic locus in CHO cells using homology-directed DNA repair.
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33
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Que Q, Chen Z, Kelliher T, Skibbe D, Dong S, Chilton MD. Plant DNA Repair Pathways and Their Applications in Genome Engineering. Methods Mol Biol 2019; 1917:3-24. [PMID: 30610624 DOI: 10.1007/978-1-4939-8991-1_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Remarkable progress in the development of technologies for sequence-specific modification of primary DNA sequences has enabled the precise engineering of crops with novel characteristics. These programmable sequence-specific modifiers include site-directed nucleases (SDNs) and base editors (BEs). Currently, these genome editing machineries can be targeted to specific chromosomal locations to induce sequence changes. However, the sequence mutation outcomes are often greatly influenced by the type of DNA damage being generated, the status of host DNA repair machinery, and the presence and structure of DNA repair donor molecule. The outcome of sequence modification from repair of DNA double-strand breaks (DSBs) is often uncontrollable, resulting in unpredictable sequence insertions or deletions of various sizes. For base editing, the precision of intended edits is much higher, but the efficiency can vary greatly depending on the type of BE used or the activity of the endogenous DNA repair systems. This article will briefly review the possible DNA repair pathways present in the plant cells commonly used for generating edited variants for genome engineering applications. We will discuss the potential use of DNA repair mechanisms for developing and improving methodologies to enhance genome engineering efficiency and to direct DNA repair processes toward the desired outcomes.
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Affiliation(s)
- Qiudeng Que
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA.
| | - Zhongying Chen
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Tim Kelliher
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - David Skibbe
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Shujie Dong
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Mary-Dell Chilton
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
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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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35
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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: 27] [Impact Index Per Article: 4.5] [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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36
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Liu X, Wang M, Qin Y, Shi X, Cong P, Chen Y, He Z. Targeted integration in human cells through single crossover mediated by ZFN or CRISPR/Cas9. BMC Biotechnol 2018; 18:66. [PMID: 30340581 PMCID: PMC6194632 DOI: 10.1186/s12896-018-0474-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/28/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Targeted DNA integration is widely used in basic research and commercial applications because it eliminates positional effects on transgene expression. Targeted integration in mammalian cells is generally achieved through a double crossover event between the genome and a linear donor containing two homology arms flanking the gene of interest. However, this strategy is generally less efficient at introducing larger DNA fragments. Using the homology-independent NHEJ mechanism has recently been shown to improve efficiency of integrating larger DNA fragments at targeted sites, but integration through this mechanism is direction-independent. Therefore, developing new methods for direction-dependent integration with improved efficiency is desired. RESULTS We generated site-specific double-strand breaks using ZFNs or CRISPR/Cas9 in the human CCR5 gene and a donor plasmid containing a 1.6-kb fragment homologous to the CCR5 gene in the genome. These DSBs efficiently drove the direction-dependent integration of 6.4-kb plasmids into the genomes of two human cell lines through single-crossover recombination. The integration was direction-dependent and resulted in the duplication of the homology region in the genome, allowing the integration of another copy of the donor plasmid. The CRISPR/Cas9 system tended to disrupt the sgRNA-binding site within the duplicated homology region, preventing the integration of another plasmid donor. In contrast, ZFNs were less likely to completely disrupt their binding sites, allowing the successive integration of additional plasmid donor copies. This could be useful in promoting multi-copy integration for high-level expression of recombinant proteins. Targeted integration through single crossover recombination was highly efficient (frequency: 33%) as revealed by Southern blot analysis of clonal cells. This is more efficient than a previously described NHEJ-based method (0.17-0.45%) that was used to knock in an approximately 5-kb long DNA fragment. CONCLUSION We developed a method for the direction-dependent integration of large DNA fragments through single crossover recombination. We compared and contrasted our method to a previously reported technique for the direction-independent integration of DNA cassettes into the genomes of cultured cells via NHEJ. Our method, due to its directionality and ability to efficiently integrate large fragments, is an attractive strategy for both basic research and industrial application.
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Affiliation(s)
- Xiaofeng Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Min Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Yufeng Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Peiqing Cong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China.
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37
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Wu H, Liu Q, Shi H, Xie J, Zhang Q, Ouyang Z, Li N, Yang Y, Liu Z, Zhao Y, Lai C, Ruan D, Peng J, Ge W, Chen F, Fan N, Jin Q, Liang Y, Lan T, Yang X, Wang X, Lei Z, Doevendans PA, Sluijter JPG, Wang K, Li X, Lai L. Engineering CRISPR/Cpf1 with tRNA promotes genome editing capability in mammalian systems. Cell Mol Life Sci 2018; 75:3593-3607. [PMID: 29637228 PMCID: PMC11105780 DOI: 10.1007/s00018-018-2810-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/20/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022]
Abstract
CRISPR/Cpf1 features a number of properties that are distinct from CRISPR/Cas9 and provides an excellent alternative to Cas9 for genome editing. To date, genome engineering by CRISPR/Cpf1 has been reported only in human cells and mouse embryos of mammalian systems and its efficiency is ultimately lower than that of Cas9 proteins from Streptococcus pyogenes. The application of CRISPR/Cpf1 for targeted mutagenesis in other animal models has not been successfully verified. In this study, we designed and optimized a guide RNA (gRNA) transcription system by inserting a transfer RNA precursor (pre-tRNA) sequence downstream of the gRNA for Cpf1, protecting gRNA from immediate digestion by 3'-to-5' exonucleases. Using this new gRNAtRNA system, genome editing, including indels, large fragment deletion and precise point mutation, was induced in mammalian systems, showing significantly higher efficiency than the original Cpf1-gRNA system. With this system, gene-modified rabbits and pigs were generated by embryo injection or somatic cell nuclear transfer (SCNT) with an efficiency comparable to that of the Cas9 gRNA system. These results demonstrated that this refined gRNAtRNA system can boost the targeting capability of CRISPR/Cpf1 toolkits.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Animals, Newborn
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Cas Systems/genetics
- Cells, Cultured
- Cloning, Molecular/methods
- Cloning, Organism/methods
- Embryo, Mammalian
- Endonucleases/genetics
- Endonucleases/metabolism
- Female
- Fetus
- Gene Editing/methods
- Genome/genetics
- HEK293 Cells
- HeLa Cells
- Humans
- Male
- Mammals/embryology
- Mammals/genetics
- Mutagenesis
- Nuclear Transfer Techniques
- Pregnancy
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Transfer/genetics
- Rabbits
- Swine
- Swine, Miniature
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Affiliation(s)
- Han Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Qishuai Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Hui Shi
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jingke Xie
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Quanjun Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Zhen Ouyang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Nan Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yi Yang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Zhaoming Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yu Zhao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Chengdan Lai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Degong Ruan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiangyun Peng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Weikai Ge
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Fangbing Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Nana Fan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Qin Jin
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yanhui Liang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ting Lan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaoyu Yang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Xiaoshan Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Zhiyong Lei
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
- Netherlands Heart Institute, 3584CX, Utrecht, The Netherlands
| | - Pieter A Doevendans
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
- Netherlands Heart Institute, 3584CX, Utrecht, The Netherlands
| | - Joost P G Sluijter
- Department of Cardiology, Experimental Cardiology Laboratory, University Medical Center Utrecht, 3584CX, Utrecht, The Netherlands
- Netherlands Heart Institute, 3584CX, Utrecht, The Netherlands
| | - Kepin Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Xiaoping Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Liangxue Lai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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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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Haupt A, Grancharova T, Arakaki J, Fuqua MA, Roberts B, Gunawardane RN. Endogenous Protein Tagging in Human Induced Pluripotent Stem Cells Using CRISPR/Cas9. J Vis Exp 2018:58130. [PMID: 30199041 PMCID: PMC6231893 DOI: 10.3791/58130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A protocol is presented for generating human induced pluripotent stem cells (hiPSCs) that express endogenous proteins fused to in-frame N- or C-terminal fluorescent tags. The prokaryotic CRISPR/Cas9 system (clustered regularly interspaced short palindromic repeats/CRISPR-associated 9) may be used to introduce large exogenous sequences into genomic loci via homology directed repair (HDR). To achieve the desired knock-in, this protocol employs the ribonucleoprotein (RNP)-based approach where wild type Streptococcus pyogenes Cas9 protein, synthetic 2-part guide RNA (gRNA), and a donor template plasmid are delivered to the cells via electroporation. Putatively edited cells expressing the fluorescently tagged proteins are enriched by fluorescence activated cell sorting (FACS). Clonal lines are then generated and can be analyzed for precise editing outcomes. By introducing the fluorescent tag at the genomic locus of the gene of interest, the resulting subcellular localization and dynamics of the fusion protein can be studied under endogenous regulatory control, a key improvement over conventional overexpression systems. The use of hiPSCs as a model system for gene tagging provides the opportunity to study the tagged proteins in diploid, nontransformed cells. Since hiPSCs can be differentiated into multiple cell types, this approach provides the opportunity to create and study tagged proteins in a variety of isogenic cellular contexts.
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Shin JH, Jung S, Ramakrishna S, Kim HH, Lee J. In vivo gene correction with targeted sequence substitution through microhomology-mediated end joining. Biochem Biophys Res Commun 2018; 502:116-122. [PMID: 29787760 DOI: 10.1016/j.bbrc.2018.05.130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 11/21/2022]
Abstract
Genome editing technology using programmable nucleases has rapidly evolved in recent years. The primary mechanism to achieve precise integration of a transgene is mainly based on homology-directed repair (HDR). However, an HDR-based genome-editing approach is less efficient than non-homologous end-joining (NHEJ). Recently, a microhomology-mediated end-joining (MMEJ)-based transgene integration approach was developed, showing feasibility both in vitro and in vivo. We expanded this method to achieve targeted sequence substitution (TSS) of mutated sequences with normal sequences using double-guide RNAs (gRNAs), and a donor template flanking the microhomologies and target sequence of the gRNAs in vitro and in vivo. Our method could realize more efficient sequence substitution than the HDR-based method in vitro using a reporter cell line, and led to the survival of a hereditary tyrosinemia mouse model in vivo. The proposed MMEJ-based TSS approach could provide a novel therapeutic strategy, in addition to HDR, to achieve gene correction from a mutated sequence to a normal sequence.
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Affiliation(s)
- Jeong Hong Shin
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea
| | - Soobin Jung
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea; Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, South Korea; Yonsei-IBS Institute, Yonsei University, Seoul, South Korea.
| | - Junwon Lee
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea; Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, Seoul, South Korea.
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41
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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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42
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Abstract
Prokaryotic type II adaptive immune systems have been developed into the versatile CRISPR technology, which has been widely applied in site-specific genome editing and has revolutionized biomedical research due to its superior efficiency and flexibility. Recent studies have greatly diversified CRISPR technologies by coupling it with various DNA repair mechanisms and targeting strategies. These new advances have significantly expanded the generation of genetically modified animal models, either by including species in which targeted genetic modification could not be achieved previously, or through introducing complex genetic modifications that take multiple steps and cost years to achieve using traditional methods. Herein, we review the recent developments and applications of CRISPR-based technology in generating various animal models, and discuss the everlasting impact of this new progress on biomedical research.
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Affiliation(s)
- Xun Ma
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Avery Sum-Yu Wong
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Hei-Yin Tam
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Samuel Yung-Kin Tsui
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Dittman Lai-Shun Chung
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Bo Feng
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Guangdong 510530, China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen Guangdong 518057, China
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43
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Woodard LE, Galvan DL, Wilson MH. Site-Directed Genome Modification with Engineered Zinc Finger Proteins. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Lauren E. Woodard
- Department of Veterans Affairs; Nashville TN 37212 USA
- Vanderbilt University Medical Center; Department of Medicine, Department of Pharmacology; Nashville TN 37232 USA
| | - Daniel L. Galvan
- University of Texas at MD Anderson Cancer Center; Section of Nephrology; Houston TX 77030 USA
| | - Matthew H. Wilson
- Department of Veterans Affairs; Nashville TN 37212 USA
- Vanderbilt University Medical Center; Department of Medicine, Department of Pharmacology; Nashville TN 37232 USA
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Yanik M, Ponnam SPG, Wimmer T, Trimborn L, Müller C, Gambert I, Ginsberg J, Janise A, Domicke J, Wende W, Lorenz B, Stieger K. Development of a Reporter System to Explore MMEJ in the Context of Replacing Large Genomic Fragments. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 11:407-415. [PMID: 29858075 PMCID: PMC5992787 DOI: 10.1016/j.omtn.2018.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/13/2018] [Accepted: 03/20/2018] [Indexed: 01/21/2023]
Abstract
Common genome-editing strategies are either based on non-homologous end joining (NHEJ) or, in the presence of a template DNA, based on homologous recombination with long (homology-directed repair [HDR]) or short (microhomology-mediated end joining [MMEJ]) homologous sequences. In the current study, we aim to develop a model system to test the activity of MMEJ after CRISPR/Cas9-mediated cleavage in cell culture. Following successful proof of concept in an episomally based reporter system, we tested template plasmids containing a promoter-less luciferase gene flanked by microhomologous sequences (mhs) of different length (5, 10, 15, 20, 30, and 50 bp) that are complementary to the mouse retinitis pigmentosa GTPase regulator (RPGR)-ORF15, which is under the control of a CMV promoter stably integrated into a HEK293 cell line. Luciferase signal appearance represented successful recombination events and was highest when the mhs were 5 bp long, while longer mhs revealed lower luciferase signal. In addition, presence of Csy4 RNase was shown to increase luciferase signaling. The luciferase reporter system is a valuable tool to study the input of the different DNA repair mechanisms in the replacement of large DNA sequences by mhs.
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Affiliation(s)
- Mert Yanik
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Surya Prakash Goud Ponnam
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany; Department of Molecular Biology & Biotechnology, Tezpur University, Napaam, Assam 784028, India
| | - Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Lennart Trimborn
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Carina Müller
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Isabel Gambert
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Johanna Ginsberg
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Annabella Janise
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Janina Domicke
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Wolfgang Wende
- Institute for Biochemistry, Justus-Liebig-University, Giessen 35392, Germany
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University, Giessen 35392, Germany.
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45
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Kim SI, Matsumoto T, Kagawa H, Nakamura M, Hirohata R, Ueno A, Ohishi M, Sakuma T, Soga T, Yamamoto T, Woltjen K. Microhomology-assisted scarless genome editing in human iPSCs. Nat Commun 2018; 9:939. [PMID: 29507284 PMCID: PMC5838097 DOI: 10.1038/s41467-018-03044-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 01/16/2018] [Indexed: 12/26/2022] Open
Abstract
Gene-edited induced pluripotent stem cells (iPSCs) provide relevant isogenic human disease models in patient-specific or healthy genetic backgrounds. Towards this end, gene targeting using antibiotic selection along with engineered point mutations remains a reliable method to enrich edited cells. Nevertheless, integrated selection markers obstruct scarless transgene-free gene editing. Here, we present a method for scarless selection marker excision using engineered microhomology-mediated end joining (MMEJ). By overlapping the homology arms of standard donor vectors, short tandem microhomologies are generated flanking the selection marker. Unique CRISPR-Cas9 protospacer sequences nested between the selection marker and engineered microhomologies are cleaved after gene targeting, engaging MMEJ and scarless excision. Moreover, when point mutations are positioned unilaterally within engineered microhomologies, both mutant and normal isogenic clones are derived simultaneously. The utility and fidelity of our method is demonstrated in human iPSCs by editing the X-linked HPRT1 locus and biallelic modification of the autosomal APRT locus, eliciting disease-relevant metabolic phenotypes.
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Affiliation(s)
- Shin-Il Kim
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Tomoko Matsumoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Harunobu Kagawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Michiko Nakamura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Ryoko Hirohata
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Ayano Ueno
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Maki Ohishi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, 739-8526, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, 739-8526, Japan
| | - Knut Woltjen
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan. .,Hakubi Center for Advanced Research, Kyoto University, Kyoto, 606-8501, Japan.
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Gutierrez-Guerrero A, Sanchez-Hernandez S, Galvani G, Pinedo-Gomez J, Martin-Guerra R, Sanchez-Gilabert A, Aguilar-González A, Cobo M, Gregory P, Holmes M, Benabdellah K, Martin F. Comparison of Zinc Finger Nucleases Versus CRISPR-Specific Nucleases for Genome Editing of the Wiskott-Aldrich Syndrome Locus. Hum Gene Ther 2018; 29:366-380. [DOI: 10.1089/hum.2017.047] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Alejandra Gutierrez-Guerrero
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Sabina Sanchez-Hernandez
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Giuseppe Galvani
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Javier Pinedo-Gomez
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Rocio Martin-Guerra
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Almudena Sanchez-Gilabert
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Araceli Aguilar-González
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Marién Cobo
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
- LentiStem Biotech, Granada, Spain
| | - Philip Gregory
- Sangamo BioSciences, Point Richmond Tech Center, Richmond, California
| | - Michael Holmes
- Sangamo BioSciences, Point Richmond Tech Center, Richmond, California
| | - Karim Benabdellah
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
- LentiStem Biotech, Granada, Spain
| | - Francisco Martin
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
- LentiStem Biotech, Granada, Spain
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47
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Pawelczak KS, Gavande NS, VanderVere-Carozza PS, Turchi JJ. Modulating DNA Repair Pathways to Improve Precision Genome Engineering. ACS Chem Biol 2018; 13:389-396. [PMID: 29210569 DOI: 10.1021/acschembio.7b00777] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Programmable nucleases like the popular CRISPR/Cas9 system allow for precision genome engineering by inducing a site-specific DNA double strand break (DSB) within a genome. The DSB is repaired by endogenous DNA repair pathways, either nonhomologous end joining (NHEJ) or homology directed repair (HDR). The predominant and error-prone NHEJ pathway often results in small nucleotide insertions or deletions that can be used to construct knockout alleles. Alternatively, HDR activity can result in precise modification incorporating exogenous DNA fragments into the cut site. However, genetic recombination in mammalian systems through the HDR pathway is an inefficient process and requires cumbersome laboratory methods to identify the desired accurate insertion events. This is further compromised by the activity of the competing DNA repair pathway, NHEJ, which repairs the majority of nuclease induced DNA DSBs and also is responsible for mutagenic insertion and deletion events at off-target locations throughout the genome. Various methodologies have been developed to increase the efficiency of designer nuclease-based HDR mediated gene editing. Here, we review these advances toward modulating the activities of the two critical DNA repair pathways, HDR and NHEJ, to enhance precision genome engineering.
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Affiliation(s)
- Katherine S. Pawelczak
- NERx Biosciences, 212 W 10th
Street, Suite A480, Indianapolis, Indiana 46202, United States
| | | | | | - John J. Turchi
- NERx Biosciences, 212 W 10th
Street, Suite A480, Indianapolis, Indiana 46202, United States
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48
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Tálas A, Kulcsár PI, Weinhardt N, Borsy A, Tóth E, Szebényi K, Krausz SL, Huszár K, Vida I, Sturm Á, Gordos B, Hoffmann OI, Bencsura P, Nyeste A, Ligeti Z, Fodor E, Welker E. A convenient method to pre-screen candidate guide RNAs for CRISPR/Cas9 gene editing by NHEJ-mediated integration of a 'self-cleaving' GFP-expression plasmid. DNA Res 2017; 24:609-621. [PMID: 28679166 PMCID: PMC5726473 DOI: 10.1093/dnares/dsx029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 06/07/2017] [Indexed: 12/20/2022] Open
Abstract
The efficacies of guide RNAs (gRNAs), the short RNA molecules that bind to and determine the sequence specificity of the Streptococcus pyogenes Cas9 nuclease, to mediate DNA cleavage vary dramatically. Thus, the selection of appropriate target sites, and hence spacer sequence, is critical for most applications. Here, we describe a simple, unparalleled method for experimentally pre-testing the efficiencies of various gRNAs targeting a gene. The method explores NHEJ-cloning, genomic integration of a GFP-expressing plasmid without homologous arms and linearized in-cell. The use of 'self-cleaving' GFP-plasmids containing universal gRNAs and corresponding targets alleviates cloning burdens when this method is applied. These universal gRNAs mediate efficient plasmid cleavage and are designed to avoid genomic targets in several model species. The method combines the advantages of the straightforward FACS detection provided by applying fluorescent reporter systems and of the PCR-based approaches being capable of testing targets in their genomic context, without necessitating any extra cloning steps. Additionally, we show that NHEJ-cloning can also be used in mammalian cells for targeted integration of donor plasmids up to 10 kb in size, with up to 30% efficiency, without any selection or enrichment.
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Affiliation(s)
- András Tálas
- School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- University of Szeged, Szeged, Hungary
| | - Nóra Weinhardt
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- University of Szeged, Szeged, Hungary
| | - Adrienn Borsy
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Kornélia Szebényi
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Sarah Laura Krausz
- School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - István Vida
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Organic Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ádám Sturm
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Bianka Gordos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Orsolya Ivett Hoffmann
- Animal Biotechnology Section, Ruminant Genome Biology Group, NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Petra Bencsura
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
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49
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Gaj T, Staahl BT, Rodrigues GMC, Limsirichai P, Ekman FK, Doudna JA, Schaffer DV. Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery. Nucleic Acids Res 2017; 45:e98. [PMID: 28334779 PMCID: PMC5499784 DOI: 10.1093/nar/gkx154] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/22/2017] [Indexed: 12/27/2022] Open
Abstract
Realizing the full potential of genome editing requires the development of efficient and broadly applicable methods for delivering programmable nucleases and donor templates for homology-directed repair (HDR). The RNA-guided Cas9 endonuclease can be introduced into cells as a purified protein in complex with a single guide RNA (sgRNA). Such ribonucleoproteins (RNPs) can facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a single-stranded DNA oligonucleotide. However, combining RNPs with transgene-containing donor templates for targeted gene addition has proven challenging, which in turn has limited the capabilities of the RNP-mediated genome editing toolbox. Here, we demonstrate that combining RNP delivery with naturally recombinogenic adeno-associated virus (AAV) donor vectors enables site-specific gene insertion by homology-directed genome editing. Compared to conventional plasmid-based expression vectors and donor templates, we show that combining RNP and AAV donor delivery increases the efficiency of gene addition by up to 12-fold, enabling the creation of lineage reporters that can be used to track the conversion of striatal neurons from human fibroblasts in real time. These results thus illustrate the potential for unifying nuclease protein delivery with AAV donor vectors for homology-directed genome editing.
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Affiliation(s)
- Thomas Gaj
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brett T Staahl
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Gonçalo M C Rodrigues
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Prajit Limsirichai
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Freja K Ekman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David V Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA.,Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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Baker O, Tsurkan S, Fu J, Klink B, Rump A, Obst M, Kranz A, Schröck E, Anastassiadis K, Stewart AF. The contribution of homology arms to nuclease-assisted genome engineering. Nucleic Acids Res 2017; 45:8105-8115. [PMID: 28582546 PMCID: PMC5570031 DOI: 10.1093/nar/gkx497] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/30/2017] [Indexed: 01/29/2023] Open
Abstract
Designer nucleases like CRISPR/Cas9 enable fluent site-directed damage or small mutations in many genomes. Strategies for their use to achieve more complex tasks like regional exchanges for gene humanization or the establishment of conditional alleles are still emerging. To optimize Cas9-assisted targeting, we measured the relationship between targeting frequency and homology length in targeting constructs using a hypoxanthine-guanine phosphoribosyl-transferase assay in mouse embryonic stem cells. Targeting frequency with supercoiled plasmids improved steeply up to 2 kb total homology and continued to increase with even longer homology arms, thereby implying that Cas9-assisted targeting efficiencies can be improved using homology arms of 1 kb or greater. To humanize the Kmt2d gene, we built a hybrid mouse/human targeting construct in a bacterial artificial chromosome by recombineering. To simplify the possible outcomes, we employed a single Cas9 cleavage strategy and best achieved the intended 42 kb regional exchange with a targeting construct including a very long homology arm to recombine ∼42 kb away from the cleavage site. We recommend the use of long homology arm targeting constructs for accurate and efficient complex genome engineering, particularly when combined with the simplifying advantages of using just one Cas9 cleavage at the genome target site.
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Affiliation(s)
- Oliver Baker
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany.,Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Sarah Tsurkan
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany.,Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Barbara Klink
- Institute for Clinical Genetics, Faculty of Medicine, Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Andreas Rump
- Institute for Clinical Genetics, Faculty of Medicine, Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Mandy Obst
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany.,Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, Faculty of Medicine, Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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