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Djedovic R, Radojkovic D, Stanojevic D, Savic R, Vukasinovic N, Popovac M, Bogdanovic V, Radovic C, Gogic M, Gligovic N, Stojic P, Mitrovic I. Base Characteristics, Preservation Methods, and Assessment of the Genetic Diversity of Autochthonous Breeds of Cattle, Sheep and Pigs in Serbia: A Review. Animals (Basel) 2024; 14:1894. [PMID: 38998006 PMCID: PMC11240667 DOI: 10.3390/ani14131894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/23/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024] Open
Abstract
Preserving local autochthonous domestic animal populations and the products derived from them is a crucial aspect of managing human utilization of the biosphere. This management approach aims to ensure sustainable benefits for both present and future generations. The diversity of autochthonous domestic animal populations plays a vital role in the functionality and sustainability of the food production system. It encompasses both productive and non-productive aspects, contributing significantly to the overall health, nutrition, and food security of the landscape by providing a wide range of animal-derived food resources. Based on the data contained in the Draft Program of Rural Development, a significant presence of more than 44 autochthonous and local breeds of domestic animals has been noted in Serbia. In order to enable the sustainable preservation of local domestic animals, the competent Ministry of Agriculture of the Republic of Serbia has, through a number of projects, implemented models for the preservation of local breeds on farms (in situ), as well as provided technical assistance to small farms that keep animal collections. It also helps the local population to procure animals, conducts product quality research, and provides opportunities to integrate conservation programs through tourism. Given that molecular characterization is a key factor for the preservation of autochthonous breeds, in the Republic of Serbia, DNA markers are used for identification and to investigate the belonging to a specific breeds or strain. All the mentioned activities led to an immediate increase in the number of animals, which is especially true for the autochthonous breeds of cattle (Busha), sheep (Sjenicka, Svrljiska, and Vlach-vitohorn) and pigs (Mangalitsa, Moravka, and Resavka) that are discussed in this paper. In addition to the significant measures undertaken to preserve animal genetic resources (AnGR), it is necessary to continue to work primarily on ex situ conservation in order to prevent the loss of their gene pools. However, regardless of the evident effort that has been made to preserve autochthonous genetic resources in Serbia, we believe that there is still a lot of room for further improvement. This primarily refers to advanced technologies that have not been applied so far, mostly related to the identification of genomic regions associated with economic traits, resistance to diseases, and adaptability to emerging climate changes. In this way, the production capacity and functional characteristics of autochthonous species and breeds of domestic animals in Serbia will be improved.
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Affiliation(s)
- Radica Djedovic
- Department of Animal Science, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia; (D.R.); (D.S.); (R.S.); (M.P.); (V.B.); (N.G.); (I.M.)
| | - Dragan Radojkovic
- Department of Animal Science, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia; (D.R.); (D.S.); (R.S.); (M.P.); (V.B.); (N.G.); (I.M.)
| | - Dragan Stanojevic
- Department of Animal Science, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia; (D.R.); (D.S.); (R.S.); (M.P.); (V.B.); (N.G.); (I.M.)
| | - Radomir Savic
- Department of Animal Science, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia; (D.R.); (D.S.); (R.S.); (M.P.); (V.B.); (N.G.); (I.M.)
| | - Natasha Vukasinovic
- Zoetis Veterinary Medicine Research and Development (VMRD), Kalamazoo, MI 49001, USA;
| | - Mladen Popovac
- Department of Animal Science, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia; (D.R.); (D.S.); (R.S.); (M.P.); (V.B.); (N.G.); (I.M.)
| | - Vladan Bogdanovic
- Department of Animal Science, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia; (D.R.); (D.S.); (R.S.); (M.P.); (V.B.); (N.G.); (I.M.)
| | - Cedomir Radovic
- Institute for Animal Husbandry, 11080 Belgrade, Serbia; (C.R.); (M.G.)
| | - Marija Gogic
- Institute for Animal Husbandry, 11080 Belgrade, Serbia; (C.R.); (M.G.)
| | - Nikolija Gligovic
- Department of Animal Science, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia; (D.R.); (D.S.); (R.S.); (M.P.); (V.B.); (N.G.); (I.M.)
| | - Petar Stojic
- Institute for Science Application in Agriculture, Bulevar Despota Stefana 68b, 11000 Belgrade, Serbia;
| | - Ivan Mitrovic
- Department of Animal Science, Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia; (D.R.); (D.S.); (R.S.); (M.P.); (V.B.); (N.G.); (I.M.)
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Barriga FM, Lowe SW. Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements). Nat Protoc 2024; 19:1381-1399. [PMID: 38326496 DOI: 10.1038/s41596-024-00953-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/21/2023] [Indexed: 02/09/2024]
Abstract
The elimination of large genomic regions has been enabled by the advent of site-specific nucleases. However, as the intended deletions get larger, the efficiency of successful engineering decreases to a point where it is not feasible to retrieve edited cells due to the rarity of on-target events. To address this issue, we developed a system called molecular alteration of chromosomes with engineered tandem elements (MACHETE). MACHETE is a CRISPR-Cas9-based system involving two stages: the initial insertion of a bicistronic positive/negative selection cassette to the locus of interest. This is followed by the introduction of single-guide RNAs flanking the knockin cassette to engineer the intended deletion, where only cells that have lost the locus survive the negative selection. In contrast to other approaches optimizing the activity of sequence-specific nucleases, MACHETE selects for the deletion event itself, thus greatly enriching for cells with the engineered alteration. The procedure routinely takes 4-6 weeks from design to selection of polyclonal populations bearing the deletion of interest. We have successfully deployed MACHETE to engineer deletions of up to 45 Mb, as well as the rapid creation of allelic series to map the relevant activities within a locus. This protocol details the design and step-by-step procedure to engineer megabase-sized deletions in cells of interest, with potential application for cancer genetics, transcriptional regulation, genome architecture and beyond.
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Affiliation(s)
- Francisco M Barriga
- Systems Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
| | - Scott W Lowe
- Cancer Biology and Genetics Program and Howard Hughes Medical Institute, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Jerabek T, Weiß L, Fahrion H, Zeh N, Raab N, Lindner B, Fischer S, Otte K. In pursuit of a minimal CHO genome: Establishment of large-scale genome deletions. N Biotechnol 2024; 79:100-110. [PMID: 38154614 DOI: 10.1016/j.nbt.2023.12.007] [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] [Received: 10/20/2023] [Revised: 11/27/2023] [Accepted: 12/24/2023] [Indexed: 12/30/2023]
Abstract
Chinese hamster ovary (CHO) cells are the most commonly used mammalian cell line for the production of complex therapeutic glycoproteins. As CHO cells have evolved as part of a multicellular organism, they harbor many cellular functions irrelevant for their application as production hosts in industrial bioprocesses. Consequently, CHO cells have been the target for numerous genetic engineering efforts in the past, but a tailored host cell chassis holistically optimized for its specific task in a bioreactor is still missing. While the concept of genome reduction has already been successfully applied to bacterial production cells, attempts to create higher eukaryotic production hosts exhibiting reduced genomes have not been reported yet. Here, we present the establishment and application of a large-scale genome deletion strategy for targeted excision of large genomic regions in CHO cells. We demonstrate the feasibility of genome reduction in CHO cells using optimized CRISPR/Cas9 based experimental protocols targeting large non-essential genomic regions with high efficiency. Achieved genome deletions of non-essential genetic regions did not introduce negative effects on bioprocess relevant parameters, although we conducted the largest reported genomic excision of 864 kilobase pairs in CHO cells so far. The concept presented serves as a directive to accelerate the development of a significantly genome-reduced CHO host cell chassis paving the way for a next generation of CHO cell factories.
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Affiliation(s)
- Tobias Jerabek
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany.
| | - Linus Weiß
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| | - Hannah Fahrion
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| | - Nikolas Zeh
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany; Boehringer Ingelheim Pharma GmbH & Co KG, Bioprocess Development Biologicals, Cell Line Development, Biberach, Germany
| | - Nadja Raab
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| | - Benjamin Lindner
- Boehringer Ingelheim Pharma GmbH & Co KG, Bioprocess Development Biologicals, Cell Line Development, Biberach, Germany
| | - Simon Fischer
- Boehringer Ingelheim Pharma GmbH & Co KG, Bioprocess Development Biologicals, Cell Line Development, Biberach, Germany
| | - Kerstin Otte
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
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Komori T, Hata S, Mabuchi A, Genova M, Harada T, Fukuyama M, Chinen T, Kitagawa D. A CRISPR-del-based pipeline for complete gene knockout in human diploid cells. J Cell Sci 2023; 136:286993. [PMID: 36762651 PMCID: PMC10038147 DOI: 10.1242/jcs.260000] [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: 03/07/2022] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
The advance of CRISPR/Cas9 technology has enabled us easily to generate gene knockout cell lines by introducing insertion-deletion mutations (indels) at the target site via the error-prone non-homologous end joining repair system. Frameshift-promoting indels can disrupt gene functions by generation of a premature stop codon. However, there is growing evidence that targeted genes are not always knocked out by the indel-based gene disruption. Here, we established a pipeline of CRISPR-del, which induces a large chromosomal deletion by cutting two different target sites, to perform 'complete' gene knockout efficiently in human diploid cells. Quantitative analyses show that the frequency of gene deletion with this approach is much higher than that of conventional CRISPR-del methods. The lengths of the deleted genomic regions demonstrated in this study are longer than those of 95% of the human protein-coding genes. Furthermore, the pipeline enabled the generation of a model cell line having a bi-allelic cancer-associated chromosomal deletion. Overall, these data lead us to propose that the CRISPR-del pipeline is an efficient and practical approach for producing 'complete' gene knockout cell lines in human diploid cells.
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Affiliation(s)
- Takuma Komori
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Shoji Hata
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO) Program, Japan Science and Technology Agency, Honcho Kawaguchi, 102-8666 Saitama, Japan
| | - Akira Mabuchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Mariya Genova
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, 69120 Heidelberg, Germany
| | - Tomoki Harada
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Masamitsu Fukuyama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Takumi Chinen
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033 Tokyo, Japan
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Jiang T, Wen K, Liao A, Wang Y, Jiao Y, Guo J, Chen Y, He Z, Cong P. Efficient editing BMP15 in porcine oocytes through microinjection of CRISPR ctRNP. Theriogenology 2023; 198:241-249. [PMID: 36621133 DOI: 10.1016/j.theriogenology.2022.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Bone morphogenetic protein 15 (BMP15) is an X-linked gene encoding an oocyte secreted factor, which plays varied functions in the female fertility between mono-ovulatory and poly-ovulatory mammalian species. We previously found that knockout of BMP15 completely blocked porcine follicular development at preantral stages. However, the specific function of BMP15 on porcine oocytes in vitro maturation remains largely unknown. Here, we injected the pre-assembled crRNA + tracrRNA + Cas9 ribonucleoprotein (ctRNP) complex into the cytoplasm of germinal vesicle stage porcine oocytes to disrupt BMP15. The ctRNP composed of Cas9 nuclease and crRNA-tracrRNA complex at 1.2/1 content ratio. The tested crRNA-tracrRNA complex concentration ranging from 50 to 200 ng/μL, all presented effective editing of BMP15 in porcine oocytes, and the 125 ng/μL crRNA-tracrRNA complex presented the highest editing efficiency (39.23 ± 3.33%). Surprisingly, we found approximately 95% edited oocytes presented monoallelic mutations, and only 5% edited oocytes harbored biallelic mutations. Interestingly, the coinjected two crRNAs guided the ctRNP complex to concurrently cut within a 10 bp window of the PAM (protospacer adjacent motif), resulting in a precise deletion within BMP15 in 85.9% edited oocytes, and additional deletion happened in 14.1% edited oocytes, which resulted in large fragment deletions in BMP15. Most deletions caused frameshift and introduced premature stop codon in BMP15, resulting in the disruption of BMP15 protein expression, which was confirmed by the Western blot analysis showing the reduced BMP15 protein expression in ctRNP injected oocytes. The disruption of BMP15 attenuated the activation of SMAD1/5/8 signaling, and impaired cumulus expansion of porcine cumulus cell-oocyte complexes (COCs). Our study proved that delivering CRISPR ctRNP into porcine oocytes by microinjection was able to edit BMP15 efficiently, providing a new strategy to investigate the functions of oocyte-specific secreted factors in oocyte in vitro maturation.
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Affiliation(s)
- Tiantuan Jiang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Keying Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Alian Liao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yixian Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yafei Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jinming Guo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Peiqing Cong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China.
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6
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CRISPR-Cas9 Technology for the Creation of Biological Avatars Capable of Modeling and Treating Pathologies: From Discovery to the Latest Improvements. Cells 2022; 11:cells11223615. [PMID: 36429042 PMCID: PMC9688409 DOI: 10.3390/cells11223615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
This is a spectacular moment for genetics to evolve in genome editing, which encompasses the precise alteration of the cellular DNA sequences within various species. One of the most fascinating genome-editing technologies currently available is Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its associated protein 9 (CRISPR-Cas9), which have integrated deeply into the research field within a short period due to its effectiveness. It became a standard tool utilized in a broad spectrum of biological and therapeutic applications. Furthermore, reliable disease models are required to improve the quality of healthcare. CRISPR-Cas9 has the potential to diversify our knowledge in genetics by generating cellular models, which can mimic various human diseases to better understand the disease consequences and develop new treatments. Precision in genome editing offered by CRISPR-Cas9 is now paving the way for gene therapy to expand in clinical trials to treat several genetic diseases in a wide range of species. This review article will discuss genome-editing tools: CRISPR-Cas9, Zinc Finger Nucleases (ZFNs), and Transcription Activator-Like Effector Nucleases (TALENs). It will also encompass the importance of CRISPR-Cas9 technology in generating cellular disease models for novel therapeutics, its applications in gene therapy, and challenges with novel strategies to enhance its specificity.
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Barriga FM, Tsanov KM, Ho YJ, Sohail N, Zhang A, Baslan T, Wuest AN, Del Priore I, Meškauskaitė B, Livshits G, Alonso-Curbelo D, Simon J, Chaves-Perez A, Bar-Sagi D, Iacobuzio-Donahue CA, Notta F, Chaligne R, Sharma R, Pe'er D, Lowe SW. MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis. NATURE CANCER 2022; 3:1367-1385. [PMID: 36344707 PMCID: PMC9701143 DOI: 10.1038/s43018-022-00443-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022]
Abstract
The most prominent homozygous deletions in cancer affect chromosome 9p21.3 and eliminate CDKN2A/B tumor suppressors, disabling a cell-intrinsic barrier to tumorigenesis. Half of 9p21.3 deletions, however, also encompass a type I interferon (IFN) gene cluster; the consequences of this co-deletion remain unexplored. To functionally dissect 9p21.3 and other large genomic deletions, we developed a flexible deletion engineering strategy, MACHETE (molecular alteration of chromosomes with engineered tandem elements). Applying MACHETE to a syngeneic mouse model of pancreatic cancer, we found that co-deletion of the IFN cluster promoted immune evasion, metastasis and immunotherapy resistance. Mechanistically, IFN co-deletion disrupted type I IFN signaling in the tumor microenvironment, leading to marked changes in infiltrating immune cells and escape from CD8+ T-cell surveillance, effects largely driven by the poorly understood interferon epsilon. These results reveal a chromosomal deletion that disables both cell-intrinsic and cell-extrinsic tumor suppression and provide a framework for interrogating large deletions in cancer and beyond.
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Affiliation(s)
- Francisco M Barriga
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Noor Sohail
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Timour Baslan
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra N Wuest
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Isabella Del Priore
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Brigita Meškauskaitė
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geulah Livshits
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Direna Alonso-Curbelo
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janelle Simon
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Almudena Chaves-Perez
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dafna Bar-Sagi
- Department of Biochemistry, New York University School of Medicine, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ronan Chaligne
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Chunduri NK, Barthel K, Storchova Z. Consequences of Chromosome Loss: Why Do Cells Need Each Chromosome Twice? Cells 2022; 11:1530. [PMID: 35563836 PMCID: PMC9101035 DOI: 10.3390/cells11091530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
Aneuploidy is a cellular state with an unbalanced chromosome number that deviates from the usual euploid status. During evolution, elaborate cellular mechanisms have evolved to maintain the correct chromosome content over generations. The rare errors often lead to cell death, cell cycle arrest, or impaired proliferation. At the same time, aneuploidy can provide a growth advantage under selective conditions in a stressful, frequently changing environment. This is likely why aneuploidy is commonly found in cancer cells, where it correlates with malignancy, drug resistance, and poor prognosis. To understand this "aneuploidy paradox", model systems have been established and analyzed to investigate the consequences of aneuploidy. Most of the evidence to date has been based on models with chromosomes gains, but chromosome losses and recurrent monosomies can also be found in cancer. We summarize the current models of chromosome loss and our understanding of its consequences, particularly in comparison to chromosome gains.
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Affiliation(s)
- Narendra Kumar Chunduri
- University Medical Center Groningen, European Research Institute for the Biology of Ageing, University of Groningen, 9713 AV Groningen, The Netherlands;
| | - Karen Barthel
- Department of molecular genetics, University of Kaiserslautern, 67663 Kaiserslautern, Germany;
| | - Zuzana Storchova
- Department of molecular genetics, University of Kaiserslautern, 67663 Kaiserslautern, Germany;
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9
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Zeng Y, Qian H, Campos MM, Li Y, Vijayasarathy C, Sieving PA. Rs1h -/y exon 3-del rat model of X-linked retinoschisis with early onset and rapid phenotype is rescued by RS1 supplementation. Gene Ther 2021; 29:431-440. [PMID: 34548657 PMCID: PMC8938309 DOI: 10.1038/s41434-021-00290-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/03/2021] [Accepted: 08/18/2021] [Indexed: 12/27/2022]
Abstract
Animal models of X-linked juvenile retinoschisis (XLRS) are valuable tools for understanding basic biochemical function of retinoschisin (RS1) protein and to investigate outcomes of preclinical efficacy and toxicity studies. In order to work with an eye larger than mouse, we generated and characterized an Rs1h−/y knockout rat model created by removing exon 3. This rat model expresses no normal RS1 protein. The model shares features of an early onset and more severe phenotype of human XLRS. The morphologic pathology includes schisis cavities at postnatal day 15 (p15), photoreceptors that are misplaced into the subretinal space and OPL, and a reduction of photoreceptor cell numbers by p21. By 6 mo age only 1–3 rows of photoreceptors nuclei remain, and the inner/outer segment layers and the OPL shows major changes. Electroretinogram recordings show functional loss with considerable reduction of both the a-wave and b-wave by p28, indicating early age loss and dysfunction of photoreceptors. The ratio of b-/a-wave amplitudes indicates impaired synaptic transmission to bipolar cells in addition. Supplementing the Rs1h−/y exon3-del retina with normal human RS1 protein using AAV8-RS1 delivery improved the retinal structure. This Rs1h−/y rat model provides a further tool to explore underlying mechanisms of XLRS pathology and to evaluate therapeutic intervention for the XLRS condition.
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Affiliation(s)
- Yong Zeng
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Haohua Qian
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Yichao Li
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Paul A Sieving
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA. .,Department of Ophthalmology, University of California Davis, Sacramento, CA, USA. .,Center for Ocular Regenerative Therapy, Department of Ophthalmology and Vision Science, University of California Davis, Sacramento, CA, USA.
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10
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Soblechero-Martín P, Albiasu-Arteta E, Anton-Martinez A, de la Puente-Ovejero L, Garcia-Jimenez I, González-Iglesias G, Larrañaga-Aiestaran I, López-Martínez A, Poyatos-García J, Ruiz-Del-Yerro E, Gonzalez F, Arechavala-Gomeza V. Duchenne muscular dystrophy cell culture models created by CRISPR/Cas9 gene editing and their application in drug screening. Sci Rep 2021; 11:18188. [PMID: 34521928 PMCID: PMC8440673 DOI: 10.1038/s41598-021-97730-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/27/2021] [Indexed: 12/28/2022] Open
Abstract
Gene editing methods are an attractive therapeutic option for Duchenne muscular dystrophy, and they have an immediate application in the generation of research models. To generate myoblast cultures that could be useful in in vitro drug screening, we have optimised a CRISPR/Cas9 gene edition protocol. We have successfully used it in wild type immortalised myoblasts to delete exon 52 of the dystrophin gene, modelling a common Duchenne muscular dystrophy mutation; and in patient's immortalised cultures we have deleted an inhibitory microRNA target region of the utrophin UTR, leading to utrophin upregulation. We have characterised these cultures by demonstrating, respectively, inhibition of dystrophin expression and overexpression of utrophin, and evaluating the expression of myogenic factors (Myf5 and MyH3) and components of the dystrophin associated glycoprotein complex (α-sarcoglycan and β-dystroglycan). To demonstrate their use in the assessment of DMD treatments, we have performed exon skipping on the DMDΔ52-Model and have used the unedited DMD cultures/ DMD-UTRN-Model combo to assess utrophin overexpression after drug treatment. While the practical use of DMDΔ52-Model is limited to the validation to our gene editing protocol, DMD-UTRN-Model presents a possible therapeutic gene edition target as well as a useful positive control in the screening of utrophin overexpression drugs.
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Affiliation(s)
- Patricia Soblechero-Martín
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain.,Osakidetza Basque Health Service, Bilbao-Basurto Integrated Health Organisation, Basurto University Hospital, Clinical Laboratory Service, Bilbao, Spain
| | - Edurne Albiasu-Arteta
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Aina Anton-Martinez
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | | | - Iker Garcia-Jimenez
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | | | - Irene Larrañaga-Aiestaran
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Andrea López-Martínez
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | | | - Estíbaliz Ruiz-Del-Yerro
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Federico Gonzalez
- Pluripotent Stem Cells and Activation of Endogenous Tissue Programs for Organ Regeneration (PR Lab), Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
| | - Virginia Arechavala-Gomeza
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain. .,Basque Foundation for Science, Bilbao, Spain.
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11
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Zhu L, Yang X, Li J, Jia X, Bai X, Zhao Y, Cheng W, Shu M, Zhu Y, Jin S. Leptin gene-targeted editing in ob/ob mouse adipose tissue based on the CRISPR/Cas9 system. J Genet Genomics 2021; 48:134-146. [PMID: 33931338 DOI: 10.1016/j.jgg.2021.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 01/13/2023]
Abstract
Gene therapy has become the most effective treatment for monogenic diseases. Congenital LEPTIN deficiency is a rare autosomal recessive monogenic obesity syndrome caused by mutations in the Leptin gene. Ob/ob mouse is a monogenic obesity model, which carries a homozygous point mutation of C to T in Exon 2 of the Leptin gene. Here, we attempted to edit the mutated Leptin gene in ob/ob mice preadipocytes and inguinal adipose tissues using CRISPR/Cas9 to correct the C to T mutation and restore the production of LEPTIN protein by adipocytes. The edited preadipocytes exhibit a correction of 5.5% of Leptin alleles and produce normal LEPTIN protein when differentiated into mature adipocytes. The ob/ob mice display correction of 1.67% of Leptin alleles, which is sufficient to restore the production and physiological functions of LEPTIN protein, such as suppressing appetite and alleviating insulin resistance. Our study suggests CRISPR/Cas9-mediated in situ genome editing as a feasible therapeutic strategy for human monogenic diseases, and paves the way for further research on efficient delivery system in potential future clinical application.
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Affiliation(s)
- Lin Zhu
- Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Pediatrics, Tongji Hospital, Tongji Medicine College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoyan Yang
- Department of Pharmacology, Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Juyi Li
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiong Jia
- Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiangli Bai
- Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Laboratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ying Zhao
- Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenzhuo Cheng
- Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Meng Shu
- Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yan Zhu
- Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Si Jin
- Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Pharmacology, Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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12
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Li D, Sun X, Yu F, Perle MA, Araten D, Boeke J. Application of counter-selectable marker PIGA in engineering designer deletion cell lines and characterization of CRISPR deletion efficiency. Nucleic Acids Res 2021; 49:2642-2654. [PMID: 33591308 PMCID: PMC7969003 DOI: 10.1093/nar/gkab035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/11/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
The CRISPR/Cas9 system is a technology for genome engineering, which has been applied to indel mutations in genes as well as targeted gene deletion and replacement. Here, we describe paired gRNA deletions along the PIGA locus on the human X chromosome ranging from 17 kb to 2 Mb. We found no compelling linear correlation between deletion size and the deletion efficiency, and there is no substantial impact of topologically associating domains on deletion frequency. Using this precise deletion technique, we have engineered a series of designer deletion cell lines, including one with deletions of two X-chromosomal counterselectable (negative selection) markers, PIGA and HPRT1, and additional cell lines bearing each individual deletion. PIGA encodes a component of the glycosylphosphatidylinositol (GPI) anchor biosynthetic apparatus. The PIGA gene counterselectable marker has unique features, including existing single cell level assays for both function and loss of function of PIGA and the existence of a potent counterselectable agent, proaerolysin, which we use routinely for selection against cells expressing PIGA. These designer cell lines may serve as a general platform with multiple selection markers and may be particularly useful for large scale genome engineering projects such as Genome Project-Write (GP-write).
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Affiliation(s)
- Donghui Li
- Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Fangzhou Yu
- Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Mary Ann Perle
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - David Araten
- Division of Hematology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, and the New York VA Medical Center, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn NY 11201, USA
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13
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Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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14
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Sheva M, Hanania U, Ariel T, Turbovski A, Rathod VKR, Oz D, Tekoah Y, Shaaltiel Y. Sequential Genome Editing and Induced Excision of the Transgene in N. tabacum BY2 Cells. FRONTIERS IN PLANT SCIENCE 2020; 11:607174. [PMID: 33324440 PMCID: PMC7723889 DOI: 10.3389/fpls.2020.607174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
While plant cells in suspension are becoming a popular platform for expressing biotherapeutic proteins, the need to pre-engineer these cells to better comply with their role as host cell lines is emerging. Heterologous DNA and selectable markers are used for transformation and genome editing designated to produce improved host cell lines for overexpression of recombinant proteins. The removal of these heterologous DNA and selectable markers, no longer needed, can be beneficial since they limit additional gene stacking in subsequent transformations and may pose excessive metabolic burden on the cell machinery. In this study we developed an innovative stepwise methodology in which the CRISPR-Cas9 is used sequentially to target genome editing, followed by its own excision. The first step included a stable insertion of a CRISPR-Cas9 cassette, targeted to knockout the β(1,2)-xylosyltranferase (XylT) and the α(1,3)-fucosyltransferase (FucT) genes in Nicotiana tabacum L. cv Bright Yellow 2 (BY2) cell suspension. The second step included the excision of the inserted cassette of 14.3 kbp by induction of specific sgRNA designed to target the T-DNA boundaries. The genome editing step and the transgene removal step are achieved in one transformation run. This mechanism enables CRISPR genome editing and subsequently eliminating the introduced transgenes thus freeing the cells from foreign DNA no longer needed.
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15
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Sheva M, Hanania U, Ariel T, Turbovski A, Rathod VKR, Oz D, Tekoah Y, Shaaltiel Y. Sequential Genome Editing and Induced Excision of the Transgene in N. tabacum BY2 Cells. FRONTIERS IN PLANT SCIENCE 2020; 11:607174. [PMID: 33324440 DOI: 10.3389/fpls.2020.60714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/04/2020] [Indexed: 05/23/2023]
Abstract
While plant cells in suspension are becoming a popular platform for expressing biotherapeutic proteins, the need to pre-engineer these cells to better comply with their role as host cell lines is emerging. Heterologous DNA and selectable markers are used for transformation and genome editing designated to produce improved host cell lines for overexpression of recombinant proteins. The removal of these heterologous DNA and selectable markers, no longer needed, can be beneficial since they limit additional gene stacking in subsequent transformations and may pose excessive metabolic burden on the cell machinery. In this study we developed an innovative stepwise methodology in which the CRISPR-Cas9 is used sequentially to target genome editing, followed by its own excision. The first step included a stable insertion of a CRISPR-Cas9 cassette, targeted to knockout the β(1,2)-xylosyltranferase (XylT) and the α(1,3)-fucosyltransferase (FucT) genes in Nicotiana tabacum L. cv Bright Yellow 2 (BY2) cell suspension. The second step included the excision of the inserted cassette of 14.3 kbp by induction of specific sgRNA designed to target the T-DNA boundaries. The genome editing step and the transgene removal step are achieved in one transformation run. This mechanism enables CRISPR genome editing and subsequently eliminating the introduced transgenes thus freeing the cells from foreign DNA no longer needed.
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Affiliation(s)
- Maor Sheva
- Protalix Biotherapeutics, Carmiel, Israel
| | | | - Tami Ariel
- Protalix Biotherapeutics, Carmiel, Israel
| | | | | | - Dina Oz
- Protalix Biotherapeutics, Carmiel, Israel
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16
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Shi X, Tang T, Lin Q, Liu H, Qin Y, Liang X, Cong P, Mo D, Liu X, Chen Y, He Z. Efficient generation of bone morphogenetic protein 15-edited Yorkshire pigs using CRISPR/Cas9†. Biol Reprod 2020; 103:1054-1068. [PMID: 32761111 DOI: 10.1093/biolre/ioaa138] [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] [Received: 02/18/2019] [Revised: 06/25/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022] Open
Abstract
Bone morphogenetic protein 15 (BMP15), a member of the transforming growth factor beta superfamily, plays an essential role in ovarian follicular development in mono-ovulatory mammalian species. Studies using a biallelic knockout mouse model revealed that BMP15 potentially has just a minimal impact on female fertility and ovarian follicular development in polyovulatory species. In contrast, our previous study demonstrated that in vivo knockdown of BMP15 significantly affected porcine female fertility, as evidenced by the dysplastic ovaries containing significantly decreased numbers of follicles and an increased number of abnormal follicles. This finding implied that BMP15 plays an important role in the regulation of female fertility and ovarian follicular development in polyovulatory species. To further investigate the regulatory role of BMP15 in porcine ovarian and follicular development, here, we describe the efficient generation of BMP15-edited Yorkshire pigs using CRISPR/Cas9. Using artificial insemination experiments, we found that the biallelically edited gilts were all infertile, regardless of different genotypes. One monoallelically edited gilt #4 (Δ66 bp/WT) was fertile and could deliver offspring with a litter size comparable to that of wild-type gilts. Further analysis established that the infertility of biallelically edited gilts was caused by the arrest of follicular development at preantral stages, with formation of numerous structurally abnormal follicles, resulting in streaky ovaries and the absence of obvious estrous cycles. Our results strongly suggest that the role of BMP15 in nonrodent polyovulatory species may be as important as that in mono-ovulatory species.
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Affiliation(s)
- Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Tao Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Qiyuan Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Hongbo Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yufeng Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xinyu Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Peiqing Cong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China
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17
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Meaker GA, Hair EJ, Gorochowski TE. Advances in engineering CRISPR-Cas9 as a molecular Swiss Army knife. Synth Biol (Oxf) 2020; 5:ysaa021. [PMID: 33344779 PMCID: PMC7737000 DOI: 10.1093/synbio/ysaa021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
The RNA-guided endonuclease system CRISPR-Cas9 has been extensively modified since its discovery, allowing its capabilities to extend far beyond double-stranded cleavage to high fidelity insertions, deletions and single base edits. Such innovations have been possible due to the modular architecture of CRISPR-Cas9 and the robustness of its component parts to modifications and the fusion of new functional elements. Here, we review the broad toolkit of CRISPR-Cas9-based systems now available for diverse genome-editing tasks. We provide an overview of their core molecular structure and mechanism and distil the design principles used to engineer their diverse functionalities. We end by looking beyond the biochemistry and toward the societal and ethical challenges that these CRISPR-Cas9 systems face if their transformative capabilities are to be deployed in a safe and acceptable manner.
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Affiliation(s)
- Grace A Meaker
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Emma J Hair
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, UK
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18
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Kotini AG, Papapetrou EP. Engineering of targeted megabase-scale deletions in human induced pluripotent stem cells. Exp Hematol 2020; 87:25-32. [PMID: 32544417 PMCID: PMC7816568 DOI: 10.1016/j.exphem.2020.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 12/29/2022]
Abstract
Recurrent chromosomal deletions spanning several megabases are often found in hematological malignancies. The ability to engineer deletions in model systems to functionally study their effects on the phenotype would enable, first, determination of whether a given deletion is pathogenic or neutral and, second, identification of the critical genes. Incomplete synteny makes modeling of deletions of megabase scale challenging or impossible in the mouse or other model organisms. Furthermore, despite the breakthroughs in targeted nuclease technologies in recent years, engineering of megabase-scale deletions remains challenging and has not been achieved in normal diploid human cells. Large deletions of the long arm of chromosome 7 (chr7q) occur frequently in myelodysplastic syndrome (MDS) and are associated with poor prognosis. We previously found that we can model chr7q deletions in human induced pluripotent stem cells (iPSCs) using a modified Cre-loxP strategy. However, this strategy did not afford control over the length and boundaries of the engineered deletions, which were initiated through random chromosome breaks. Here we developed strategies enabling the generation of defined and precise chromosomal deletions of up to 22 Mb, using two different strategies: "classic" Cre-loxP recombination and CRISPR/Cas9-mediated DNA cleavage. As proof of principle, we illustrate that phenotypic characterization of the hematopoiesis derived from these iPSCs upon in vitro differentiation allows further definition of the critical region of chr7q whose hemizygosity impairs hematopoietic differentiation potential. The strategies we present here can be broadly applicable to engineering of diverse chromosomal deletions in human cells.
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Affiliation(s)
- Andriana G Kotini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eirini P Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.
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19
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Pimenova AA, Goate AM. Novel presenilin 1 and 2 double knock-out cell line for in vitro validation of PSEN1 and PSEN2 mutations. Neurobiol Dis 2020; 138:104785. [PMID: 32032730 PMCID: PMC7515654 DOI: 10.1016/j.nbd.2020.104785] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/05/2020] [Accepted: 01/31/2020] [Indexed: 12/23/2022] Open
Abstract
Mutations in APP (amyloid precursor protein), PSEN1 (presenilin 1) or PSEN2 (presenilin 2) are the main cause of early-onset familial forms of Alzheimer's disease (autosomal dominant AD or ADAD). These genes affect γ-secretase-dependent generation of Amyloid β (Aβ) peptides, the main constituent of amyloid plaques and one of the pathological hallmarks of AD. Evaluation of patients with ADAD includes assessment of family history, clinical presentation, biomarkers, neuropathology when available and DNA sequencing data. These analyses frequently uncover novel variants of unknown significance in ADAD genes. This presents a barrier to recruitment of such individuals into clinical trials, unless a biochemical test can demonstrate that a novel mutation results in altered APP processing in a manner consistent with pathogenicity. Here we describe generation and characterization of a novel presenilin 1 and 2 double knock-out in N2A mouse neuroblastoma cells using CRISPR/Cas9, which results in complete ablation of Aβ production, decreased Pen-2 expression and Nicastrin glycosylation. Because of the absence of background Aβ secretion from endogenous γ-secretases, these cells can be used for validation of PSEN1 and PSEN2 variant effects on production of Aβ or other γ-secretase substrates and for biochemical studies of γ-secretase function using novel variants. We examined several PSEN1 and PSEN2 mutations of known and unknown pathogenicity. Known mutants increased Aβ42/Aβ40 ratio with varying effect on Aβ40, Aβ42, total Aβ levels and Pen-2 expression, which aligns with previous work on these mutants. Our data on novel PSEN1 V142F, G206V and G206D mutations suggest that these mutations underlie the reported clinical observations in ADAD patients. We believe our novel cell line will be valuable for the scientific community for reliable validation of presenilin mutations and helpful in defining their pathogenicity to improve and facilitate evaluation of ADAD patients, particularly in the context of enrollment in clinical trials.
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Affiliation(s)
- Anna A Pimenova
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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20
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Oh Y, Lee B, Kim H, Kim SG. A multiplex guide RNA expression system and its efficacy for plant genome engineering. PLANT METHODS 2020; 16:37. [PMID: 32190101 PMCID: PMC7069183 DOI: 10.1186/s13007-020-00580-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/04/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The Streptococcus pyogenes CRISPR system is composed of a Cas9 endonuclease (SpCas9) and a single-stranded guide RNA (gRNA) harboring a target-specific sequence. Theoretically, SpCas9 proteins could cleave as many targeted loci as gRNAs bind in a genome. RESULTS We introduce a PCR-free multiple gRNA cloning system for editing plant genomes. This method consists of two steps: (1) cloning the annealed products of two single-stranded oligonucleotide fragments harboring a complimentary target-binding sequence on each strand between tRNA and gRNA scaffold sequences in a pGRNA vector; and (2) assembling tRNA-gRNA units from several pGRNA vectors with a plant binary vector containing a SpCas9 expression cassette using the Golden Gate assembly method. We validated the editing efficiency and patterns of the multiplex gRNA expression system in wild tobacco (Nicotiana attenuata) protoplasts and in transformed plants by performing targeted deep sequencing. Two proximal cleavages by SpCas9-gRNA largely increased the editing efficiency and induced large deletions between two cleavage sites. CONCLUSIONS This multiplex gRNA expression system enables high-throughput production of a single binary vector and increases the efficiency of plant genome editing.
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Affiliation(s)
- Youngbin Oh
- Department of Biological Sciences, KAIST, Daejeon, 34141 Republic of Korea
| | - Bora Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141 Republic of Korea
| | - Hyeonjin Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141 Republic of Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141 Republic of Korea
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Mallett DR, Chang M, Cheng X, Bezanilla M. Efficient and modular CRISPR-Cas9 vector system for Physcomitrella patens. PLANT DIRECT 2019; 3:e00168. [PMID: 31523744 PMCID: PMC6739617 DOI: 10.1002/pld3.168] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/29/2019] [Accepted: 08/20/2019] [Indexed: 05/20/2023]
Abstract
CRISPR-Cas9 has been shown to be a valuable tool in recent years, allowing researchers to precisely edit the genome using an RNA-guided nuclease to initiate double-strand breaks. Until recently, classical RAD51-mediated homologous recombination has been a powerful tool for gene targeting in the moss Physcomitrella patens. However, CRISPR-Cas9-mediated genome editing in P. patens was shown to be more efficient than traditional homologous recombination (Plant Biotechnology Journal, 15, 2017, 122). CRISPR-Cas9 provides the opportunity to efficiently edit the genome at multiple loci as well as integrate sequences at precise locations in the genome using a simple transient transformation. To fully take advantage of CRISPR-Cas9 genome editing in P. patens, here we describe the generation and use of a flexible and modular CRISPR-Cas9 vector system. Without the need for gene synthesis, this vector system enables editing of up to 12 loci simultaneously. Using this system, we generated multiple lines that had null alleles at four distant loci. We also found that targeting multiple sites within a single locus can produce larger deletions, but the success of this depends on individual protospacers. To take advantage of homology-directed repair, we developed modular vectors to rapidly generate DNA donor plasmids to efficiently introduce DNA sequences encoding for fluorescent proteins at the 5' and 3' ends of gene coding regions. With regard to homology-directed repair experiments, we found that if the protospacer sequence remains on the DNA donor plasmid, then Cas9 cleaves the plasmid target as well as the genomic target. This can reduce the efficiency of introducing sequences into the genome. Furthermore, to ensure the generation of a null allele near the Cas9 cleavage site, we generated a homology plasmid harboring a "stop codon cassette" with downstream near-effortless genotyping.
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Affiliation(s)
- Darren R. Mallett
- Department of Biological SciencesDartmouth CollegeHanoverNew Hampshire
| | - Mingqin Chang
- Department of Biological SciencesDartmouth CollegeHanoverNew Hampshire
- Plant Biology Graduate ProgramUniversity of MassachusettsAmherstMassachusetts
| | - Xiaohang Cheng
- Department of Biological SciencesDartmouth CollegeHanoverNew Hampshire
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We have entered the era of genome-edited farmed animals. Emerg Top Life Sci 2019; 3:645-649. [PMID: 33523167 DOI: 10.1042/etls20190057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/17/2019] [Accepted: 07/01/2019] [Indexed: 11/17/2022]
Abstract
Genome editing technology provides a transformative approach to animal breeding. Otherwise difficult or impossible-to-access genetic variation can now be used in a given target population, with leading examples focussing on animal health and welfare. The race is on for the first food from genome-edited farm animals to reach the shops.
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Qin K, Liang X, Sun G, Shi X, Wang M, Liu H, Chen Y, Liu X, He Z. Highly efficient correction of structural mutations of 450 kb KIT locus in kidney cells of Yorkshire pig by CRISPR/Cas9. BMC Mol Cell Biol 2019; 20:4. [PMID: 31041890 PMCID: PMC6446502 DOI: 10.1186/s12860-019-0184-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 03/11/2019] [Indexed: 11/23/2022] Open
Abstract
The white coat colour of Yorkshire and Landrace pig breeds is caused by the dominant white I allele of KIT, associated with 450-kb duplications and a splice mutation (G > A) at the first base in intron 17. To test whether genome editing can be employed to correct this structural mutation, and to investigate the role of KIT in the control of porcine coat colour, we designed sgRNAs targeting either intron 16 or intron 17 of KIT, and transfected Cas9/sgRNA co-expression plasmids into the kidney cells of Yorkshire pigs. The copy number of KIT was reduced by about 13%, suggesting the possibility of obtaining cells with corrected structural mutations of the KIT locus. Using single cell cloning, from 24 successfully expanded single cell clones derived from cells transfected with sgRNA targeting at intron 17, we obtained 3 clones with a single copy of KIT without the splice mutation. Taken together, the 12.5% (3/24) efficiency of correction of structural mutations of 450 kb fragments is highly efficient, providing a solid basis for the generation of genome edited Yorkshire pigs with a normal KIT locus. This provides an insight into the underlying genetic mechanisms of porcine coat colour.
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Affiliation(s)
- Ke Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Xinyu Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Guanjie Sun
- 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
| | - Min Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Hongbo Liu
- 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
| | - Xiaohong Liu
- 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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Cai Y, Chen L, Sun S, Wu C, Yao W, Jiang B, Han T, Hou W. CRISPR/Cas9-Mediated Deletion of Large Genomic Fragments in Soybean. Int J Mol Sci 2018; 19:E3835. [PMID: 30513774 PMCID: PMC6321276 DOI: 10.3390/ijms19123835] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/23/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023] Open
Abstract
At present, the application of CRISPR/Cas9 in soybean (Glycine max (L.) Merr.) has been mainly focused on knocking out target genes, and most site-directed mutagenesis has occurred at single cleavage sites and resulted in short deletions and/or insertions. However, the use of multiple guide RNAs for complex genome editing, especially the deletion of large DNA fragments in soybean, has not been systematically explored. In this study, we employed CRISPR/Cas9 technology to specifically induce targeted deletions of DNA fragments in GmFT2a (Glyma16g26660) and GmFT5a (Glyma16g04830) in soybean using a dual-sgRNA/Cas9 design. We achieved a deletion frequency of 15.6% for target fragments ranging from 599 to 1618 bp in GmFT2a. We also achieved deletion frequencies of 12.1% for target fragments exceeding 4.5 kb in GmFT2a and 15.8% for target fragments ranging from 1069 to 1161 bp in GmFT5a. In addition, we demonstrated that these CRISPR/Cas9-induced large fragment deletions can be inherited. The T2 'transgene-free' homozygous ft2a mutants with a 1618 bp deletion exhibited the late-flowering phenotype. In this study, we developed an efficient system for deleting large fragments in soybean using CRISPR/Cas9; this system could benefit future research on gene function and improve agriculture via chromosome engineering or customized genetic breeding in soybean.
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Affiliation(s)
- Yupeng Cai
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Shi Sun
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Cunxiang Wu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Weiwei Yao
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Bingjun Jiang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Wensheng Hou
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Schmieder V, Bydlinski N, Strasser R, Baumann M, Kildegaard HF, Jadhav V, Borth N. Enhanced Genome Editing Tools For Multi-Gene Deletion Knock-Out Approaches Using Paired CRISPR sgRNAs in CHO Cells. Biotechnol J 2017; 13:e1700211. [PMID: 28976642 DOI: 10.1002/biot.201700211] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/31/2017] [Indexed: 12/26/2022]
Abstract
Since the establishment of clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9, powerful strategies for engineering of CHO cell lines have emerged. Nevertheless, there is still room to expand the scope of the CRISPR tool box for further applications to improve CHO cell factories. Here, the authors demonstrate activity of the alternative CRISPR endonuclease Cpf1 in CHO-K1 for the first time and that it can be used in parallel to CRISPR/Cas9 without any interference. Both, Cas9 and Cpf1, can be effectively used for multi-gene engineering with a strategy based on paired single guide RNAs (sgRNAs) for full gene deletions. This strategy also enables the targeting of regulatory regions, which would not respond to the conventional frameshift mutations, as shown by removing the α-1,6-Fucosyltransferase 8 (FUT8) promoter resulting in a functional knock-out. FUT8 also served as model to verify that deletion efficiency is size-independent (2-150 kb). To test the suitability for multi-gene approaches in combination with gene deletion, clones harboring triple deletions in β-1,4-Galactosyltransferase (B4GALT) isozymes are identified using solely conventional PCR/qPCR. In addition, two bicistronic transcription strategies are implemented to enable unequivocal pairing of sgRNAs: a CHO-derived tRNA linker that works for both, Cas9 and Cpf1, as well as paired sgRNAs in an array format, which can be used with Cpf1 due to its RNA processing ability. These strategies broaden the range of application of CRISPR for novel gene editing approaches in CHO cells and also enable the efficient realization of a genome-wide deletion library.
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Affiliation(s)
- Valerie Schmieder
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria.,ACIB GmbH, Austrian Center of Industrial Biotechnology, Graz, Austria
| | - Nina Bydlinski
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Martina Baumann
- ACIB GmbH, Austrian Center of Industrial Biotechnology, Graz, Austria
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Vaibhav Jadhav
- ACIB GmbH, Austrian Center of Industrial Biotechnology, Graz, Austria
| | - Nicole Borth
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria
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Du J, Shang J, Chen F, Zhang Y, Yin N, Xie T, Zhang H, Yu J, Liu F. A CRISPR/Cas9–Based Screening for Non-Homologous End Joining Inhibitors Reveals Ouabain and Penfluridol as Radiosensitizers. Mol Cancer Ther 2017; 17:419-431. [DOI: 10.1158/1535-7163.mct-17-0090] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/20/2017] [Accepted: 08/25/2017] [Indexed: 11/16/2022]
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Voloshanenko O, Gmach P, Winter J, Kranz D, Boutros M. Mapping of Wnt-Frizzled interactions by multiplex CRISPR targeting of receptor gene families. FASEB J 2017; 31:4832-4844. [PMID: 28733458 PMCID: PMC5636703 DOI: 10.1096/fj.201700144r] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 07/05/2017] [Indexed: 12/19/2022]
Abstract
Signaling pathway modules are often encoded by several closely related paralogous genes that can have redundant roles and are therefore difficult to analyze by loss-of-function analysis. A typical example is the Wnt signaling pathway, which in mammals is mediated by 19 Wnt ligands that can bind to 10 Frizzled (FZD) receptors. Although significant progress in understanding Wnt-FZD receptor interactions has been made in recent years, tools to generate systematic interaction maps have been largely lacking. Here we generated cell lines with multiplex mutant alleles of FZD1, FZD2, and FZD7 and demonstrate that these cells are unresponsive to canonical Wnt ligands. Subsequently, we performed genetic rescue experiments with combinations of FZDs and canonical Wnts to create a functional ligand–receptor interaction map. These experiments showed that whereas several Wnt ligands, such as Wnt3a, induce signaling through a broad spectrum of FZD receptors, others, such as Wnt8a, act through a restricted set of FZD genes. Together, our results map functional interactions of FZDs and 10 Wnt ligands and demonstrate how multiplex targeting by clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 can be used to systematically elucidate the functions of multigene families.—Voloshanenko, O., Gmach, P., Winter, J., Kranz, D., Boutros, M. Mapping of Wnt-Frizzled interactions by multiplex CRISPR targeting of receptor gene families.
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Affiliation(s)
- Oksana Voloshanenko
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany; and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Philipp Gmach
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany; and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Jan Winter
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany; and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Dominique Kranz
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany; and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany; and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
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28
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[Chromosomal large fragment deletion induced by CRISPR/Cas9 gene editing system]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2017; 38:427-431. [PMID: 28565744 PMCID: PMC7354198 DOI: 10.3760/cma.j.issn.0253-2727.2017.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Objective: Using CRISPR-Cas9 gene editing technology to achieve a number of genes co-deletion on the same chromosome. Methods: CRISPR-Cas9 lentiviral plasmid that could induce deletion of Aloxe3-Alox12b-Alox8 cluster genes located on mouse 11B3 chromosome was constructed via molecular clone. HEK293T cells were transfected to package lentivirus of CRISPR or Cas9 cDNA, then mouse NIH3T3 cells were infected by lentivirus and genomic DNA of these cells was extracted. The deleted fragment was amplified by PCR, TA clone, Sanger sequencing and other techniques were used to confirm the deletion of Aloxe3-Alox12b-Alox8 cluster genes. Results: The CRISPR-Cas9 lentiviral plasmid, which could induce deletion of Aloxe3-Alox12b-Alox8 cluster genes, was successfully constructed. Deletion of target chromosome fragment (Aloxe3-Alox12b-Alox8 cluster genes) was verified by PCR. The deletion of Aloxe3-Alox12b-Alox8 cluster genes was affirmed by TA clone, Sanger sequencing, and the breakpoint junctions of the CRISPR-Cas9 system mediate cutting events were accurately recombined, insertion mutation did not occur between two cleavage sites at all. Conclusion: Large fragment deletion of Aloxe3-Alox12b-Alox8 cluster genes located on mouse chromosome 11B3 was successfully induced by CRISPR-Cas9 gene editing system.
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Ouellet DL, Cherif K, Rousseau J, Tremblay JP. Deletion of the GAA repeats from the human frataxin gene using the CRISPR-Cas9 system in YG8R-derived cells and mouse models of Friedreich ataxia. Gene Ther 2017; 24:265-274. [PMID: 28024081 DOI: 10.1038/gt.2016.89] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/19/2016] [Indexed: 02/07/2023]
Abstract
The Friedreich ataxia is a monogenic disease due to a hyperexpanded GAA triplet located within the first intron of the frataxin gene that causes transcriptional issues. The resulting frataxin protein deficiency leads to a Fe-S cluster biosynthesis dysfunction in the mitochondria and to oxidative stress and cell death. Here we use the CRISPR-Cas9 system to remove the mutated GAA expansion and restore the frataxin gene transcriptional activity and protein level. Both YG8R and YG8sR mouse models and cell lines derived from these mice were used to CRISPR-edited successfully the GAA expansion in vitro and in vivo. Nevertheless, our results suggest the YG8sR as a better and more suitable model for the study of the CRISPR-Cas9 edition of the mutated frataxin gene.
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Affiliation(s)
- D L Ouellet
- Centre de Recherche, Centre Hospitalier, Universitaire de Québec, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - K Cherif
- Centre de Recherche, Centre Hospitalier, Universitaire de Québec, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - J Rousseau
- Centre de Recherche, Centre Hospitalier, Universitaire de Québec, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - J P Tremblay
- Centre de Recherche, Centre Hospitalier, Universitaire de Québec, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, CHU de Québec, Université Laval, Québec City, QC, Canada
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Abstract
With the introduction of precision genome editing using CRISPR-Cas9 technology, we have entered a new era of genetic engineering and gene therapy. With RNA-guided endonucleases, such as Cas9, it is possible to engineer DNA double strand breaks (DSB) at specific genomic loci. DSB repair by the error-prone non-homologous end-joining (NHEJ) pathway can disrupt a target gene by generating insertions and deletions. Alternatively, Cas9-mediated DSBs can be repaired by homology-directed repair (HDR) using an homologous DNA repair template, thus allowing precise gene editing by incorporating genetic changes into the repair template. HDR can introduce gene sequences for protein epitope tags, delete genes, make point mutations, or alter enhancer and promoter activities. In anticipation of adapting this technology for gene therapy in human somatic cells, much focus has been placed on increasing the fidelity of CRISPR-Cas9 and increasing HDR efficiency to improve precision genome editing. In this review, we will discuss applications of CRISPR technology for gene inactivation and genome editing with a focus on approaches to enhancing CRISPR-Cas9-mediated HDR for the generation of cell and animal models, and conclude with a discussion of recent advances and challenges towards the application of this technology for gene therapy in humans.
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Affiliation(s)
- Jayme Salsman
- a Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Graham Dellaire
- a Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- b Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- c Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
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Ordon J, Gantner J, Kemna J, Schwalgun L, Reschke M, Streubel J, Boch J, Stuttmann J. Generation of chromosomal deletions in dicotyledonous plants employing a user-friendly genome editing toolkit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:155-168. [PMID: 27579989 DOI: 10.1111/tpj.13319] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 05/20/2023]
Abstract
Genome editing facilitated by Cas9-based RNA-guided nucleases (RGNs) is becoming an increasingly important and popular technique for reverse genetics in both model and non-model species. So far, RGNs were mainly applied for the induction of point mutations, and one major challenge consists in the detection of genome-edited individuals from a mutagenized population. Also, point mutations are not appropriate for functional dissection of non-coding DNA. Here, the multiplexing capacity of a newly developed genome editing toolkit was exploited for the induction of inheritable chromosomal deletions at six different loci in Nicotiana benthamiana and Arabidopsis. In both species, the preferential formation of small deletions was observed, suggesting reduced efficiency with increasing deletion size. Importantly, small deletions (<100 bp) were detected at high frequencies in N. benthamiana T0 and Arabidopsis T2 populations. Thus, targeting of small deletions by paired nucleases represents a simple approach for the generation of mutant alleles segregating as size polymorphisms in subsequent generations. Phenotypically selected deletions of up to 120 kb occurred at low frequencies in Arabidopsis, suggesting larger population sizes for the discovery of valuable alleles from addressing gene clusters or non-coding DNA for deletion by programmable nucleases.
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Affiliation(s)
- Jana Ordon
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Johannes Gantner
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Jan Kemna
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Lennart Schwalgun
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Maik Reschke
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Jana Streubel
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Jens Boch
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
| | - Johannes Stuttmann
- Department of Genetics, Martin Luther University Halle (Saale), Weinbergweg 10, 06120, Halle, Germany
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Wang G, Zhao N, Berkhout B, Das AT. A Combinatorial CRISPR-Cas9 Attack on HIV-1 DNA Extinguishes All Infectious Provirus in Infected T Cell Cultures. Cell Rep 2016; 17:2819-2826. [PMID: 27974196 DOI: 10.1016/j.celrep.2016.11.057] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/07/2016] [Accepted: 11/18/2016] [Indexed: 01/24/2023] Open
Abstract
Current drug therapies effectively suppress HIV-1 replication but do not inactivate the provirus that persists in latent reservoirs. Recent studies have found that the guide RNA (gRNA)-directed CRISPR/Cas9 system can be used for sequence-specific attack on this proviral DNA. Although potent inhibition of virus replication was reported, HIV-1 can escape from a single antiviral gRNA by mutation of the target sequence. Here, we demonstrate that combinations of two antiviral gRNAs delay viral escape, and identify two gRNA combinations that durably block virus replication. When viral escape is prevented, repeated Cas9 cleavage leads to saturation of major mutations in the conserved target sequences that encode critical proteins. This hypermutation coincides with the loss of replication-competent virus as scored in sensitive co-cultures with unprotected cells, demonstrating complete virus inactivation. These results provide a proof-of-principle that HIV-1-infected cells can be functionally cured by dual-gRNA CRISPR/Cas9 treatment.
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Affiliation(s)
- Gang Wang
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Na Zhao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.
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Altering the Anti-inflammatory Lipoxin Microenvironment: a New Insight into Kaposi's Sarcoma-Associated Herpesvirus Pathogenesis. J Virol 2016; 90:11020-11031. [PMID: 27681120 DOI: 10.1128/jvi.01491-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/23/2016] [Indexed: 12/29/2022] Open
Abstract
Lipoxins are host anti-inflammatory molecules that play a vital role in restoring tissue homeostasis. The efficacy of lipoxins and their analog epilipoxins in treating inflammation and its associated diseases has been well documented. Kaposi's sarcoma (KS) and primary effusion lymphoma (PEL) are two well-known inflammation related diseases caused by Kaposi's sarcoma-associated herpesvirus (KSHV). Controlling inflammation is one of the strategies adopted to treat KS and PEL, a primary motivation for exploring and evaluating the therapeutic potential of using lipoxins. This study documents how KSHV manipulates and downregulates the secretion of the anti-inflammatory lipoxin A4 in host cells and the viral factors involved in this process using in vitro KS and PEL cells as models. The presence of the lipoxin A4 receptor/formyl peptidyl receptor (ALX/FPR) in KS patient tissue sections and in vitro KS and PEL cell models offers a novel possibility for treating KS and PEL with lipoxins. Treating de novo KSHV-infected endothelial cells with lipoxin and epilipoxin creates an anti-inflammatory environment by decreasing the levels of NF-κB, AKT, ERK1/2, COX-2, and 5-lipoxygenase. Lipoxin treatment on CRISPR/CAS9 technology-mediated ALX/FPR gene deletion revealed the importance of the lipoxin receptor ALX for effective lipoxin signaling. A viral microRNA (miRNA) cluster was identified as the primary factor contributing to the downregulation of lipoxin A4 secretion in host cells. The KSHV miRNA cluster probably targets enzyme 15-lipoxygenase, which is involved in lipoxin A4 synthesis. This study provides a new insight into the potential treatment of KS and PEL using nature's own anti-inflammatory molecule, lipoxin. IMPORTANCE KSHV infection has been shown to upregulate several host proinflammatory factors, which aid in its survival and pathogenesis. The influence of KSHV infection on anti-inflammatory molecules is not well studied. Since current treatment methods for KS and PEL are fraught with unwanted side effects and low efficiency, the search for new therapeutics is therefore imperative. The use of nature's own molecule lipoxin as a drug is promising. This study opens up new domains in KSHV research focusing on how the virus modulates lipoxin secretion and warrants further investigation of the therapeutic potential of lipoxin using in vitro cell models for KS and PEL.
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Huang CH, Shen CR, Li H, Sung LY, Wu MY, Hu YC. CRISPR interference (CRISPRi) for gene regulation and succinate production in cyanobacterium S. elongatus PCC 7942. Microb Cell Fact 2016; 15:196. [PMID: 27846887 PMCID: PMC5111286 DOI: 10.1186/s12934-016-0595-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/06/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Cyanobacterium Synechococcus elongatus PCC 7942 holds promise for biochemical conversion, but gene deletion in PCC 7942 is time-consuming and may be lethal to cells. CRISPR interference (CRISPRi) is an emerging technology that exploits the catalytically inactive Cas9 (dCas9) and single guide RNA (sgRNA) to repress sequence-specific genes without the need of gene knockout, and is repurposed to rewire metabolic networks in various procaryotic cells. RESULTS To employ CRISPRi for the manipulation of gene network in PCC 7942, we integrated the cassettes expressing enhanced yellow fluorescent protein (EYFP), dCas9 and sgRNA targeting different regions on eyfp into the PCC 7942 chromosome. Co-expression of dCas9 and sgRNA conferred effective and stable suppression of EYFP production at efficiencies exceeding 99%, without impairing cell growth. We next integrated the dCas9 and sgRNA targeting endogenous genes essential for glycogen accumulation (glgc) and succinate conversion to fumarate (sdhA and sdhB). Transcription levels of glgc, sdhA and sdhB were effectively suppressed with efficiencies depending on the sgRNA binding site. Targeted suppression of glgc reduced the expression to 6.2%, attenuated the glycogen accumulation to 4.8% and significantly enhanced the succinate titer. Targeting sdhA or sdhB also effectively downregulated the gene expression and enhanced the succinate titer ≈12.5-fold to ≈0.58-0.63 mg/L. CONCLUSIONS These data demonstrated that CRISPRi-mediated gene suppression allowed for re-directing the cellular carbon flow, thus paving a new avenue to rationally fine-tune the metabolic pathways in PCC 7942 for the production of biotechnological products.
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Affiliation(s)
- Chun-Hung Huang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Claire R Shen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Hung Li
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Li-Yu Sung
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Meng-Ying Wu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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Li H, Shen CR, Huang CH, Sung LY, Wu MY, Hu YC. CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production. Metab Eng 2016; 38:293-302. [DOI: 10.1016/j.ymben.2016.09.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/03/2016] [Accepted: 09/27/2016] [Indexed: 10/20/2022]
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Abu-Bonsrah KD, Zhang D, Newgreen DF. CRISPR/Cas9 Targets Chicken Embryonic Somatic Cells In Vitro and In Vivo and generates Phenotypic Abnormalities. Sci Rep 2016; 6:34524. [PMID: 27694906 PMCID: PMC5046125 DOI: 10.1038/srep34524] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 09/15/2016] [Indexed: 12/16/2022] Open
Abstract
Chickens are an invaluable model for studying human diseases, physiology and especially development, but have lagged in genetic applications. With the advent of Programmable Engineered Nucleases, genetic manipulation has become efficient, specific and rapid. Here, we show that the CRISPR/Cas9 system can precisely edit the chicken genome. We generated HIRA, TYRP1, DICER, MBD3, EZH2, and 6 other gene knockouts in two chicken cell lines using the CRISPR/Cas9 system, with no off-target effects detected. We also showed that very large deletions (>75 kb) could be achieved. We also achieved targeted modification by homology-directed repair (HDR), producing MEN2A and MEN2B mutations of the RET gene. We also targeted DGCR8 in neural cells of the chicken embryo by in vivo electroporation. After FACS isolation of transfected cells, we observed appropriate sequence changes in DGCR8. Wholemount and frozen section antibody labelling showed reduction of DGCR8 levels in transfected cells. In addition, there was reduced expression levels of DGCR8-associated genes DROSHA, YPEL1 and NGN2. We also observed morphological differences in neural tissue and cardiac-related tissues of transfected embryos. These findings demonstrate that precisely targeted genetic manipulation of the genome using the CRISPR/Cas9 system can be extended to the highly adaptable in vivo chicken embryo model.
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Affiliation(s)
- Kwaku Dad Abu-Bonsrah
- Department of Paediatrics, University of Melbourne, Parkville 3052, Australia.,Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, 3052, Australia
| | - Dongcheng Zhang
- Department of Paediatrics, University of Melbourne, Parkville 3052, Australia.,Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, 3052, Australia
| | - Donald F Newgreen
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, 3052, Australia
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Zhang T, Yin Y, Liu H, Du W, Ren C, Wang L, Lu H, Zhang Z. Generation of VDR Knock-Out Mice via Zygote Injection of CRISPR/Cas9 System. PLoS One 2016; 11:e0163551. [PMID: 27685656 PMCID: PMC5042489 DOI: 10.1371/journal.pone.0163551] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 09/11/2016] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 system has become a new versatile technology for genome engineering in various species. To achieve targeted modifications at the same site in both human and mice genomes by a CRISPR/Cas9 nuclease, we designed two target sites in conserved regions of vitamin D receptor (VDR) gene, which cover more than 17 kb of chromosome region depending on the species. We first validated the efficacy of single sgRNA mediated gene specific modifications were 36% and 31% in HEK293T cells. Concurrently, targeted of the intervening genomic segments deletions were generated in chromosomes when two sgRNAs worked simultaneously. The large genomic DNA segments up to 23.4 Kb could be precisely deleted in human chromosomes. Subsequently, Cas9 mRNA and sgRNAs targeting VDRT1 and VDRT2 were co-microinjected into one-cell-stage embryos of C57BL/6 mice. Verified by T7E1 assay and DNA sequencing analysis, 12 mice showed VDR targeted disruption and 8 of which were biallelic knock-out, which demonstrated obvious phenotype of hair thinning. Furthermore, expression changes of Vitamin D metabolism genes in VDR-/-mice were detected. These results indicated that CRISPR/Cas9 mediated knock-out of VDR diminished its gene function in vivo. The off-target effects of CRISPR/Cas9 in VDR-/- founder mice were analyzed. Our results showed that CRISPR/Cas9 system could be employed to target the same sites in different species, when sgRNAs are designed within conserved regions, and therefore will be critically important and applicable for human disease model.
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Affiliation(s)
- Tao Zhang
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- School of Bioscience and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, People's Republic of China
| | - Yajun Yin
- School of Bioscience and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, People's Republic of China
| | - Huan Liu
- School of Bioscience and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, People's Republic of China
| | - Weili Du
- School of Bioscience and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, People's Republic of China
| | - Chonghua Ren
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ling Wang
- School of Bioscience and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, People's Republic of China
| | - Hongzhao Lu
- School of Bioscience and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, People's Republic of China
| | - Zhiying Zhang
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- * E-mail:
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38
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Sasano Y, Nagasawa K, Kaboli S, Sugiyama M, Harashima S. CRISPR-PCS: a powerful new approach to inducing multiple chromosome splitting in Saccharomyces cerevisiae. Sci Rep 2016; 6:30278. [PMID: 27530680 PMCID: PMC4987674 DOI: 10.1038/srep30278] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/27/2016] [Indexed: 12/31/2022] Open
Abstract
PCR-mediated chromosome splitting (PCS) was developed in the yeast Saccharomyces cerevisiae. It is based on homologous recombination and enables division of a chromosome at any point to form two derived and functional chromosomes. However, because of low homologous recombination activity, PCS is limited to a single site at a time, which makes the splitting of multiple loci laborious and time-consuming. Here we have developed a highly efficient and versatile chromosome engineering technology named CRISPR-PCS that integrates PCS with the novel genome editing CRISPR/Cas9 system. This integration allows PCS to utilize induced double strand breaks to activate homologous recombination. CRISPR-PCS enhances the efficiency of chromosome splitting approximately 200-fold and enables generation of simultaneous multiple chromosome splits. We propose that CRISPR-PCS will be a powerful tool for breeding novel yeast strains with desirable traits for specific industrial applications and for investigating genome function.
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Affiliation(s)
- Yu Sasano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Koki Nagasawa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Saeed Kaboli
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Minetaka Sugiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Satoshi Harashima
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, Ikeda 4-22-1, Kumamoto, 860-0082, Japan
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Comparison of CRISPR/Cas9 and TALENs on editing an integrated EGFP gene in the genome of HEK293FT cells. SPRINGERPLUS 2016; 5:814. [PMID: 27390654 PMCID: PMC4916124 DOI: 10.1186/s40064-016-2536-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/07/2016] [Indexed: 11/12/2022]
Abstract
Background Genome editors such as CRISPR/Cas9 and TALENs are at the forefront of research into methodologies for targeted modification of the mammalian genome. To date few comparative studies have been carried out to investigate the difference of genome editing characteristics between CRISPR/Cas9 and TALENs. While the CRISPR/Cas9 system has overtaken TALENs as the tool of choice for most research groups working in this field, we hypothesized that there could be certain applications whereby the application of TALENs would have specific benefits. Here we compare CRISPR/Cas9 and TALEN as tools for introducing site-specific editing events at an integrated EGFP gene in the genome of HEK293FT cells. Results Guide RNAs and TALEN pairs were designed to target two loci within the EGFP gene. We found that paired Cas9 nucleases induced targeted genomic deletion more efficiently and precisely than two TALEN pairs. However, when concurrently supplied with a plasmid template spanning the two DNA double-strand breaks (DSBs) within EGFP, TALENs stimulated homology directed repair (HDR) more efficiently than CRISPR/Cas9 and caused fewer targeted genomic deletions. Conclusions Our data suggest that the choice of genome editing tool should be determined by the desired genome editing outcome. Such a rational approach is likely to benefit research outputs for groups working in fields as diverse as modification of cell lines, to animal models for disease studies, or gene therapy strategies. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2536-3) contains supplementary material, which is available to authorized users.
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40
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Abstract
The Cas9 protein (CRISPR-associated protein 9), derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms. As an RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, and its development as a tool has made sequence-specific gene editing several magnitudes easier. The nuclease-deactivated form of Cas9 further provides a versatile RNA-guided DNA-targeting platform for regulating and imaging the genome, as well as for rewriting the epigenetic status, all in a sequence-specific manner. With all of these advances, we have just begun to explore the possible applications of Cas9 in biomedical research and therapeutics. In this review, we describe the current models of Cas9 function and the structural and biochemical studies that support it. We focus on the applications of Cas9 for genome editing, regulation, and imaging, discuss other possible applications and some technical considerations, and highlight the many advantages that CRISPR/Cas9 technology offers.
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Affiliation(s)
- Haifeng Wang
- Department of Bioengineering, Stanford University, Stanford, California 94305; , ,
| | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, California 94305; , ,
- Biomedical Sciences Graduate Program, University of California, San Francisco, California 94158
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, California 94305; , ,
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305
- Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305
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41
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Tan W, Proudfoot C, Lillico SG, Whitelaw CBA. Gene targeting, genome editing: from Dolly to editors. Transgenic Res 2016; 25:273-87. [PMID: 26847670 PMCID: PMC4882362 DOI: 10.1007/s11248-016-9932-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/06/2016] [Indexed: 12/25/2022]
Abstract
One of the most powerful strategies to investigate biology we have as scientists, is the ability to transfer genetic material in a controlled and deliberate manner between organisms. When applied to livestock, applications worthy of commercial venture can be devised. Although initial methods used to generate transgenic livestock resulted in random transgene insertion, the development of SCNT technology enabled homologous recombination gene targeting strategies to be used in livestock. Much has been accomplished using this approach. However, now we have the ability to change a specific base in the genome without leaving any other DNA mark, with no need for a transgene. With the advent of the genome editors this is now possible and like other significant technological leaps, the result is an even greater diversity of possible applications. Indeed, in merely 5 years, these 'molecular scissors' have enabled the production of more than 300 differently edited pigs, cattle, sheep and goats. The advent of genome editors has brought genetic engineering of livestock to a position where industry, the public and politicians are all eager to see real use of genetically engineered livestock to address societal needs. Since the first transgenic livestock reported just over three decades ago the field of livestock biotechnology has come a long way-but the most exciting period is just starting.
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Affiliation(s)
- Wenfang Tan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - Chris Proudfoot
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - Simon G. Lillico
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - C. Bruce A. Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
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42
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Hu Z, Zhang H, Haley B, Macchi F, Yang F, Misaghi S, Elich J, Yang R, Tang Y, Joly JC, Snedecor BR, Shen A. Carboxypeptidase D is the only enzyme responsible for antibody C-terminal lysine cleavage in Chinese hamster ovary (CHO) cells. Biotechnol Bioeng 2016; 113:2100-6. [DOI: 10.1002/bit.25977] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/20/2016] [Accepted: 03/07/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Zhilan Hu
- Department of Early Stage Cell Culture; Genentech Inc.; 1 DNA Way; South San Francisco California 94080
| | - Henry Zhang
- Department of Early Stage Cell Culture; Genentech Inc.; 1 DNA Way; South San Francisco California 94080
| | - Benjamin Haley
- Department of Molecular Biology; Genentech Inc.; 1 DNA Way; South San Francisco California
| | - Frank Macchi
- Department of Analytical Development and Quality Control; Genentech Inc.; 1 DNA Way; South San Francisco California
| | - Feng Yang
- Department of Analytical Development and Quality Control; Genentech Inc.; 1 DNA Way; South San Francisco California
| | - Shahram Misaghi
- Department of Early Stage Cell Culture; Genentech Inc.; 1 DNA Way; South San Francisco California 94080
| | - Joseph Elich
- Department of Early Stage Cell Culture; Genentech Inc.; 1 DNA Way; South San Francisco California 94080
| | - Renee Yang
- Department of Analytical Development and Quality Control; Genentech Inc.; 1 DNA Way; South San Francisco California
| | - Yun Tang
- Department of Analytical Development and Quality Control; Genentech Inc.; 1 DNA Way; South San Francisco California
| | - John C. Joly
- Department of Early Stage Cell Culture; Genentech Inc.; 1 DNA Way; South San Francisco California 94080
| | - Bradley R. Snedecor
- Department of Early Stage Cell Culture; Genentech Inc.; 1 DNA Way; South San Francisco California 94080
| | - Amy Shen
- Department of Early Stage Cell Culture; Genentech Inc.; 1 DNA Way; South San Francisco California 94080
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43
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He Z, Shi X, Liu M, Sun G, Proudfoot C, Whitelaw CBA, Lillico SG, Chen Y. Comparison of surrogate reporter systems for enrichment of cells with mutations induced by genome editors. J Biotechnol 2016; 221:49-54. [PMID: 26778541 DOI: 10.1016/j.jbiotec.2016.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 01/01/2023]
Abstract
Genome editors are powerful tools that allow modification of the nuclear DNA in eukaryotic cells both in vitro and in vivo. In vitro modified cells are often phenotypically indistinguishable from unmodified cells, hampering their isolation for analysis. Episomal reporters encoding fluorescent proteins can be used for enrichment of modified cells by flow cytometry. Here we compare two surrogate reporters, RGS and SSA, for the enrichment of porcine embryonic fibroblasts containing mutations induced by ZFNs or CRISPR/Cas9. Both systems were effective for enrichment of edited porcine cells with the RGS reporter proving more effective than the SSA reporter. We noted a higher-fold enrichment when editing events were induced by Cas9 compared to those induced by ZFNs, allowing selection at frequencies as high as 70%.
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Affiliation(s)
- Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, PR China
| | - Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, PR China
| | - Meirui Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, PR China
| | - Guangjie Sun
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, PR China
| | - Chris Proudfoot
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - C Bruce A Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Simon G Lillico
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK.
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, PR China.
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44
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Whitelaw CBA, Sheets TP, Lillico SG, Telugu BP. Engineering large animal models of human disease. J Pathol 2015; 238:247-56. [PMID: 26414877 PMCID: PMC4737318 DOI: 10.1002/path.4648] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/15/2015] [Accepted: 09/22/2015] [Indexed: 12/17/2022]
Abstract
The recent development of gene editing tools and methodology for use in livestock enables the production of new animal disease models. These tools facilitate site‐specific mutation of the genome, allowing animals carrying known human disease mutations to be produced. In this review, we describe the various gene editing tools and how they can be used for a range of large animal models of diseases. This genomic technology is in its infancy but the expectation is that through the use of gene editing tools we will see a dramatic increase in animal model resources available for both the study of human disease and the translation of this knowledge into the clinic. Comparative pathology will be central to the productive use of these animal models and the successful translation of new therapeutic strategies. © 2015 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- C Bruce A Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Science, Easter Bush Campus, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Timothy P Sheets
- Animal Bioscience and Biotechnology Laboratory, ARS, Beltsville, MD, 20705, USA.,Department of Animal and Avian Sciences, Beltsville, MD, 20742, USA
| | - Simon G Lillico
- The Roslin Institute and Royal (Dick) School of Veterinary Science, Easter Bush Campus, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Bhanu P Telugu
- Animal Bioscience and Biotechnology Laboratory, ARS, Beltsville, MD, 20705, USA.,Department of Animal and Avian Sciences, Beltsville, MD, 20742, USA
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45
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Tremblay JP. [The CRISPR system can correct or modify the expression of genes responsible for hereditary diseases]. Med Sci (Paris) 2015; 31:1014-22. [PMID: 26576609 DOI: 10.1051/medsci/20153111016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new technology, called CRISPR, derived from the immune system of bacteria, uses a Cas9 nuclease and a guided RNA complementary to a 20 nucleotides sequence of a gene to induce double strand DNA breaks. This permits to modify specifically the targeted gene in plant, animal and human cells. Variants of the technique also permit to reduce or increase the expression of a selected gene. This technology may thus be used not only to understand the role of a gene but also to develop therapies for hereditary and acquired diseases.
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Affiliation(s)
- Jacques P Tremblay
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Centre de Recherche du CHU de Québec, 2705 boulevard Laurier, G1V Québec, Canada
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46
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Wiles MV, Qin W, Cheng AW, Wang H. CRISPR-Cas9-mediated genome editing and guide RNA design. Mamm Genome 2015; 26:501-10. [PMID: 25991564 PMCID: PMC4602062 DOI: 10.1007/s00335-015-9565-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 03/27/2015] [Indexed: 12/26/2022]
Abstract
CRISPR and CRISPR-associated (Cas) proteins, which in nature comprise the RNA-based adaptive immune system in bacteria and archaea, have emerged as particularly powerful genome editing tools owing to their unrivaled ease of use and ability to modify genomes across mammalian model systems. As such, the CRISPR-Cas9 system holds promise as a "system of choice" for functional mammalian genetic studies across biological disciplines. Here we briefly review this fast moving field, introduce the CRISPR-Cas9 system and its application to genome editing, with a focus on the basic considerations in designing the targeting guide RNA sequence.
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Affiliation(s)
- Michael V Wiles
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609-1500, USA
| | - Wenning Qin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609-1500, USA
| | - Albert W Cheng
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609-1500, USA
| | - Haoyi Wang
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609-1500, USA.
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China.
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47
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Crispo M, Mulet AP, Tesson L, Barrera N, Cuadro F, dos Santos-Neto PC, Nguyen TH, Crénéguy A, Brusselle L, Anegón I, Menchaca A. Efficient Generation of Myostatin Knock-Out Sheep Using CRISPR/Cas9 Technology and Microinjection into Zygotes. PLoS One 2015; 10:e0136690. [PMID: 26305800 PMCID: PMC4549068 DOI: 10.1371/journal.pone.0136690] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 08/05/2015] [Indexed: 01/01/2023] Open
Abstract
While CRISPR/Cas9 technology has proven to be a valuable system to generate gene-targeted modified animals in several species, this tool has been scarcely reported in farm animals. Myostatin is encoded by MSTN gene involved in the inhibition of muscle differentiation and growth. We determined the efficiency of the CRISPR/Cas9 system to edit MSTN in sheep and generate knock-out (KO) animals with the aim to promote muscle development and body growth. We generated CRISPR/Cas9 mRNAs specific for ovine MSTN and microinjected them into the cytoplasm of ovine zygotes. When embryo development of CRISPR/Cas9 microinjected zygotes (n = 216) was compared with buffer injected embryos (n = 183) and non microinjected embryos (n = 173), cleavage rate was lower for both microinjected groups (P<0.05) and neither was affected by CRISPR/Cas9 content in the injected medium. Embryo development to blastocyst was not affected by microinjection and was similar among the experimental groups. From 20 embryos analyzed by Sanger sequencing, ten were mutant (heterozygous or mosaic; 50% efficiency). To obtain live MSTN KO lambs, 53 blastocysts produced after zygote CRISPR/Cas9 microinjection were transferred to 29 recipient females resulting in 65.5% (19/29) of pregnant ewes and 41.5% (22/53) of newborns. From 22 born lambs analyzed by T7EI and Sanger sequencing, ten showed indel mutations at MSTN gene. Eight showed mutations in both alleles and five of them were homozygous for indels generating out-of frame mutations that resulted in premature stop codons. Western blot analysis of homozygous KO founders confirmed the absence of myostatin, showing heavier body weight than wild type counterparts. In conclusion, our results demonstrate that CRISPR/Cas9 system was a very efficient tool to generate gene KO sheep. This technology is quick and easy to perform and less expensive than previous techniques, and can be applied to obtain genetically modified animal models of interest for biomedicine and livestock.
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Affiliation(s)
- M. Crispo
- Unidad de Animales Transgénicos y de Experimentación (UATE), Institut Pasteur de Montevideo, Montevideo, Uruguay
- * E-mail: (MC); (IA); (AM)
| | - A. P. Mulet
- Unidad de Animales Transgénicos y de Experimentación (UATE), Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - L. Tesson
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
| | - N. Barrera
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - F. Cuadro
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | | | - T. H. Nguyen
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
| | - A. Crénéguy
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
| | - L. Brusselle
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
| | - I. Anegón
- INSERM UMR 1064, Center for Research in Transplantation and Immunology-ITUN, Nantes, France
- * E-mail: (MC); (IA); (AM)
| | - A. Menchaca
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
- * E-mail: (MC); (IA); (AM)
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48
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Li Y, Park AI, Mou H, Colpan C, Bizhanova A, Akama-Garren E, Joshi N, Hendrickson EA, Feldser D, Yin H, Anderson DG, Jacks T, Weng Z, Xue W. A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome Biol 2015; 16:111. [PMID: 26018130 PMCID: PMC4465146 DOI: 10.1186/s13059-015-0680-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/19/2015] [Indexed: 01/23/2023] Open
Abstract
Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous end-joining enzyme LIG4. We also engineer deletions and inversions for a 50 kb Pten genomic region in mouse liver. We discover diverse yet sequence-specific indels at the rearrangement fusion sites. Moreover, we detect Cas9 cleavage at the fourth nucleotide on the non-complementary strand, leading to staggered instead of blunt DNA breaks. These reporters allow mechanisms of chromosomal rearrangements to be investigated.
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Affiliation(s)
- Yingxiang Li
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, P. R. China.
| | - Angela I Park
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Haiwei Mou
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Cansu Colpan
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Aizhan Bizhanova
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Elliot Akama-Garren
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Nik Joshi
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
| | - David Feldser
- Abramson Family Cancer Research Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Hao Yin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. .,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. .,Harvard-MIT Division of Health Sciences & Technology, Cambridge, MA, 02139, USA. .,Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Zhiping Weng
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, P. R. China. .,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Wen Xue
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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