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Bisht D, Salave S, Desai N, Gogoi P, Rana D, Biswal P, Sarma G, Benival D, Kommineni N, Desai D. Genome editing and its role in vaccine, diagnosis, and therapeutic advancement. Int J Biol Macromol 2024; 269:131802. [PMID: 38670178 DOI: 10.1016/j.ijbiomac.2024.131802] [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: 11/05/2023] [Revised: 02/25/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024]
Abstract
Genome editing involves precise modification of specific nucleotides in the genome using nucleases like CRISPR/Cas, ZFN, or TALEN, leading to increased efficiency of homologous recombination (HR) for gene editing, and it can result in gene disruption events via non-homologous end joining (NHEJ) or homology-driven repair (HDR). Genome editing, particularly CRISPR-Cas9, revolutionizes vaccine development by enabling precise modifications of pathogen genomes, leading to enhanced vaccine efficacy and safety. It allows for tailored antigen optimization, improved vector design, and deeper insights into host genes' impact on vaccine responses, ultimately enhancing vaccine development and manufacturing processes. This review highlights different types of genome editing methods, their associated risks, approaches to overcome the shortcomings, and the diverse roles of genome editing.
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Affiliation(s)
- Deepanker Bisht
- ICAR- Indian Veterinary Research Institute, Izatnagar 243122, Bareilly, India
| | - Sagar Salave
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Nimeet Desai
- Indian Institute of Technology Hyderabad, Kandi 502285, Telangana, India
| | - Purnima Gogoi
- School of Medicine and Public Health, University of Wisconsin and Madison, Madison, WI 53726, USA
| | - Dhwani Rana
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Prachurya Biswal
- College of Veterinary and Animal Sciences, Bihar Animal Sciences University, Kishanganj 855115, Bihar, India
| | - Gautami Sarma
- College of Veterinary & Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, U.S. Nagar, Uttarakhand, India
| | - Derajram Benival
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India.
| | | | - Dhruv Desai
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Liu Y, Liu S, Sheng H, Feng X, Wang S, Hu Y, Zhang L, Cai B, Ma Y. Revolutionizing cattle breeding: Gene editing advancements for enhancing economic traits. Gene 2024; 927:148595. [PMID: 38795857 DOI: 10.1016/j.gene.2024.148595] [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: 02/28/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Beef and dairy products are rich in protein and amino acids, making them highly nutritious for human consumption. The increasing use of gene editing technology in agriculture has paved the way for genetic improvement in cattle breeding via the development of the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system. Gene sequences are artificially altered and employed in the pursuit of improving bovine breeding research through targeted knockout, knock-in, substitution, and mutation methods. This review offers a comprehensive analysis of the advancements in gene editing technology and its diverse applications in enhancing both quantitative and qualitative traits across livestock. These applications encompass areas such as meat quality, milk quality, fertility, disease resistance, environmental adaptability, sex control, horn development, and coat colour. Furthermore, the review considers prospective ideas and insights that may be employed to refine breeding traits, enhance editing efficiency, and navigate the ethical considerations associated with these advancements. The review's focus on improving the quality of beef and milk is intended to enhance the economic viability of these products. Furthermore, it constitutes a valuable resource for scholars and researchers engaged in the fields of cattle genetic improvement and breeding.
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Affiliation(s)
- Yuan Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, Yinchuan 750021, China.
| | - Shuang Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, Yinchuan 750021, China.
| | - Hui Sheng
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, Yinchuan 750021, China.
| | - Xue Feng
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, Yinchuan 750021, China.
| | - Shuzhe Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, Yinchuan 750021, China.
| | - Yamei Hu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, Yinchuan 750021, China.
| | - Lingkai Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, Yinchuan 750021, China.
| | - Bei Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, Yinchuan 750021, China
| | - Yun Ma
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, Ningxia University, Yinchuan 750021, China.
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Morooka N, Gui N, Ando K, Sako K, Fukumoto M, Hasegawa U, Hußmann M, Schulte-Merker S, Mochizuki N, Nakajima H. Angpt1 binding to Tie1 regulates the signaling required for lymphatic vessel development in zebrafish. Development 2024; 151:dev202269. [PMID: 38742432 DOI: 10.1242/dev.202269] [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: 08/16/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024]
Abstract
Development of the vascular system is regulated by multiple signaling pathways mediated by receptor tyrosine kinases. Among them, angiopoietin (Ang)/Tie signaling regulates lymphatic and blood vessel development in mammals. Of the two Tie receptors, Tie2 is well known as a key mediator of Ang/Tie signaling, but, unexpectedly, recent studies have revealed that the Tie2 locus has been lost in many vertebrate species, whereas the Tie1 gene is more commonly present. However, Tie1-driven signaling pathways, including ligands and cellular functions, are not well understood. Here, we performed comprehensive mutant analyses of angiopoietins and Tie receptors in zebrafish and found that only angpt1 and tie1 mutants show defects in trunk lymphatic vessel development. Among zebrafish angiopoietins, only Angpt1 binds to Tie1 as a ligand. We indirectly monitored Ang1/Tie1 signaling and detected Tie1 activation in sprouting endothelial cells, where Tie1 inhibits nuclear import of EGFP-Foxo1a. Angpt1/Tie1 signaling functions in endothelial cell migration and proliferation, and in lymphatic specification during early lymphangiogenesis, at least in part by modulating Vegfc/Vegfr3 signaling. Thus, we show that Angpt1/Tie1 signaling constitutes an essential signaling pathway for lymphatic development in zebrafish.
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Affiliation(s)
- Nanami Morooka
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
- Department of Medical Physiology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Ning Gui
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Koji Ando
- Department of Cardiac Regeneration Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Keisuke Sako
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Moe Fukumoto
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Urara Hasegawa
- Department of Materials Science and Engineering, The Pennsylvania State University, Steidle Building, University Park, Pennsylvania 16802, United States
| | - Melina Hußmann
- Institute of Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WU Münster, 48149 Münster, Germany
| | - Stefan Schulte-Merker
- Institute of Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WU Münster, 48149 Münster, Germany
| | - Naoki Mochizuki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Hiroyuki Nakajima
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
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Yuan YG, Liu SZ, Farhab M, Lv MY, Zhang T, Cao SX. Genome editing: An insight into disease resistance, production efficiency, and biomedical applications in livestock. Funct Integr Genomics 2024; 24:81. [PMID: 38709433 DOI: 10.1007/s10142-024-01364-5] [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: 03/04/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/07/2024]
Abstract
One of the primary concerns for the survival of the human species is the growing demand for food brought on by an increasing global population. New developments in genome-editing technology present promising opportunities for the growth of wholesome and prolific farm animals. Genome editing in large animals is used for a variety of purposes, including biotechnology to improve food production, animal health, and pest management, as well as the development of animal models for fundamental research and biomedicine. Genome editing entails modifying genetic material by removing, adding, or manipulating particular DNA sequences from a particular locus in a way that does not happen naturally. The three primary genome editors are CRISPR/Cas 9, TALENs, and ZFNs. Each of these enzymes is capable of precisely severing nuclear DNA at a predetermined location. One of the most effective inventions is base editing, which enables single base conversions without the requirement for a DNA double-strand break (DSB). As reliable methods for precise genome editing in studies involving animals, cytosine and adenine base editing are now well-established. Effective zygote editing with both cytosine and adenine base editors (ABE) has resulted in the production of animal models. Both base editors produced comparable outcomes for the precise editing of point mutations in somatic cells, advancing the field of gene therapy. This review focused on the principles, methods, recent developments, outstanding applications, the advantages and disadvantages of ZFNs, TALENs, and CRISPR/Cas9 base editors, and prime editing in diverse lab and farm animals. Additionally, we address the methodologies that can be used for gene regulation, base editing, and epigenetic alterations, as well as the significance of genome editing in animal models to better reflect real disease. We also look at methods designed to increase the effectiveness and precision of gene editing tools. Genome editing in large animals is used for a variety of purposes, including biotechnology to improve food production, animal health, and pest management, as well as the development of animal models for fundamental research and biomedicine. This review is an overview of the existing knowledge of the principles, methods, recent developments, outstanding applications, the advantages and disadvantages of zinc finger nucleases (ZFNs), transcription-activator-like endonucleases (TALENs), and clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR/Cas 9), base editors and prime editing in diverse lab and farm animals, which will offer better and healthier products for the entire human race.
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Affiliation(s)
- Yu-Guo Yuan
- College of Veterinary Medicine/Key Laboratory of Animal Genetic Engineering, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Song-Zi Liu
- College of Veterinary Medicine/Key Laboratory of Animal Genetic Engineering, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Muhammad Farhab
- College of Veterinary Medicine/Key Laboratory of Animal Genetic Engineering, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Mei-Yun Lv
- College of Veterinary Medicine/Key Laboratory of Animal Genetic Engineering, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Ting Zhang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212499, China
| | - Shao-Xiao Cao
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- Jiangsu Provincial Engineering Research Center for Precision animal Breeding, Nanjing, 210014, China
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AMJAD ELHAM, PEZZANI RAFFAELE, SOKOUTI BABAK. A review of the literature on the use of CRISPR/Cas9 gene therapy to treat hepatocellular carcinoma. Oncol Res 2024; 32:439-461. [PMID: 38361756 PMCID: PMC10865741 DOI: 10.32604/or.2023.044473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/24/2023] [Indexed: 02/17/2024] Open
Abstract
Noncoding RNAs instruct the Cas9 nuclease to site-specifically cleave DNA in the CRISPR/Cas9 system. Despite the high incidence of hepatocellular carcinoma (HCC), the patient's outcome is poor. As a result of the emergence of therapeutic resistance in HCC patients, clinicians have faced difficulties in treating such tumor. In addition, CRISPR/Cas9 screens were used to identify genes that improve the clinical response of HCC patients. It is the objective of this article to summarize the current understanding of the use of the CRISPR/Cas9 system for the treatment of cancer, with a particular emphasis on HCC as part of the current state of knowledge. Thus, in order to locate recent developments in oncology research, we examined both the Scopus database and the PubMed database. The ability to selectively interfere with gene expression in combinatorial CRISPR/Cas9 screening can lead to the discovery of new effective HCC treatment regimens by combining clinically approved drugs. Drug resistance can be overcome with the help of the CRISPR/Cas9 system. HCC signature genes and resistance to treatment have been uncovered by genome-scale CRISPR activation screening, although this method is not without limitations. It has been extensively examined whether CRISPR can be used as a tool for disease research and gene therapy. CRISPR and its applications to tumor research, particularly in HCC, are examined in this study through a review of the literature.
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Affiliation(s)
- ELHAM AMJAD
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165665813, Iran
| | - RAFFAELE PEZZANI
- Phytotherapy Lab, Endocrinology Unit, Dipartimento di Medicina (DIMED), University of Padova, Via Ospedale 105, Padova, 35128, Italy
- Associazione Italiana Per La Ricerca Oncologica Di Base, Associazione Italiana Per La Ricerca Oncologica Di Base, Padova, 35128, Italy
| | - BABAK SOKOUTI
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165665813, Iran
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Dong Y, Zhang B, Wei Y, Murashev A, Wang S, Wu Y, Ma W, Liu T. Development of Cas13a-based therapy for cancer treatment. Mol Biol Rep 2024; 51:94. [PMID: 38194206 DOI: 10.1007/s11033-023-09129-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024]
Abstract
Gene therapy has become a major focus of current biomedical research. CRISPR (Clustered Regularly Inter spaced Short Palindromic Repeats) systems have been extensively researched for disease treatment applications through genome editing specificity. Compared with Cas9 (CRISPR-associated proteins, Cas), a commonly used tool enzyme for genome editing, Cas13a exhibits RNA-dependent endonuclease activity, including collateral cleavage without obvious potential genetic risks. With its high specificity, Cas13a has significantly improved the sensitivity of viral diagnosis and shown potential to eliminate viruses. However, its efficacy in tumor therapy has not been determined. This review introduces the mechanism and research developments associated with the CRISPR-Cas13a system in tumor treatments and its potential to be used as a new tool for gene therapy. We hope more research would apply Cas13a-based therapy in cancer treatment in the future.
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Affiliation(s)
- Ying Dong
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1023 Shatai Rd, Guangzhou, 510515, China
| | - Bingyang Zhang
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1023 Shatai Rd, Guangzhou, 510515, China
| | - Yi Wei
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1023 Shatai Rd, Guangzhou, 510515, China
| | - Arkady Murashev
- Biological Testing Center of Shamyakin and Ovchimnikov Institute of Bioorganic Chemistry, Moscow, 142290, Russian Federation
| | - Suihai Wang
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1023 Shatai Rd, Guangzhou, 510515, China
| | - Yingsong Wu
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1023 Shatai Rd, Guangzhou, 510515, China
| | - Weifeng Ma
- Department of Microbiology, School of Public Health, Southern Medical University, 1023 Shatai Rd, Guangzhou, 510515, China.
| | - Tiancai Liu
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1023 Shatai Rd, Guangzhou, 510515, China.
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- Provincial Key Laboratory of Immune Regulation and Immunotherapy, Southern Medical University, Guangzhou, 510515, China.
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Gim GM, Jang G. Outlook on genome editing application to cattle. J Vet Sci 2024; 25:e10. [PMID: 38311323 PMCID: PMC10839183 DOI: 10.4142/jvs.23133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/04/2023] [Accepted: 08/20/2023] [Indexed: 02/07/2024] Open
Abstract
In livestock industry, there is growing interest in methods to increase the production efficiency of livestock to address food shortages, given the increasing global population. With the advancements in gene engineering technology, it is a valuable tool and has been intensively utilized in research specifically focused on human disease. In historically, this technology has been used with livestock to create human disease models or to produce recombinant proteins from their byproducts. However, in recent years, utilizing gene editing technology, cattle with identified genes related to productivity can be edited, thereby enhancing productivity in response to climate change or specific disease instead of producing recombinant proteins. Furthermore, with the advancement in the efficiency of gene editing, it has become possible to edit multiple genes simultaneously. This cattle breed improvement has been achieved by discovering the genes through the comprehensive analysis of the entire genome of cattle. The cattle industry has been able to address gene bottlenecks that were previously impossible through conventional breeding systems. This review concludes that gene editing is necessary to expand the cattle industry, improving productivity in the future. Additionally, the enhancement of cattle through gene editing is expected to contribute to addressing environmental challenges associated with the cattle industry. Further research and development in gene editing, coupled with genomic analysis technologies, will significantly contribute to solving issues that conventional breeding systems have not been able to address.
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Affiliation(s)
| | - Goo Jang
- LARTBio Inco, Seoul 06221, Korea
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul 08826, Korea
- Comparative medicine Disease Research Center, Seoul National University, Seoul 08826, Korea
- Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia.
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Yum SY, Choi W, Kim S, Jang G, Koo O. Identification AAVS1-like locus from the porcine genome and site-specific integration of recombinase-mediated cassette exchange using CRISPR/Cas9. Anim Biotechnol 2023; 34:4730-4735. [PMID: 36905152 DOI: 10.1080/10495398.2023.2187408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Gene integration at site-specific loci is a critical approach for understanding the function of a gene in cells or animals. The AAVS1 locus is a well-known safe harbor for human and mouse studies. In this study, we found an AAVS1-like sequence (pAAVS1) in the porcine genome using the Genome Browser and designed TALEN and CRISPR/Cas9 to target the pAAVS1. The efficiency of CRISPR/Cas9 in porcine cells was superior to that of TALEN. We added a loxP-lox2272 sequences to the pAAVS1 targeting donor vector containing GFP for further exchange of various transgenes via recombinase-mediated cassette exchange (RMCE). The donor vector and CRISPR/Cas9 components were transfected into porcine fibroblasts. Targeted cells of CRISPR/Cas9-mediated homologous recombination were identified by antibiotic selection. Gene knock-in was confirmed by PCR. To induce RMCE, another donor vector containing the loxP-lox2272 and inducible Cre recombinase was cloned. The Cre-donor vector was transfected into the pAAVS1 targeted cell line, and RMCE was induced by adding doxycycline to the culture medium. RMCE in porcine fibroblasts was confirmed using PCR. In conclusion, gene targeting at the pAAVS1 and RMCE in porcine fibroblasts was successful. This technology will be useful for future porcine transgenesis studies and the generation of stable transgenic pigs.
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Affiliation(s)
- Soo-Young Yum
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul, Republic of Korea
- LARTBio Incorp, Seoul, Republic of Korea
| | - Woojae Choi
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | | | - Goo Jang
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul, Republic of Korea
- LARTBio Incorp, Seoul, Republic of Korea
- BK21 Plus program, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- Institute of Green Bio Science Technology, Seoul National University, Pyeongchang-gun, Republic of Korea
- Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Okjae Koo
- ToolGen, Inc, Seoul, South Korea
- nSAGE Inc., Incheon, South Korea
- SeaWith Inc., Daegu, South Korea
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Wang M, Ding F, Wang H, Li L, Dai Y, Sun Z, Li N. Versatile generation of precise gene edits in bovines using SEGCPN. BMC Biol 2023; 21:226. [PMID: 37864194 PMCID: PMC10589966 DOI: 10.1186/s12915-023-01677-0] [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: 01/16/2022] [Accepted: 08/07/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Gene knockout and knock-in have been widely performed in large farm animals based on genome editing systems. However, many types of precise gene editing, including targeted deletion, gene tagging, and large gene fragment replacement, remain a challenge in large farm animals. RESULTS Here, we established versatile self-excising gene-targeting technology in combination with programmable nucleases (SEGCPN) to efficiently generate various types of precise gene editing in bovine. First, we used this versatile method to successfully generate bovine embryos with point mutations and 11-bp deletions at the MSTN locus. Second, we successfully generated bulls with EGFP labeling at the SRY locus. Finally, we successfully generated humanized cows in which the endogenous 18-kb α-casein gene was replaced with a 2.6-kb human α-lactalbumin gene. CONCLUSIONS In summary, our new SEGCPN method offers unlimited possibilities for various types of precise gene editing in large animals for application both in agriculture and disease models.
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Affiliation(s)
- Ming Wang
- College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, No. 75 Bingjiaokou Hutong, Beijing, 100088, China
| | - Fangrong Ding
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Haiping Wang
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Ling Li
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Yunping Dai
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
| | - ZhaoLin Sun
- College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, No. 75 Bingjiaokou Hutong, Beijing, 100088, China.
| | - Ning Li
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, No. 75 Bingjiaokou Hutong, Beijing, 100088, China.
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Popova J, Bets V, Kozhevnikova E. Perspectives in Genome-Editing Techniques for Livestock. Animals (Basel) 2023; 13:2580. [PMID: 37627370 PMCID: PMC10452040 DOI: 10.3390/ani13162580] [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: 07/07/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Genome editing of farm animals has undeniable practical applications. It helps to improve production traits, enhances the economic value of livestock, and increases disease resistance. Gene-modified animals are also used for biomedical research and drug production and demonstrate the potential to be used as xenograft donors for humans. The recent discovery of site-specific nucleases that allow precision genome editing of a single-cell embryo (or embryonic stem cells) and the development of new embryological delivery manipulations have revolutionized the transgenesis field. These relatively new approaches have already proven to be efficient and reliable for genome engineering and have wide potential for use in agriculture. A number of advanced methodologies have been tested in laboratory models and might be considered for application in livestock animals. At the same time, these methods must meet the requirements of safety, efficiency and availability of their application for a wide range of farm animals. This review aims at covering a brief history of livestock animal genome engineering and outlines possible future directions to design optimal and cost-effective tools for transgenesis in farm species.
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Affiliation(s)
- Julia Popova
- Laboratory of Bioengineering, Novosibirsk State Agrarian University, 630039 Novosibirsk, Russia; (J.P.); (V.B.)
| | - Victoria Bets
- Laboratory of Bioengineering, Novosibirsk State Agrarian University, 630039 Novosibirsk, Russia; (J.P.); (V.B.)
- Center of Technological Excellence, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
| | - Elena Kozhevnikova
- Laboratory of Bioengineering, Novosibirsk State Agrarian University, 630039 Novosibirsk, Russia; (J.P.); (V.B.)
- Laboratory of Experimental Models of Cognitive and Emotional Disorders, Scientific-Research Institute of Neurosciences and Medicine, 630117 Novosibirsk, Russia
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Salama II, Sami SM, Salama SI, Abdel-Latif GA, Shaaban FA, Fouad WA, Abdelmohsen AM, Raslan HM. Current and novel modalities for management of chronic hepatitis B infection. World J Hepatol 2023; 15:585-608. [PMID: 37305370 PMCID: PMC10251278 DOI: 10.4254/wjh.v15.i5.585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 03/13/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Over 296 million people are estimated to have chronic hepatitis B viral infection (CHB), and it poses unique challenges for elimination. CHB is the result of hepatitis B virus (HBV)-specific immune tolerance and the presence of covalently closed circular DNA as mini chromosome inside the nucleus and the integrated HBV. Serum hepatitis B core-related antigen is the best surrogate marker for intrahepatic covalently closed circular DNA. Functional HBV “cure” is the durable loss of hepatitis B surface antigen (HBsAg), with or without HBsAg seroconversion and undetectable serum HBV DNA after completing a course of treatment. The currently approved therapies are nucleos(t)ide analogues, interferon-alpha, and pegylated-interferon. With these therapies, functional cure can be achieved in < 10% of CHB patients. Any variation to HBV or the host immune system that disrupts the interaction between them can lead to reactivation of HBV. Novel therapies may allow efficient control of CHB. They include direct acting antivirals and immunomodulators. Reduction of the viral antigen load is a crucial factor for success of immune-based therapies. Immunomodulatory therapy may lead to modulation of the host immune system. It may enhance/restore innate immunity against HBV (as toll-like-receptors and cytosolic retinoic acid inducible gene I agonist). Others may induce adaptive immunity as checkpoint inhibitors, therapeutic HBV vaccines including protein (HBsAg/preS and hepatitis B core antigen), monoclonal or bispecific antibodies and genetically engineered T cells to generate chimeric antigen receptor-T or T-cell receptor-T cells and HBV-specific T cells to restore T cell function to efficiently clear HBV. Combined therapy may successfully overcome immune tolerance and lead to HBV control and cure. Immunotherapeutic approaches carry the risk of overshooting immune responses causing uncontrolled liver damage. The safety of any new curative therapies should be measured in relation to the excellent safety of currently approved nucleos(t)ide analogues. Development of novel antiviral and immune modulatory therapies should be associated with new diagnostic assays used to evaluate the effectiveness or to predict response.
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Affiliation(s)
- Iman Ibrahim Salama
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Samia M Sami
- Department of Child Health, National Research Centre, Giza 12411, Dokki, Egypt
| | - Somaia I Salama
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Ghada A Abdel-Latif
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Fatma A Shaaban
- Department of Child Health, National Research Centre, Giza 12411, Dokki, Egypt
| | - Walaa A Fouad
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Aida M Abdelmohsen
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Hala M Raslan
- Department of Internal Medicine, National Research Centre, Giza 12411, Dokki, Egypt
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12
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Kalds P, Zhou S, Huang S, Gao Y, Wang X, Chen Y. When Less Is More: Targeting the Myostatin Gene in Livestock for Augmenting Meat Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4216-4227. [PMID: 36862946 DOI: 10.1021/acs.jafc.2c08583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
How to increase meat production is one of the main questions in animal breeding. Selection for improved body weight has been made and, due to recent genomic advances, naturally occurring variants that are responsible for controlling economically relevant phenotypes have been revealed. The myostatin (MSTN) gene, a superstar gene in animal breeding, was discovered as a negative controller of muscle mass. In some livestock species, natural mutations in the MSTN gene could generate the agriculturally desirable double-muscling phenotype. However, some other livestock species or breeds lack these desirable variants. Genetic modification, particularly gene editing, offers an unprecedented opportunity to induce or mimic naturally occurring mutations in livestock genomes. To date, various MSTN-edited livestock species have been generated using different gene modification tools. These MSTN gene-edited models have higher growth rates and increased muscle mass, suggesting the high potential of utilizing MSTN gene editing in animal breeding. Additionally, post-editing investigations in most livestock species support the favorable influence of targeting the MSTN gene on meat quantity and quality. In this Review, we provide a collective discussion on targeting the MSTN gene in livestock to further encourage its utilization opportunities. It is expected that, shortly, MSTN gene-edited livestock will be commercialized, and MSTN-edited meat will be on the tables of ordinary customers.
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Affiliation(s)
- Peter Kalds
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Shiwei Zhou
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Shuhong Huang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yawei Gao
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling 712100, China
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling 712100, China
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13
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Watanabe M, Nagashima H. Genome Editing of Pig. Methods Mol Biol 2023; 2637:269-292. [PMID: 36773154 DOI: 10.1007/978-1-0716-3016-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Pigs have anatomical and physiological characteristics similar to humans; therefore, genetically modified pigs have the potential to become a valuable bioresource in biomedical research. In fact, considering the increasing need for translational research, pigs are useful for studying intractable diseases, organ transplantation, and regenerative medicine as large-scale experimental animals with excellent potential for extrapolation to humans. With the advent of zinc finger nucleases (ZFNs), breakthroughs in genome editing tools such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9) have facilitated the efficient generation of genetically modified pigs. Genome editing has been used in pigs for more than 10 years; now, along with knockout pigs, knock-in pigs are also gaining increasing importance. In this chapter, we describe the establishment of gene-modified cells (nuclear donor cells), which are necessary for gene knockout and production of knock-in pigs via somatic cell nuclear transplantation, as well as the production of gene knockout pigs using a simple cytoplasmic injection method.
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Affiliation(s)
- Masahito Watanabe
- Meiji University International Institute for Bio-Resource Research, Kawasaki, Kanagawa, Japan.,PorMedTec Co., Ltd., Kawasaki, Kanagawa, Japan
| | - Hiroshi Nagashima
- Meiji University International Institute for Bio-Resource Research, Kawasaki, Kanagawa, Japan. .,Laboratory of Medical Bioengineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan.
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14
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Nair A, Greeny A, Rajendran R, Abdelgawad MA, Ghoneim MM, Raghavan RP, Sudevan ST, Mathew B, Kim H. KIF1A-Associated Neurological Disorder: An Overview of a Rare Mutational Disease. Pharmaceuticals (Basel) 2023; 16:147. [PMID: 37259299 PMCID: PMC9962247 DOI: 10.3390/ph16020147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 10/03/2023] Open
Abstract
KIF1A-associated neurological diseases (KANDs) are a group of inherited conditions caused by changes in the microtubule (MT) motor protein KIF1A as a result of KIF1A gene mutations. Anterograde transport of membrane organelles is facilitated by the kinesin family protein encoded by the MT-based motor gene KIF1A. Variations in the KIF1A gene, which primarily affect the motor domain, disrupt its ability to transport synaptic vesicles containing synaptophysin and synaptotagmin leading to various neurological pathologies such as hereditary sensory neuropathy, autosomal dominant and recessive forms of spastic paraplegia, and different neurological conditions. These mutations are frequently misdiagnosed because they result from spontaneous, non-inherited genomic alterations. Whole-exome sequencing (WES), a cutting-edge method, assists neurologists in diagnosing the illness and in planning and choosing the best course of action. These conditions are simple to be identified in pediatric and have a life expectancy of 5-7 years. There is presently no permanent treatment for these illnesses, and researchers have not yet discovered a medicine to treat them. Scientists have more hope in gene therapy since it can be used to cure diseases brought on by mutations. In this review article, we discussed some of the experimental gene therapy methods, including gene replacement, gene knockdown, symptomatic gene therapy, and cell suicide gene therapy. It also covered its clinical symptoms, pathogenesis, current diagnostics, therapy, and research advances currently occurring in the field of KAND-related disorders. This review also explained the impact that gene therapy can be designed in this direction and afford the remarkable benefits to the patients and society.
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Affiliation(s)
- Ayushi Nair
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Alosh Greeny
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Rajalakshmi Rajendran
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Mohamed A. Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf 72341, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
| | - Roshni Pushpa Raghavan
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Sachithra Thazhathuveedu Sudevan
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682 041, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682 041, India
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
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15
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Montoliu L. Transgenesis and Genome Engineering: A Historical Review. Methods Mol Biol 2023; 2631:1-32. [PMID: 36995662 DOI: 10.1007/978-1-0716-2990-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Our ability to modify DNA molecules and to introduce them into mammalian cells or embryos almost appears in parallel, starting from the 1970s of the last century. Genetic engineering techniques rapidly developed between 1970 and 1980. In contrast, robust procedures to microinject or introduce DNA constructs into individuals did not take off until 1980 and evolved during the following two decades. For some years, it was only possible to add transgenes, de novo, of different formats, including artificial chromosomes, in a variety of vertebrate species or to introduce specific mutations essentially in mice, thanks to the gene-targeting methods by homologous recombination approaches using mouse embryonic stem (ES) cells. Eventually, genome-editing tools brought the possibility to add or inactivate DNA sequences, at specific sites, at will, irrespective of the animal species involved. Together with a variety of additional techniques, this chapter will summarize the milestones in the transgenesis and genome engineering fields from the 1970s to date.
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Affiliation(s)
- Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC) and Center for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain.
- National Centre for Biotechnology (CNB-CSIC), Madrid, Spain.
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16
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Wani AK, Akhtar N, Singh R, Prakash A, Raza SHA, Cavalu S, Chopra C, Madkour M, Elolimy A, Hashem NM. Genome centric engineering using ZFNs, TALENs and CRISPR-Cas9 systems for trait improvement and disease control in Animals. Vet Res Commun 2023; 47:1-16. [PMID: 35781172 DOI: 10.1007/s11259-022-09967-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/24/2022] [Indexed: 01/27/2023]
Abstract
Livestock is an essential life commodity in modern agriculture involving breeding and maintenance. The farming practices have evolved mainly over the last century for commercial outputs, animal welfare, environment friendliness, and public health. Modifying genetic makeup of livestock has been proposed as an effective tool to create farmed animals with characteristics meeting modern farming system goals. The first technique used to produce transgenic farmed animals resulted in random transgene insertion and a low gene transfection rate. Therefore, genome manipulation technologies have been developed to enable efficient gene targeting with a higher accuracy and gene stability. Genome editing (GE) with engineered nucleases-Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) regulates the targeted genetic alterations to facilitate multiple genomic modifications through protein-DNA binding. The application of genome editors indicates usefulness in reproduction, animal models, transgenic animals, and cell lines. Recently, CRISPR/Cas system, an RNA-dependent genome editing tool (GET), is considered one of the most advanced and precise GE techniques for on-target modifications in the mammalian genome by mediating knock-in (KI) and knock-out (KO) of several genes. Lately, CRISPR/Cas9 tool has become the method of choice for genome alterations in livestock species due to its efficiency and specificity. The aim of this review is to discuss the evolution of engineered nucleases and GETs as a powerful tool for genome manipulation with special emphasis on its applications in improving economic traits and conferring resistance to infectious diseases of animals used for food production, by highlighting the recent trends for maintaining sustainable livestock production.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina, 120 Mason Farm Road, CB# 7260, 3093 Genetic Medicine, Chapel Hill, NC, 27599-2760, USA
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, P -ta 1Decembrie 10, 410073, Oradea, Romania
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Mahmoud Madkour
- Animal Production Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Ahmed Elolimy
- Animal Production Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Nesrein M Hashem
- Department of Animal and Fish Production, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, 21545, Egypt.
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17
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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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18
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Leonova EI, Reshetnikov VV, Sopova JV. CRISPR/Cas-edited pigs for personalized medicine: more than preclinical test-system. RESEARCH RESULTS IN PHARMACOLOGY 2022. [DOI: 10.3897/rrpharmacology.8.83872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Novel CRISPR-Cas-based genome editing tools made it feasible to introduce a variety of precise genomic modifications in the pig genome, including introducing multiple edits simultaneously, inserting long DNA sequences into specifically targeted loci, and performing nucleotide transitions and transversions. Pigs serve as a vital agricultural resource and animal model in biomedical studies, given their advantages over the other models. Pigs share high similarities to humans regarding body/organ size, anatomy, physiology, and a metabolic profile. The pig genome can be modified to carry the same genetic mutations found in humans to replicate inherited diseases to provide preclinical trials of drugs. Moreover, CRISPR-based modification of pigs antigen profile makes it possible to offer porcine organs for xenotransplantation with minimal transplant rejection responses. This review summarizes recent advances in endonuclease-mediated genome editing tools and research progress of genome-edited pigs as personalized test-systems for preclinical trials and as donors of organs with human-fit antigen profile.
Graphical abstract:
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19
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Sarvari P, Sarvari P, Ramírez-Díaz I, Mahjoubi F, Rubio K. Advances of Epigenetic Biomarkers and Epigenome Editing for Early Diagnosis in Breast Cancer. Int J Mol Sci 2022; 23:ijms23179521. [PMID: 36076918 PMCID: PMC9455804 DOI: 10.3390/ijms23179521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Epigenetic modifications are known to regulate cell phenotype during cancer progression, including breast cancer. Unlike genetic alterations, changes in the epigenome are reversible, thus potentially reversed by epi-drugs. Breast cancer, the most common cause of cancer death worldwide in women, encompasses multiple histopathological and molecular subtypes. Several lines of evidence demonstrated distortion of the epigenetic landscape in breast cancer. Interestingly, mammary cells isolated from breast cancer patients and cultured ex vivo maintained the tumorigenic phenotype and exhibited aberrant epigenetic modifications. Recent studies indicated that the therapeutic efficiency for breast cancer regimens has increased over time, resulting in reduced mortality. Future medical treatment for breast cancer patients, however, will likely depend upon a better understanding of epigenetic modifications. The present review aims to outline different epigenetic mechanisms including DNA methylation, histone modifications, and ncRNAs with their impact on breast cancer, as well as to discuss studies highlighting the central role of epigenetic mechanisms in breast cancer pathogenesis. We propose new research areas that may facilitate locus-specific epigenome editing as breast cancer therapeutics.
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Affiliation(s)
- Pourya Sarvari
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Frouzandeh Mahjoubi
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Correspondence:
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20
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Coorey B, Haase F, Ellaway C, Clarke A, Lisowski L, Gold WA. Gene Editing and Rett Syndrome: Does It Make the Cut? CRISPR J 2022; 5:490-499. [PMID: 35881862 DOI: 10.1089/crispr.2022.0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rett syndrome (RTT) is a rare neurogenetic disorder caused by pathogenic variants of the Methyl CpG binding protein 2 (MECP2) gene. The RTT is characterized by apparent normal early development followed by regression of communicative and fine motor skills. Comorbidities include epilepsy, severe cognitive impairment, and autonomic and motor dysfunction. Despite almost 60 clinical trials and the promise of a gene therapy, no cure has yet emerged with treatment remaining symptomatic. Advances in understanding RTT has provided insight into the complexity and exquisite control of MECP2 expression, where loss of expression leads to RTT and overexpression leads to MECP2 duplication syndrome. Therapy development requires regulated expression that matches the spatiotemporal endogenous expression of MECP2 in the brain. Gene editing has revolutionized gene therapy and promises an exciting strategy for many incurable monogenic disorders, including RTT, by editing the native locus and retaining endogenous gene expression. Here, we review the literature on the currently available editing technologies and discuss their limitations and applicability to the treatment of RTT.
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Affiliation(s)
- Bronte Coorey
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, Australia.,Molecular Neurobiology Research Laboratory, Kid's Research, Westmead, Australia.,Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, Australia
| | - Florencia Haase
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, Australia.,Molecular Neurobiology Research Laboratory, Kid's Research, Westmead, Australia.,Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, Australia
| | - Carolyn Ellaway
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network Sydney, Westmead, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Angus Clarke
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.,Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland
| | - Wendy A Gold
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, Australia.,Molecular Neurobiology Research Laboratory, Kid's Research, Westmead, Australia.,Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Children's Medical Research Institute, Westmead, Australia
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21
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Application of Gene Editing Technology in Resistance Breeding of Livestock. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071070. [PMID: 35888158 PMCID: PMC9325061 DOI: 10.3390/life12071070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 02/06/2023]
Abstract
As a new genetic engineering technology, gene editing can precisely modify the specific gene sequence of the organism’s genome. In the last 10 years, with the rapid development of gene editing technology, zinc-finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs), and CRISPR/Cas9 systems have been applied to modify endogenous genes in organisms accurately. Now, gene editing technology has been used in mice, zebrafish, pigs, cattle, goats, sheep, rabbits, monkeys, and other species. Breeding for disease-resistance in agricultural animals tends to be a difficult task for traditional breeding, but gene editing technology has made this easier. In this work, we overview the development and application of gene editing technology in the resistance breeding of livestock. Also, we further discuss the prospects and outlooks of gene editing technology in disease-resistance breeding.
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22
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Ogun OJ, Thaller G, Becker D. An Overview of the Importance and Value of Porcine Species in Sialic Acid Research. BIOLOGY 2022; 11:biology11060903. [PMID: 35741423 PMCID: PMC9219854 DOI: 10.3390/biology11060903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 11/19/2022]
Abstract
Simple Summary Humans frequently interact with pigs and porcine meat is the most consumed red meat in the world. In addition, due to the many physiological and anatomical similarities shared between pigs and humans, in contrast to most mammalian species, pigs are a suitable model organism and pig organs can be used for xenotransplantation. However, one major challenge of porcine meat consumption and xenotransplantation is the xenoreactivity between red meat Neu5Gc sialic acid and human anti-Neu5Gc antibodies, which are associated with certain diseases and disorders. Furthermore, pigs express both α2-3 and α2-6 Sia linkages that could serve as viable receptors for viral infections, reassortments, and cross-species transmission of viruses. Therefore, pigs play a significant role in sialic acid research and, in general, in human health. Abstract Humans frequently interact with pigs, whose meat is also one of the primary sources of animal protein. They are one of the main species at the center of sialic acid (Sia) research. Sias are sugars at terminals of glycoconjugates, are expressed at the cell surfaces of mammals, and are important in cellular interactions. N-glycolylneuraminic acid (Neu5Gc) and N-acetylneuraminic acid (Neu5Ac) are notable Sias in mammals. Cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) encodes the CMAH enzyme that biosynthesizes Neu5Gc. Although humans cannot endogenously synthesize Neu5Gc due to the inactivation of this gene by a mutation, Neu5Gc can be metabolically incorporated into human tissues from red meat consumption. Interactions between Neu5Gc and human anti-Neu5Gc antibodies have been associated with certain diseases and disorders. In this review, we summarized the sialic acid metabolic pathway, its regulation and link to viral infections, as well as the importance of the pig as a model organism in Sia research, making it a possible source of Neu5Gc antigens affecting human health. Future research in solving the structures of crucial enzymes involved in Sia metabolism, as well as their regulation and interactions with other enzymes, especially CMAH, could help to understand their function and reduce the amount of Neu5Gc.
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Affiliation(s)
- Oluwamayowa Joshua Ogun
- Institute of Animal Breeding and Husbandry, University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany;
- Correspondence: (O.J.O.); (D.B.)
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany;
| | - Doreen Becker
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
- Correspondence: (O.J.O.); (D.B.)
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23
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Negi C, Vasistha NK, Singh D, Vyas P, Dhaliwal HS. Application of CRISPR-Mediated Gene Editing for Crop Improvement. Mol Biotechnol 2022; 64:1198-1217. [PMID: 35672603 DOI: 10.1007/s12033-022-00507-y] [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: 12/08/2021] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
Plant gene editing has become an important molecular tool to revolutionize modern breeding of crops. Over the past years, remarkable advancement has been made in developing robust and efficient editing methods for plants. Despite a variety of available genome editing methods, the discovery of most recent system of clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) has been one of the biggest advancement in this path, with being the most efficient approach for genome manipulation. Until recently, genetic manipulations were confined to methods, like Agrobacterium-mediated transformations, zinc-finger nucleases, and TAL effector nucleases. However this technology supersedes all other methods for genetic modification. This RNA-guided CRISPR-Cas system is being rapidly developed with enhanced functionalities for better use and greater possibilities in biological research. In this review, we discuss and sum up the application of this simple yet powerful tool of CRISPR-Cas system for crop improvement with recent advancement in this technology.
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Affiliation(s)
- Chandranandani Negi
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India
| | | | - Pritesh Vyas
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India.
| | - H S Dhaliwal
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, 173101, India
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24
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Raza SHA, Hassanin AA, Pant SD, Bing S, Sitohy MZ, Abdelnour SA, Alotaibi MA, Al-Hazani TM, Abd El-Aziz AH, Cheng G, Zan L. Potentials, prospects and applications of genome editing technologies in livestock production. Saudi J Biol Sci 2022; 29:1928-1935. [PMID: 35531207 PMCID: PMC9072931 DOI: 10.1016/j.sjbs.2021.11.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022] Open
Abstract
In recent years, significant progress has been achieved in genome editing applications using new programmable DNA nucleases such as zinc finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs) and the clustered regularly interspaced short palindromic repeats/Cas9 system (CRISPR/Cas9). These genome editing tools are capable of nicking DNA precisely by targeting specific sequences, and enable the addition, removal or substitution of nucleotides via double-stranded breakage at specific genomic loci. CRISPR/Cas system, one of the most recent genome editing tools, affords the ability to efficiently generate multiple genomic nicks in single experiment. Moreover, CRISPR/Cas systems are relatively easy and cost effective when compared to other genome editing technologies. This is in part because CRISPR/Cas systems rely on RNA-DNA binding, unlike other genome editing tools that rely on protein–DNA interactions, which affords CRISPR/Cas systems higher flexibility and more fidelity. Genome editing tools have significantly contributed to different aspects of livestock production such as disease resistance, improved performance, alterations of milk composition, animal welfare and biomedicine. However, despite these contributions and future potential, genome editing technologies also have inherent risks, and therefore, ethics and social acceptance are crucial factors associated with implementation of these technologies. This review emphasizes the impact of genome editing technologies in development of livestock breeding and production in numerous species such as cattle, pigs, sheep and goats. This review also discusses the mechanisms behind genome editing technologies, their potential applications, risks and associated ethics that should be considered in the context of livestock.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, PR China.,National Beef Cattle Improvement Center, Northwest A&F University, 712100 Yangling, Shaanxi, PR China
| | - Abdallah A Hassanin
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Sameer D Pant
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650 Australia
| | - Sun Bing
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Mahmoud Z Sitohy
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Sameh A Abdelnour
- Animal Production Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | | | - Tahani Mohamed Al-Hazani
- Biology Department, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box: 83, Al-Kharj 11940, Saudi Arabia
| | - Ayman H Abd El-Aziz
- Animal Husbandry and Animal Wealth Development Department, Faculty of Veterinary Medicine, Daman Hour University, Damanhour, Egypt
| | - Gong Cheng
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Linsen Zan
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, PR China.,National Beef Cattle Improvement Center, Northwest A&F University, 712100 Yangling, Shaanxi, PR China
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25
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Abstract
For four decades, genetically altered laboratory animals have provided invaluable information. Originally, genetic modifications were performed on only a few animal species, often chosen because of the ready accessibility of embryonic materials and short generation times. The methods were often slow, inefficient and expensive. In 2013, a new, extremely efficient technology, namely CRISPR/Cas9, not only made the production of genetically altered organisms faster and cheaper, but also opened it up to non-conventional laboratory animal species. CRISPR/Cas9 relies on a guide RNA as a 'location finder' to target DNA double strand breaks induced by the Cas9 enzyme. This is a prerequisite for non-homologous end joining repair to occur, an error prone mechanism often generating insertion or deletion of genetic material. If a DNA template is also provided, this can lead to homology directed repair, allowing precise insertions, deletions or substitutions. Due to its high efficiency in targeting DNA, CRISPR/Cas9-mediated genetic modification is now possible in virtually all animal species for which we have genome sequence data. Furthermore, modifications of Cas9 have led to more refined genetic alterations from targeted single base-pair mutations to epigenetic modifications. The latter offer altered gene expression without genome alteration. With this ever growing genetic toolbox, the number and range of genetically altered conventional and non-conventional laboratory animals with simple or complex genetic modifications is growing exponentially.
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26
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Spencer TE, Wells KD, Lee K, Telugu BP, Hansen PJ, Bartol FF, Blomberg L, Schook LB, Dawson H, Lunney JK, Driver JP, Davis TA, Donovan SM, Dilger RN, Saif LJ, Moeser A, McGill JL, Smith G, Ireland JJ. Future of biomedical, agricultural, and biological systems research using domesticated animals. Biol Reprod 2022; 106:629-638. [PMID: 35094055 PMCID: PMC9189970 DOI: 10.1093/biolre/ioac019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 01/31/2023] Open
Abstract
Increased knowledge of reproduction and health of domesticated animals is integral to sustain and improve global competitiveness of U.S. animal agriculture, understand and resolve complex animal and human diseases, and advance fundamental research in sciences that are critical to understanding mechanisms of action and identifying future targets for interventions. Historically, federal and state budgets have dwindled and funding for the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) competitive grants programs remained relatively stagnant from 1985 through 2010. This shortage in critical financial support for basic and applied research, coupled with the underappreciated knowledge of the utility of non-rodent species for biomedical research, hindered funding opportunities for research involving livestock and limited improvements in both animal agriculture and animal and human health. In 2010, the National Institutes of Health and USDA NIFA established an interagency partnership to promote the use of agriculturally important animal species in basic and translational research relevant to both biomedicine and agriculture. This interagency program supported 61 grants totaling over $107 million with 23 awards to new or early-stage investigators. This article will review the success of the 9-year Dual Purpose effort and highlight opportunities for utilizing domesticated agricultural animals in research.
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Affiliation(s)
- Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA,Correspondence: Division of Animal Sciences, University of Missouri, Columbia, MO, USA. Tel: +15738823467; E-mail:
| | - Kevin D Wells
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Kiho Lee
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Bhanu P Telugu
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Peter J Hansen
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Frank F Bartol
- Department of Anatomy, Physiology and Pharmacology, Cellular and Molecular Biosciences Program, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - LeAnn Blomberg
- The Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705 USA
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Harry Dawson
- USDA, ARS, Beltsville Human Nutrition Research Center, Diet, Genomics & Immunology Laboratory, Beltsville, MD 20705-2350, USA
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center (BARC), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Beltsville, MD, USA
| | - John P Driver
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Teresa A Davis
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Sharon M Donovan
- Department of Food Science and Human Nutrition, College of Agricultural, Consumer and Environmental Sciences, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Ryan N Dilger
- The Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705 USA
| | - Linda J Saif
- Center for Food Animal Health Research, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, USA
| | - Adam Moeser
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Jodi L McGill
- Department of Veterinary Microbiology and Preventative Medicine, Iowa State University, Ames, IA, USA
| | - George Smith
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - James J Ireland
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
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27
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Montoliu L. Historical DNA Manipulation Overview. Methods Mol Biol 2022; 2495:3-28. [PMID: 35696025 DOI: 10.1007/978-1-0716-2301-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The history of DNA manipulation for the creation of genetically modified animals began in the 1970s, using viruses as the first DNA molecules microinjected into mouse embryos at different preimplantation stages. Subsequently, simple DNA plasmids were used to microinject into the pronuclei of fertilized mouse oocytes and that method became the reference for many years. The isolation of embryonic stem cells together with advances in genetics allowed the generation of gene-specific knockout mice, later on improved with conditional mutations. Cloning procedures expanded the gene inactivation to livestock and other non-model mammalian species. Lentiviruses, artificial chromosomes, and intracytoplasmic sperm injections expanded the toolbox for DNA manipulation. The last chapter of this short but intense history belongs to programmable nucleases, particularly CRISPR-Cas systems, triggering the development of genomic-editing techniques, the current revolution we are living in.
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Affiliation(s)
- Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC) and Center for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain.
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28
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Xian X, Wang Y, Liu G. Genetically Engineered Hamster Models of Dyslipidemia and Atherosclerosis. Methods Mol Biol 2022; 2419:433-459. [PMID: 35237980 DOI: 10.1007/978-1-0716-1924-7_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Animal models of human diseases play an extremely important role in biomedical research. Among them, mice are widely used animal models for translational research, especially because of ease of generation of genetically engineered mice. However, because of the great differences in biology between mice and humans, translation of findings to humans remains a major issue. Therefore, the exploration of models with biological and metabolic characteristics closer to those of humans has never stopped.Although pig and nonhuman primates are biologically similar to humans, their genetic engineering is technically difficult, the cost of breeding is high, and the experimental time is long. As a result, the application of these species as model animals, especially genetically engineered model animals, in biomedical research is greatly limited.In terms of lipid metabolism and cardiovascular diseases, hamsters have several characteristics different from rats and mice, but similar to those in humans. The hamster is therefore an ideal animal model for studying lipid metabolism and cardiovascular disease because of its small size and short reproduction period. However, the phenomenon of zygote division, which was unexpectedly blocked during the manipulation of hamster embryos for some unknown reasons, had plagued researchers for decades and no genetically engineered hamsters have therefore been generated as animal models of human diseases for a long time. After solving the problem of in vitro development of hamster zygotes, we successfully prepared enhanced green fluorescent protein (eGFP) transgenic hamsters by microinjection of lentiviral vectors into the zona pellucida space of zygotes. On this basis, we started the development of cardiovascular disease models using the hamster embryo culture system combined with the novel genome editing technique of clustered regularly interspaced short palindromic repeats (CRISPR )/CRISPR associated protein 9 (Cas9). In this chapter, we will introduce some of the genetically engineered hamster models with dyslipidemia and the corresponding characteristics of these models. We hope that the genetically engineered hamster models can be further recognized and complement other genetically engineered animal models such as mice, rats, and rabbits. This will lead to new avenues and pathways for the study of lipid metabolism and its related diseases.
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Affiliation(s)
- Xunde Xian
- Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuhui Wang
- Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University, Beijing, China
| | - George Liu
- Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, School of Basic Medical Sciences, Peking University, Beijing, China.
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29
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Okasato R, Kano K, Kise R, Inoue A, Fukuhara S, Aoki J. An ATX-LPA 6-Gα 13-ROCK axis shapes and maintains caudal vein plexus in zebrafish. iScience 2021; 24:103254. [PMID: 34755093 PMCID: PMC8564058 DOI: 10.1016/j.isci.2021.103254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/06/2021] [Accepted: 10/08/2021] [Indexed: 12/31/2022] Open
Abstract
Lysophosphatidic acid (LPA) is a potential regulator of vascular formation derived from blood. In this study, we utilized zebrafish as a model organism to monitor the blood vessel formation in detail. Zebrafish mutant of ATX, an LPA-producing enzyme, had a defect in the caudal vein plexus (CVP). Pharmacological inhibition of ATX resulted in a fusion of the delicate vessels in the CVP to form large sac-like vessels. Mutant embryos of LPA6 receptor and downstream Gα13 showed the same phenotype. Administration of OMPT, a stable LPA-analog, induced rapid CVP constriction, which was attenuated significantly in the LPA6 mutant. We also found that blood flow-induced CVP formation was dependent on ATX. The present study demonstrated that the ATX-LPA6 axis acts cooperatively with blood flow and contributes to the formation and maintenance of the CVP by generating contractive force in endothelial cells. Blocking an ATX-LPA6-Gα13-ROCK axis causes malformation of the caudal vein plexus The axis also contributes to maintaining the fine structure of the caudal vein plexus Activation of LPA6 induces vasoconstriction Caudal vein plexus formation evoked by blood flow is dependent on an ATX-LPA6 axis
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Affiliation(s)
- Ryohei Okasato
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.,AMED-LEAP, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Kuniyuki Kano
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.,AMED-LEAP, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Ryoji Kise
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.,AMED-LEAP, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute of Advanced Medical Sciences, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.,AMED-LEAP, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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30
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Coorey BA, Gold WA. Breaking Boundaries in the Brain-Advances in Editing Tools for Neurogenetic Disorders. Front Genome Ed 2021; 3:623519. [PMID: 34713252 PMCID: PMC8525368 DOI: 10.3389/fgeed.2021.623519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
Monogenic neurological disorders are devastating, affecting hundreds of millions of people globally and present a substantial burden to individuals, carers, and healthcare systems. These disorders are predominantly caused by inherited or de novo variants that result in impairments to nervous system development, neurodegeneration, or impaired neuronal function. No cure exists for these disorders with many being refractory to medication. However, since monogenic neurological disorders have a single causal factor, they are also excellent targets for innovative, therapies such as gene therapy. Despite this promise, gene transfer therapies are limited in that they are only suitable for neurogenetic disorders that fit within the technological reach of these therapies. The limitations include the size of the coding region of the gene, the regulatory control of expression (dosage sensitivity), the mode of expression (e.g., dominant negative) and access to target cells. Gene editing therapies are an alternative strategy to gene transfer therapy as they have the potential of overcoming some of these hurdles, enabling the retention of physiological expression of the gene and offers precision medicine-based therapies where individual variants can be repaired. This review focusses on the existing gene editing technologies for neurogenetic disorders and how these propose to overcome the challenges common to neurogenetic disorders with gene transfer therapies as well as their own challenges.
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Affiliation(s)
- Bronte A Coorey
- School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia.,Molecular Neurobiology Research Laboratory, Kid's Research, Children's Hospital at Westmead, Westmead, NSW, Australia.,Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Wendy A Gold
- School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia.,Molecular Neurobiology Research Laboratory, Kid's Research, Children's Hospital at Westmead, Westmead, NSW, Australia.,Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine and Health, Camperdown, NSW, Australia.,Molecular Neurobiology, The Children's Medical Research Institute, Westmead, NSW, Australia
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31
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Dehdilani N, Taemeh SY, Goshayeshi L, Dehghani H. Genetically engineered birds; pre-CRISPR and CRISPR era. Biol Reprod 2021; 106:24-46. [PMID: 34668968 DOI: 10.1093/biolre/ioab196] [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: 08/12/2021] [Revised: 10/08/2021] [Accepted: 10/14/2021] [Indexed: 11/14/2022] Open
Abstract
Generating biopharmaceuticals in genetically engineered bioreactors continues to reign supreme. Hence, genetically engineered birds have attracted considerable attention from the biopharmaceutical industry. Fairly recent genome engineering methods have made genome manipulation an easy and affordable task. In this review, we first provide a broad overview of the approaches and main impediments ahead of generating efficient and reliable genetically engineered birds, and various factors that affect the fate of a transgene. This section provides an essential background for the rest of the review, in which we discuss and compare different genome manipulation methods in the pre-CRISPR and CRISPR era in the field of avian genome engineering.
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Affiliation(s)
- Nima Dehdilani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sara Yousefi Taemeh
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Lena Goshayeshi
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hesam Dehghani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.,Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.,Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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32
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Rubinstein CD, McLean DT, Lehman BP, Meudt JJ, Schomberg DT, Krentz KJ, Reichert JL, Meyer MB, Adams M, Konsitzke CM, Shanmuganayagam D. Assessment of Mosaicism and Detection of Cryptic Alleles in CRISPR/Cas9-Engineered Neurofibromatosis Type 1 and TP53 Mutant Porcine Models Reveals Overlooked Challenges in Precision Modeling of Human Diseases. Front Genet 2021; 12:721045. [PMID: 34630515 PMCID: PMC8495252 DOI: 10.3389/fgene.2021.721045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/18/2021] [Indexed: 12/20/2022] Open
Abstract
Genome editing in pigs has been made efficient, practical, and economically viable by the CRISPR/Cas9 platform, representing a promising new era in translational modeling of human disease for research and preclinical development of therapies and devices. Porcine embryo microinjection provides a universally available, efficient option over somatic-cell nuclear transfer, but requires that critical considerations be made in genotypic validation of the models that routinely go unaddressed. Accurate validation of genotypes is especially important when modeling genetic disorders, such as neurofibromatosis type 1 (NF1) that exhibits complex genotype–phenotypic relationships. NF1, an autosomal dominant disorder, is particularly hard to model as it manifests very differently across patients, and even within families, with over 3,000 disease-associated mutations of the neurofibromin 1 (NF1) gene identified. The precise nature of the mutations plays a role in the complex phenotypic presentation of the disorder that includes benign and malignant peripheral and central nervous system tumors, a variety of motor deficits and debilitating cognitive impairments and musculoskeletal, cardiovascular, and gastrointestinal disorders. NF1 can also often involve mutations in passenger genes such as TP53. In this manuscript, we describe the creation of three novel porcine models of NF1 and a model additionally harboring a mutation in TP53 by embryo microinjection of CRISPR/Cas9. We present the challenges encountered in validation of genotypes and the methodological strategies developed to counter the hurdles. We present simple options for quantifying level of mosaicism: a quantitative method (targeted amplicon sequencing) for small edits such as SNPs and indels and a semiquantitative method (competitive PCR) for large edits. Characterization of mosaicism allowed for strategic selection of founder pigs for rapid, economical expansion of genetically defined lines. We also present commonly observed unexpected DNA repair products (i.e., structural variants or cryptic alleles) that are refractory to PCR amplification and thus evade detection. We present the use of copy number variance assays to overcome hurdles in detecting cryptic alleles. The report provides a framework for genotypic validation of porcine models created by embryo microinjection and the expansion of lines in an efficient manner.
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Affiliation(s)
| | - Dalton T McLean
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Brent P Lehman
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jennifer J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Dominic T Schomberg
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Kathy J Krentz
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jamie L Reichert
- Swine Research and Teaching Center, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Charles M Konsitzke
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States.,Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
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33
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Chuang CK, Lin WM. Points of View on the Tools for Genome/Gene Editing. Int J Mol Sci 2021; 22:9872. [PMID: 34576035 PMCID: PMC8470269 DOI: 10.3390/ijms22189872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/26/2021] [Accepted: 09/09/2021] [Indexed: 12/25/2022] Open
Abstract
Theoretically, a DNA sequence-specific recognition protein that can distinguish a DNA sequence equal to or more than 16 bp could be unique to mammalian genomes. Long-sequence-specific nucleases, such as naturally occurring Homing Endonucleases and artificially engineered ZFN, TALEN, and Cas9-sgRNA, have been developed and widely applied in genome editing. In contrast to other counterparts, which recognize DNA target sites by the protein moieties themselves, Cas9 uses a single-guide RNA (sgRNA) as a template for DNA target recognition. Due to the simplicity in designing and synthesizing a sgRNA for a target site, Cas9-sgRNA has become the most current tool for genome editing. Moreover, the RNA-guided DNA recognition activity of Cas9-sgRNA is independent of both of the nuclease activities of it on the complementary strand by the HNH domain and the non-complementary strand by the RuvC domain, and HNH nuclease activity null mutant (H840A) and RuvC nuclease activity null mutant (D10A) were identified. In accompaniment with the sgRNA, Cas9, Cas9(D10A), Cas9(H840A), and Cas9(D10A, H840A) can be used to achieve double strand breakage, complementary strand breakage, non-complementary strand breakage, and no breakage on-target site, respectively. Based on such unique characteristics, many engineered enzyme activities, such as DNA methylation, histone methylation, histone acetylation, cytidine deamination, adenine deamination, and primer-directed mutation, could be introduced within or around the target site. In order to prevent off-targeting by the lasting expression of Cas9 derivatives, a lot of transient expression methods, including the direct delivery of Cas9-sgRNA riboprotein, were developed. The issue of biosafety is indispensable in in vivo applications; Cas9-sgRNA packaged into virus-like particles or extracellular vesicles have been designed and some in vivo therapeutic trials have been reported.
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Affiliation(s)
- Chin-Kai Chuang
- Animal Technology Research Center, Division of Animal Technology, Agricultural Technology Research Institute, No. 52, Kedong 2nd Rd., Zhunan Township, Miaoli County 35053, Taiwan;
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Howland D, Ellederova Z, Aronin N, Fernau D, Gallagher J, Taylor A, Hennebold J, Weiss AR, Gray-Edwards H, McBride J. Large Animal Models of Huntington's Disease: What We Have Learned and Where We Need to Go Next. J Huntingtons Dis 2021; 9:201-216. [PMID: 32925082 PMCID: PMC7597371 DOI: 10.3233/jhd-200425] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genetically modified rodent models of Huntington’s disease (HD) have been especially valuable to our understanding of HD pathology and the mechanisms by which the mutant HTT gene alters physiology. However, due to inherent differences in genetics, neuroanatomy, neurocircuitry and neurophysiology, animal models do not always faithfully or fully recapitulate human disease features or adequately predict a clinical response to treatment. Therefore, conducting translational studies of candidate HD therapeutics only in a single species (i.e. mouse disease models) may not be sufficient. Large animal models of HD have been shown to be valuable to the HD research community and the expectation is that the need for translational studies that span rodent and large animal models will grow. Here, we review the large animal models of HD that have been created to date, with specific commentary on differences between the models, the strengths and disadvantages of each, and how we can advance useful models to study disease pathophysiology, biomarker development and evaluation of promising therapeutics.
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Affiliation(s)
| | - Zdenka Ellederova
- Institute of Animal Physiology and Genetics, Libechov, Czech Republic
| | - Neil Aronin
- Horae Gene Therapy Center and RNA Therapeutics Institute at The University of Massachusetts Medical School, Worcester, MA, USA
| | - Deborah Fernau
- Horae Gene Therapy Center and RNA Therapeutics Institute at The University of Massachusetts Medical School, Worcester, MA, USA
| | - Jill Gallagher
- Horae Gene Therapy Center and RNA Therapeutics Institute at The University of Massachusetts Medical School, Worcester, MA, USA
| | - Amanda Taylor
- Diplomate, MedVet, American College of Veterinary Internal Medicine - Neurology, Columbus, OH, USA
| | - Jon Hennebold
- Oregon National Primate Research Center at The Oregon Health and Science University, Portland, OR, USA
| | - Alison R Weiss
- Oregon National Primate Research Center at The Oregon Health and Science University, Portland, OR, USA
| | - Heather Gray-Edwards
- Horae Gene Therapy Center and RNA Therapeutics Institute at The University of Massachusetts Medical School, Worcester, MA, USA
| | - Jodi McBride
- Oregon National Primate Research Center at The Oregon Health and Science University, Portland, OR, USA
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Lu J, Fang W, Huang J, Li S. The application of genome editing technology in fish. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:326-346. [PMID: 37073287 PMCID: PMC10077250 DOI: 10.1007/s42995-021-00091-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/11/2021] [Indexed: 05/03/2023]
Abstract
The advent and development of genome editing technology has opened up the possibility of directly targeting and modifying genomic sequences in the field of life sciences with rapid developments occurring in the last decade. As a powerful tool to decipher genome data at the molecular biology level, genome editing technology has made important contributions to elucidating many biological problems. Currently, the three most widely used genome editing technologies include: zinc finger nucleases (ZFN), transcription activator like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR). Researchers are still striving to create simpler, more efficient, and accurate techniques, such as engineered base editors and new CRISPR/Cas systems, to improve editing efficiency and reduce off-target rate, as well as a near-PAMless SpCas9 variants to expand the scope of genome editing. As one of the important animal protein sources, fish has significant economic value in aquaculture. In addition, fish is indispensable for research as it serves as the evolutionary link between invertebrates and higher vertebrates. Consequently, genome editing technologies were applied extensively in various fish species for basic functional studies as well as applied research in aquaculture. In this review, we focus on the application of genome editing technologies in fish species detailing growth, gender, and pigmentation traits. In addition, we have focused on the construction of a zebrafish (Danio rerio) disease model and high-throughput screening of functional genes. Finally, we provide some of the future perspectives of this technology.
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Affiliation(s)
- Jianguo Lu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080 China
| | - Wenyu Fang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Shizhu Li
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
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Jakutis G, Stainier DYR. Genotype-Phenotype Relationships in the Context of Transcriptional Adaptation and Genetic Robustness. Annu Rev Genet 2021; 55:71-91. [PMID: 34314597 DOI: 10.1146/annurev-genet-071719-020342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic manipulations with a robust and predictable outcome are critical to investigate gene function, as well as for therapeutic genome engineering. For many years, knockdown approaches and reagents including RNA interference and antisense oligonucleotides dominated functional studies; however, with the advent of precise genome editing technologies, CRISPR-based knockout systems have become the state-of-the-art tools for such studies. These technologies have helped decipher the role of thousands of genes in development and disease. Their use has also revealed how limited our understanding of genotype-phenotype relationships is. The recent discovery that certain mutations can trigger the transcriptional modulation of other genes, a phenomenon called transcriptional adaptation, has provided an additional explanation for the contradicting phenotypes observed in knockdown versus knockout models and increased awareness about the use of each of these approaches. In this review, we first cover the strengths and limitations of different gene perturbation strategies. Then we highlight the diverse ways in which the genotype-phenotype relationship can be discordant between these different strategies. Finally, we review the genetic robustness mechanisms that can lead to such discrepancies, paying special attention to the recently discovered phenomenon of transcriptional adaptation. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gabrielius Jakutis
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany;
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany; .,German Centre for Cardiovascular Research (DZHK), Partner site Rhine-Main, 60590 Frankfurt am Main, Germany.,Excellence Cluster Cardio-Pulmonary Institute (CPI), 35392 Giessen, Germany
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Welker JM, Wierson WA, Almeida MP, Mann CM, Torrie ME, Ming Z, Ekker SC, Clark KJ, Dobbs DL, Essner JJ, McGrail M. GeneWeld: Efficient Targeted Integration Directed by Short Homology in Zebrafish. Bio Protoc 2021; 11:e4100. [PMID: 34395736 PMCID: PMC8329467 DOI: 10.21769/bioprotoc.4100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/23/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022] Open
Abstract
Efficient precision genome engineering requires high frequency and specificity of integration at the genomic target site. Multiple design strategies for zebrafish gene targeting have previously been reported with widely varying frequencies for germline recovery of integration alleles. The GeneWeld protocol and pGTag (plasmids for Gene Tagging) vector series provide a set of resources to streamline precision gene targeting in zebrafish. Our approach uses short homology of 24-48 bp to drive targeted integration of DNA reporter cassettes by homology-mediated end joining (HMEJ) at a CRISPR/Cas induced DNA double-strand break. The pGTag vectors contain reporters flanked by a universal CRISPR sgRNA sequence to liberate the targeting cassette in vivo and expose homology arms for homology-driven integration. Germline transmission rates for precision-targeted integration alleles range 22-100%. Our system provides a streamlined, straightforward, and cost-effective approach for high-efficiency gene targeting applications in zebrafish. Graphic abstract: GeneWeld method for CRISPR/Cas9 targeted integration.
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Affiliation(s)
- Jordan M. Welker
- Department of Genetics, Development and Cell Biology, Iowa State University, IA, USA
| | - Wesley A. Wierson
- Department of Genetics, Development and Cell Biology, Iowa State University, IA, USA
| | - Maira P. Almeida
- Department of Genetics, Development and Cell Biology, Iowa State University, IA, USA
| | - Carla M. Mann
- Department of Genetics, Development and Cell Biology, Iowa State University, IA, USA
| | - Melanie E. Torrie
- Department of Genetics, Development and Cell Biology, Iowa State University, IA, USA
| | - Zhitao Ming
- Department of Genetics, Development and Cell Biology, Iowa State University, IA, USA
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Drena L. Dobbs
- Department of Genetics, Development and Cell Biology, Iowa State University, IA, USA
| | - Jeffrey J. Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, IA, USA
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, IA, USA
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Singh P, Ali SA. Impact of CRISPR-Cas9-Based Genome Engineering in Farm Animals. Vet Sci 2021; 8:122. [PMID: 34209174 PMCID: PMC8309983 DOI: 10.3390/vetsci8070122] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/26/2022] Open
Abstract
Humans are sorely over-dependent on livestock for their daily basic need of food in the form of meat, milk, and eggs. Therefore, genetic engineering and transgenesis provide the opportunity for more significant gains and production in a short span of time. One of the best strategies is the genetic alteration of livestock to enhance the efficiency of food production (e.g., meat and milk), animal health, and welfare (animal population and disease). Moreover, genome engineering in the bovine is majorly focused on subjects such as disease resistance (e.g., tuberculosis), eradicate allergens (e.g., beta-lactoglobulin knock-out), products generation (e.g., meat from male and milk from female), male or female birth specifically (animal sexing), the introduction of valuable traits (e.g., stress tolerance and disease resistance) and their wellbeing (e.g., hornlessness). This review addressed the impressive genome engineering method CRISPR, its fundamental principle for generating highly efficient target-specific guide RNA, and the accompanying web-based tools. However, we have covered the remarkable roadmap of the CRISPR method from its conception to its use in cattle. Additionally, we have updated the comprehensive information on CRISPR-based gene editing in cattle.
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Affiliation(s)
| | - Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal 132001, India;
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Wang M, Sun Z, Ding F, Wang H, Li L, Li X, Zheng X, Li N, Dai Y, Wu C. Efficient TALEN-mediated gene knockin at the bovine Y chromosome and generation of a sex-reversal bovine. Cell Mol Life Sci 2021; 78:5415-5425. [PMID: 34047803 PMCID: PMC8257526 DOI: 10.1007/s00018-021-03855-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 05/05/2021] [Accepted: 05/14/2021] [Indexed: 11/30/2022]
Abstract
Functional elucidation of bovine Y-chromosome genes requires available genome editing technologies. Meanwhile, it has yet to be proven whether the bovine Sry gene is the main or single factor involved in the development of the male phenotype in bovine. Here, we efficiently knocked out four Y-linked genes (Sry, ZFY, DDX3Y, and EIF2S3Y) in bovine fetal fibroblasts (BFFs) with transcription activator-like effector nucleases (TALENs) individually. Furthermore, we used TALEN-mediated gene knockin at the Sry gene and generated a sex-reversal bovine by somatic cell nuclear transfer (SCNT). The resulting bovine had only one ovary and was sterile. We demonstrate, for the first time, that the Sry gene is an important sex-determining gene in bovine. Our method lays a solid foundation for detecting the biology of the bovine Y chromosome, as it may provide an alternative biological model system for the study of mammalian sex determination, and new methods for the practical application in agricultural, especially for sex predetermination.
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Affiliation(s)
- Ming Wang
- College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.,College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - ZhaoLin Sun
- College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China. .,College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China. .,Beijing Capital Agribusiness Future Biotechnology Co, 75 Bingjiaokou Hutong, Ltd, 100088, No, China.
| | - Fangrong Ding
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Haiping Wang
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Ling Li
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Xue Li
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Xianjin Zheng
- Cattle Breeding Research Institute of Beijing Shunxin Xinyuan Co, 3 Anping Street, LtdShunyi District, 101318, No, China
| | - Ning Li
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
| | - Yunping Dai
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
| | - Changxin Wu
- College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
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Jabbar A, Zulfiqar F, Mahnoor M, Mushtaq N, Zaman MH, Din ASU, Khan MA, Ahmad HI. Advances and Perspectives in the Application of CRISPR-Cas9 in Livestock. Mol Biotechnol 2021; 63:757-767. [PMID: 34041717 DOI: 10.1007/s12033-021-00347-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/20/2021] [Indexed: 10/21/2022]
Abstract
The sophistication and revolution in genome editing and manipulation have revolutionized livestock by harvesting essential biotechnological products such as drugs, proteins, and serum. It laid down areas for the large production of transgenic food, resistance against certain diseases such as mastitis, and large production of milk and leaner meat. Nowadays, the increasing demand for animal food and protein is fulfilled using genome-editing technologies. The recent genome-editing techniques have overcome the earlier methods of animal reproduction, such as cloning and artificial embryo transfer. The genome of animals now is modified using the recent alteration techniques such as ZFNs, TALENS technique, and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR-Cas9) system. The literature was illustrated for identifying the researchers to address the advances and perspectives in the application of Cas9 in Livestock. Cas9 is considered better than the previously identified techniques in livestock because of the production of resilience against diseases, improvement of reproductive traits, and animal production to act as a model biomedical research.
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Affiliation(s)
- Abdul Jabbar
- Department of Clinical Medicine, Faculty of Veterinary Science, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Farheen Zulfiqar
- Department of Food Science and Human Nutrition, Faculty of Bio Science, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Mahnoor Mahnoor
- Department of Food Science and Human Nutrition, Faculty of Bio Science, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Nadia Mushtaq
- Department of Biological Sciences, Faculty of Fisheries and Wildlife, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Muhammad Hamza Zaman
- College of Earth and Environmental Sciences, University of the Punjab, Lahore, 54590, Punjab, Pakistan
| | - Anum Salah Ud Din
- College of Earth and Environmental Sciences, University of the Punjab, Lahore, 54590, Punjab, Pakistan
| | - Musarrat Abbas Khan
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Science, The Islamia University, Bahawalpur, Pakistan
| | - Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki, Punjab, Pakistan.
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Cheng C, Zhou M, Su Q, Steigmeyer A, Niu J. Genome editor-directed in vivo library diversification. Cell Chem Biol 2021; 28:1109-1118. [PMID: 34107297 DOI: 10.1016/j.chembiol.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/08/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
The generation of a library of variant genes is a prerequisite of directed evolution, a powerful tool for biomolecular engineering. As the number of all possible sequences often far exceeds the diversity of a practical library, methods that allow efficient library diversification in living cells are essential for in vivo directed evolution technologies to effectively sample the sequence space and allow hits to emerge. While traditional whole-genome mutagenesis often results in toxicity and the emergence of "cheater" mutations, recent developments that exploit the targeting and editing abilities of genome editors to facilitate in vivo library diversification have allowed for precise mutagenesis focused on specific genes of interest, higher mutational density, and reduced the occurrence of cheater mutations. This minireview summarizes recent advances in genome editor-directed in vivo library diversification and provides an outlook on their future applications in chemical biology.
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Affiliation(s)
- Cristina Cheng
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Mi Zhou
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Qiwen Su
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Jia Niu
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.
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Abstract
Germline editing, the process by which the genome of an individual is edited in such a way that the change is heritable, has been applied to a wide variety of animals [D. A. Sorrell, A. F. Kolb, Biotechnol. Adv. 23, 431-469 (2005); D. Baltimore et al., Science 348, 36-38 (2015)]. Because of its relevancy in agricultural and biomedical research, the pig genome has been extensively modified using a multitude of technologies [K. Lee, K. Farrell, K. Uh, Reprod. Fertil. Dev. 32, 40-49 (2019); C. Proudfoot, S. Lillico, C. Tait-Burkard, Anim. Front. 9, 6-12 (2019)]. In this perspective, we will focus on using pigs as the model system to review the current methodologies, applications, and challenges of mammalian germline genome editing. We will also discuss the broad implications of animal germline editing and its clinical potential.
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Abstract
Genetically modified animals, especially rodents, are widely used in biomedical research. However, non-rodent models are required for efficient translational medicine and preclinical studies. Owing to the similarity in the physiological traits of pigs and humans, genetically modified pigs may be a valuable resource for biomedical research. Somatic cell nuclear transfer (SCNT) using genetically modified somatic cells has been the primary method for the generation of genetically modified pigs. However, site-specific gene modification in porcine cells is inefficient and requires laborious and time-consuming processes. Recent improvements in gene-editing systems, such as zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas) system, represent major advances. The efficient introduction of site-specific modifications into cells via gene editors dramatically reduces the effort and time required to generate genetically modified pigs. Furthermore, gene editors enable direct gene modification during embryogenesis, bypassing the SCNT procedure. The application of gene editors has progressively expanded, and a range of strategies is now available for porcine gene engineering. This review provides an overview of approaches for the generation of genetically modified pigs using gene editors, and highlights the current trends, as well as the limitations, of gene editing in pigs.
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Affiliation(s)
- Fuminori Tanihara
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima 770-8513, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, Tochigi 329-0498, Japan
| | - Maki Hirata
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima 770-8513, Japan
| | - Takeshige Otoi
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima 770-8513, Japan
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Ratner LD, La Motta GE, Briski O, Salamone DF, Fernandez-Martin R. Practical Approaches for Knock-Out Gene Editing in Pigs. Front Genet 2021; 11:617850. [PMID: 33747029 PMCID: PMC7973260 DOI: 10.3389/fgene.2020.617850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022] Open
Abstract
Pigs are an important resource for meat production and serve as a model for human diseases. Due to their physiological and anatomical similarities to humans, these animals can recapitulate symptoms of human diseases, becoming an effective model for biomedical research. Although, in the past pig have not been widely used partially because of the difficulty in genetic modification; nowadays, with the new revolutionary technology of programmable nucleases, and fundamentally of the CRISPR-Cas9 systems, it is possible for the first time to precisely modify the porcine genome as never before. To this purpose, it is necessary to introduce the system into early stage zygotes or to edit cells followed by somatic cell nuclear transfer. In this review, several strategies for pig knock-out gene editing, using the CRISPR-Cas9 system, will be summarized, as well as genotyping methods and different delivery techniques to introduce these tools into the embryos. Finally, the best approaches to produce homogeneous, biallelic edited animals will be discussed.
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Affiliation(s)
- Laura Daniela Ratner
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gaston Emilio La Motta
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Olinda Briski
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniel Felipe Salamone
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rafael Fernandez-Martin
- Laboratorio Biotecnología Animal (LabBA), Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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Webster D, Bondareva A, Solin S, Goldsmith T, Su L, Lara NDLEM, Carlson DF, Dobrinski I. Targeted Gene Editing in Porcine Spermatogonia. Front Genet 2021; 11:627673. [PMID: 33584819 PMCID: PMC7876475 DOI: 10.3389/fgene.2020.627673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/31/2020] [Indexed: 01/15/2023] Open
Abstract
To study the pathophysiology of human diseases, develop innovative treatments, and refine approaches for regenerative medicine require appropriate preclinical models. Pigs share physiologic and anatomic characteristics with humans and are genetically more similar to humans than are mice. Genetically modified pigs are essential where rodent models do not mimic the human disease phenotype. The male germline stem cell or spermatogonial stem cell (SSC) is unique; it is the only cell type in an adult male that divides and contributes genes to future generations, making it an ideal target for genetic modification. Here we report that CRISPR/Cas9 ribonucleoprotein (RNP)-mediated gene editing in porcine spermatogonia that include SSCs is significantly more efficient than previously reported editing with TALENs and allows precise gene editing by homology directed repair (HDR). We also established homology-mediated end joining (HMEJ) as a second approach to targeted gene editing to enable introduction of larger transgenes and/or humanizing parts of the pig genome for disease modeling or regenerative medicine. In summary, the approaches established in the current study result in efficient targeted genome editing in porcine germ cells for precise replication of human disease alleles.
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Affiliation(s)
| | - Alla Bondareva
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, AB, Canada
| | - Staci Solin
- Recombinetics, Inc., St. Paul, MN, United States
| | | | - Lin Su
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, AB, Canada
| | | | | | - Ina Dobrinski
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, AB, Canada
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Kaiser RA, Carlson DF, Allen KL, Webster DA, VanLith CJ, Nicolas CT, Hillin LG, Yu Y, Kaiser CW, Wahoff WR, Hickey RD, Watson AL, Winn SR, Thöny B, Kern DR, Harding CO, Lillegard JB. Development of a porcine model of phenylketonuria with a humanized R408W mutation for gene editing. PLoS One 2021; 16:e0245831. [PMID: 33493163 PMCID: PMC7833140 DOI: 10.1371/journal.pone.0245831] [Citation(s) in RCA: 4] [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: 03/02/2020] [Accepted: 01/08/2021] [Indexed: 12/15/2022] Open
Abstract
Phenylketonuria (PKU) is a metabolic disorder whereby phenylalanine metabolism is deficient due to allelic variations in the gene for phenylalanine hydroxylase (PAH). There is no cure for PKU other than orthotopic liver transplantation, and the standard of care for patients is limited to dietary restrictions and key amino acid supplementation. Therefore, Pah was edited in pig fibroblasts for the generation of PKU clone piglets that harbor a common and severe human mutation, R408W. Additionally, the proximal region to the mutation was further humanized by introducing 5 single nucleotide polymorphisms (SNPs) to allow for development of gene editing machinery that could be translated directly from the pig model to human PKU patients that harbor at least one classic R408W allele. Resulting piglets were hypopigmented (a single Ossabaw piglet) and had low birthweight (all piglets). The piglets had similar levels of PAH expression, but no detectable enzymatic activity, consistent with the human phenotype. The piglets were fragile and required extensive neonatal care to prevent failure to thrive and early demise. Phenylalanine levels rose sharply when dietary Phe was unrestricted but could be rapidly reduced with a low Phe diet. Fibroblasts isolated from R408W piglets show susceptibility to correction using CRISPR or TALEN, with subsequent homology-directed recombination to correct Pah. This pig model of PKU provides a powerful new tool for development of all classes of therapeutic candidates to treat or cure PKU, as well as unique value for proof-of-concept studies for in vivo human gene editing platforms in the context of this humanized PKU allele.
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Affiliation(s)
- Robert A. Kaiser
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
- Midwest Fetal Care Center, Children’s Hospitals and Clinics of Minnesota, Minneapolis, Minnesota, United States of America
| | | | - Kari L. Allen
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | | | - Caitlin J. VanLith
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Clara T. Nicolas
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
- Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Lori G. Hillin
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Yue Yu
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Catherine W. Kaiser
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | - William R. Wahoff
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Raymond D. Hickey
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | | | - Shelley R. Winn
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Beat Thöny
- Department of Pediatrics, University of Zurich, Zurich, Switzerland
| | - Douglas R. Kern
- Recombinetics, Inc., St. Paul, Minnesota, United States of America
| | - Cary O. Harding
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Joseph B. Lillegard
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
- Midwest Fetal Care Center, Children’s Hospitals and Clinics of Minnesota, Minneapolis, Minnesota, United States of America
- Pediatric Surgical Associates, Minneapolis, Minnesota, United States of America
- * E-mail:
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47
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Almeida MP, Welker JM, Siddiqui S, Luiken J, Ekker SC, Clark KJ, Essner JJ, McGrail M. Endogenous zebrafish proneural Cre drivers generated by CRISPR/Cas9 short homology directed targeted integration. Sci Rep 2021; 11:1732. [PMID: 33462297 PMCID: PMC7813866 DOI: 10.1038/s41598-021-81239-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 01/04/2021] [Indexed: 01/04/2023] Open
Abstract
We previously reported efficient precision targeted integration of reporter DNA in zebrafish and human cells using CRISPR/Cas9 and short regions of homology. Here, we apply this strategy to isolate zebrafish Cre recombinase drivers whose spatial and temporal restricted expression mimics endogenous genes. A 2A-Cre recombinase transgene with 48 bp homology arms was targeted into proneural genes ascl1b, olig2 and neurod1. We observed high rates of germline transmission ranging from 10 to 100% (2/20 olig2; 1/5 neurod1; 3/3 ascl1b). The transgenic lines Tg(ascl1b-2A-Cre)is75, Tg(olig2-2A-Cre)is76, and Tg(neurod1-2A-Cre)is77 expressed functional Cre recombinase in the expected proneural cell populations. Somatic targeting of 2A-CreERT2 into neurod1 resulted in tamoxifen responsive recombination in the nervous system. The results demonstrate Cre recombinase expression is driven by the native promoter and regulatory elements of the targeted genes. This approach provides a straightforward, efficient, and cost-effective method to generate cell type specific zebrafish Cre and CreERT2 drivers, overcoming challenges associated with promoter-BAC and transposon mediated transgenics.
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Affiliation(s)
- Maira P Almeida
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA
| | - Jordan M Welker
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA.,Department III - Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sahiba Siddiqui
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA
| | - Jon Luiken
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jeffrey J Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA. .,Genetics and Genomics Interdepartmental Graduate Program, Iowa State University, Ames, IA, USA.
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48
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Tatetsu H, Tenen DG, Chai L. The Interplay between Transcription Factor SALL4 and Histone Modifiers in Hematopoietic Stem and Progenitor Cells. JOURNAL OF CELLULAR IMMUNOLOGY 2021; 3:26-30. [PMID: 33884376 PMCID: PMC8057709 DOI: 10.33696/immunology.3.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Hiro Tatetsu
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University Hospital, Kumamoto, Japan, 860-8556
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Daniel G. Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine (MD6), #12-01, 14 Medical Drive, Singapore 117599
- Harvard Stem Cell Institute, Center for Life Science Room 437, 3 Blackfan Circle Room 437, Boston, MA 02115, USA
| | - Li Chai
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
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49
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Schwarze LI, Głów D, Sonntag T, Uhde A, Fehse B. Optimisation of a TALE nuclease targeting the HIV co-receptor CCR5 for clinical application. Gene Ther 2021; 28:588-601. [PMID: 34112993 PMCID: PMC8455333 DOI: 10.1038/s41434-021-00271-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023]
Abstract
Disruption of the C-C-Chemokine-receptor-5 (CCR5) gene induces resistance towards CCR5-tropic HIV. Here we optimised our previously described CCR5-Uco-TALEN and its delivery by mRNA electroporation. The novel variant, CCR5-Uco-hetTALEN features an obligatory heterodimeric Fok1-cleavage domain, which resulted in complete abrogation of off-target activity at previously found homodimeric as well as 7/8 in silico predicted, potential heterodimeric off-target sites, the only exception being highly homologous CCR2. Prevailing 18- and 10-bp deletions at the on-target site revealed microhomology-mediated end-joining as a major repair pathway. Notably, the CCR5Δ55-60 protein resulting from the 18-bp deletion was almost completely retained in the cytosol. Simultaneous cutting at CCR5 and CCR2 induced rearrangements, mainly 15-kb deletions between the cut sites, in up to 2% of T cells underlining the necessity to restrict TALEN expression. We optimised in vitro mRNA production and showed that CCR5-on- and CCR2 off-target activities of CCR5-Uco-hetTALEN were limited to the first 72 and 24-48 h post-mRNA electroporation, respectively. Using single-cell HRMCA, we discovered high rates of TALEN-induced biallelic gene editing of CCR5, which translated in large numbers of CCR5-negative cells resistant to HIVenv-pseudotyped lentiviral vectors. We conclude that CCR5-Uco-hetTALEN transfected by mRNA electroporation facilitates specific, high-efficiency CCR5 gene-editing (30%-56%) and it is highly suited for clinical translation subject to further characterisation of off-target effects.
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Affiliation(s)
- Lea Isabell Schwarze
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.452463.2German Centre for Infection Research (DZIF), partner site Hamburg, Hamburg, Germany
| | - Dawid Głów
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Tanja Sonntag
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Almut Uhde
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Boris Fehse
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.452463.2German Centre for Infection Research (DZIF), partner site Hamburg, Hamburg, Germany
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50
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Hennig SL, Owen JR, Lin JC, Young AE, Ross PJ, Van Eenennaam AL, Murray JD. Evaluation of mutation rates, mosaicism and off target mutations when injecting Cas9 mRNA or protein for genome editing of bovine embryos. Sci Rep 2020; 10:22309. [PMID: 33339870 PMCID: PMC7749171 DOI: 10.1038/s41598-020-78264-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
The CRISPR/Cas9 genome editing tool has the potential to improve the livestock breeding industry by allowing for the introduction of desirable traits. Although an efficient and targeted tool, the CRISPR/Cas9 system can have some drawbacks, including off-target mutations and mosaicism, particularly when used in developing embryos. Here, we introduced genome editing reagents into single-cell bovine embryos to compare the effect of Cas9 mRNA and protein on the mutation efficiency, level of mosaicism, and evaluate potential off-target mutations utilizing next generation sequencing. We designed guide-RNAs targeting three loci (POLLED, H11, and ZFX) in the bovine genome and saw a significantly higher rate of mutation in embryos injected with Cas9 protein (84.2%) vs. Cas9 mRNA (68.5%). In addition, the level of mosaicism was higher in embryos injected with Cas9 mRNA (100%) compared to those injected with Cas9 protein (94.2%), with little to no unintended off-target mutations detected. This study demonstrated that the use of gRNA/Cas9 ribonucleoprotein complex resulted in a high editing efficiency at three different loci in bovine embryos and decreased levels of mosaicism relative to Cas9 mRNA. Additional optimization will be required to further reduce mosaicism to levels that make single-step embryo editing in cattle commercially feasible.
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Affiliation(s)
- Sadie L Hennig
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Joseph R Owen
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Jason C Lin
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Amy E Young
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | - Pablo J Ross
- Department of Animal Science, University of California - Davis, Davis, CA, USA
| | | | - James D Murray
- Department of Animal Science, University of California - Davis, Davis, CA, USA.,Department of Population Health and Reproduction, University of California - Davis, Davis, CA, USA
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