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Redel BK, Yoon J, Reese E, An H, Uh K, Chen PR, Prather RS, Lee K. Novel off-Targeting Events Identified after Genome Wide Analysis of CRISPR-Cas Edited Pigs. CRISPR J 2024; 7:141-149. [PMID: 38770737 DOI: 10.1089/crispr.2024.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
CRISPR-Cas technology has transformed our ability to introduce targeted modifications, allowing unconventional animal models such as pigs to model human diseases and improve its value for food production. The main concern with using the technology is the possibility of introducing unwanted modifications in the genome. In this study, we illustrate a pipeline to comprehensively identify off-targeting events on a global scale in the genome of three different gene-edited pig models. Whole genome sequencing paired with an off-targeting prediction software tool filtered off-targeting events amongst natural variations present in gene-edited pigs. This pipeline confirmed two known off-targeting events in IGH knockout pigs, AR and RBFOX1, and identified other presumably off-targeted loci. Independent validation of the off-targeting events using other gene-edited DNA confirmed two novel off-targeting events in RAG2/IL2RG knockout pig models. This unique strategy offers a novel tool to detect off-targeting events in genetically heterogeneous species after genome editing.
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Affiliation(s)
- Bethany K Redel
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri, USA
| | - Junchul Yoon
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Emily Reese
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, USA
| | - Kyungjun Uh
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Chungcheongbuk-do, Republic of Korea
| | - Paula R Chen
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri, USA
| | - Randall S Prather
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
- National Swine Resource and Research Center, Columbia, Missouri, USA
| | - Kiho Lee
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
- National Swine Resource and Research Center, Columbia, Missouri, USA
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Profiling development of abdominal organs in the pig. Sci Rep 2022; 12:16245. [PMID: 36171243 PMCID: PMC9519580 DOI: 10.1038/s41598-022-19960-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
The pig is an ideal model system for studying human development and disease due to its similarities to human anatomy, physiology, size, and genome. Further, advances in CRISPR gene editing have made genetically engineered pigs viable models for the study of human pathologies and congenital anomalies. However, a detailed atlas illustrating pig development is necessary for identifying and modeling developmental defects. Here we describe normal development of the pig abdominal system and show examples of congenital defects that can arise in CRISPR gene edited SAP130 mutant pigs. Normal pigs at different gestational ages from day 20 (D20) to term were examined and the configuration of the abdominal organs was studied using 3D histological reconstructions with episcopic confocal microscopy, magnetic resonance imaging (MRI) and necropsy. This revealed prominent mesonephros, a transient embryonic organ present only during embryogenesis, at D20, while the developing metanephros that will form the permanent kidney are noted at D26. By D64 the mesonephroi are absent and only the metanephroi remain. The formation of the liver and pancreas was observed by D20 and complete by D30 and D35 respectively. The spleen and adrenal glands are first identified at D26 and completed by D42. The developing bowel and the gonads are identified at D20. The bowel appears completely rotated by D42, and testes in the male were descended at D64. This atlas and the methods used are excellent tools for identifying developmental pathologies of the abdominal organs in the pig at different stages of development.
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Whitworth KM, Green JA, Redel BK, Geisert RD, Lee K, Telugu BP, Wells KD, Prather RS. Improvements in pig agriculture through gene editing. CABI AGRICULTURE AND BIOSCIENCE 2022; 3:41. [PMID: 35755158 PMCID: PMC9209828 DOI: 10.1186/s43170-022-00111-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/12/2022] [Indexed: 05/06/2023]
Abstract
Genetic modification of animals via selective breeding is the basis for modern agriculture. The current breeding paradigm however has limitations, chief among them is the requirement for the beneficial trait to exist within the population. Desirable alleles in geographically isolated breeds, or breeds selected for a different conformation and commercial application, and more importantly animals from different genera or species cannot be introgressed into the population via selective breeding. Additionally, linkage disequilibrium results in low heritability and necessitates breeding over successive generations to fix a beneficial trait within a population. Given the need to sustainably improve animal production to feed an anticipated 9 billion global population by 2030 against a backdrop of infectious diseases and a looming threat from climate change, there is a pressing need for responsive, precise, and agile breeding strategies. The availability of genome editing tools that allow for the introduction of precise genetic modification at a single nucleotide resolution, while also facilitating large transgene integration in the target population, offers a solution. Concordant with the developments in genomic sequencing approaches, progress among germline editing efforts is expected to reach feverish pace. The current manuscript reviews past and current developments in germline engineering in pigs, and the many advantages they confer for advancing animal agriculture.
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Affiliation(s)
- Kristin M. Whitworth
- Division of Animal Science, College of Agriculture Food and Natural Resources, University of Missouri, 920 East Campus Drive, Columbia, MO 65211 USA
| | - Jonathan A. Green
- Division of Animal Science, College of Agriculture Food and Natural Resources, University of Missouri, 920 East Campus Drive, Columbia, MO 65211 USA
| | - Bethany K. Redel
- United States Department of Agriculture – Agriculture Research Service, Plant Genetics Research Unit, Columbia, MO 65211 USA
| | - Rodney D. Geisert
- Division of Animal Science, College of Agriculture Food and Natural Resources, University of Missouri, 920 East Campus Drive, Columbia, MO 65211 USA
| | - Kiho Lee
- Division of Animal Science, College of Agriculture Food and Natural Resources, University of Missouri, 920 East Campus Drive, Columbia, MO 65211 USA
| | - Bhanu P. Telugu
- Division of Animal Science, College of Agriculture Food and Natural Resources, University of Missouri, 920 East Campus Drive, Columbia, MO 65211 USA
| | - Kevin D. Wells
- Division of Animal Science, College of Agriculture Food and Natural Resources, University of Missouri, 920 East Campus Drive, Columbia, MO 65211 USA
| | - Randall S. Prather
- Division of Animal Science, College of Agriculture Food and Natural Resources, University of Missouri, 920 East Campus Drive, Columbia, MO 65211 USA
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Lucas CG, Redel BK, Chen PR, Spate LD, Prather RS, Wells KD. Effects of RAD51-stimulatory compound 1 (RS-1) and its vehicle, DMSO, on pig embryo culture. Reprod Toxicol 2021; 105:44-52. [PMID: 34407461 DOI: 10.1016/j.reprotox.2021.08.002] [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: 05/28/2021] [Revised: 08/01/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
Pigs have become an important model for agricultural and biomedical purposes. The advent of genomic engineering tools, such as the CRISPR/Cas9 system, has facilitated the production of livestock models with desired modifications. However, precise site-specific modifications in pigs through the homology-directed repair (HDR) pathway remains a challenge. In mammalian embryos, the use of small molecules to inhibit non-homologous end joining (NHEJ) or to improve HDR have been tested, but little is known about their toxicity. The compound RS-1 stimulates the activity of the RAD51 protein, which plays a key role in the HDR mechanism, demonstrating enhancement of HDR events in rabbit and bovine zygotes. Thus, in this study, we evaluated the dosage and temporal effects of RS-1 on porcine embryo development and viability. Additionally, we assessed the effects of its vehicle, DMSO, during embryo in vitro culture. Transient exposure to 7.5 μM of RS-1 did not adversely affect early embryo development and was compatible with subsequent development to term. Additionally, low concentrations of its vehicle, DMSO, did not show any toxicity to in vitro produced embryos. The transient use of RS-1 at 7.5 μM during in vitro culture seems to be the best protocol of choice to reduce the potentially toxic effects of RS-1 while attempting to improve HDR in the pig. Direct injection of the CRISPR/Cas9 system, combined with strategies to increase the frequency of targeted modifications via HDR, have become an important tool to simplify and accelerate the production of genetically modified livestock models.
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Affiliation(s)
- C G Lucas
- National Swine Resource and Research Center, University of Missouri, Columbia, MO, USA; Division of Animal Science, University of Missouri, Columbia, MO, USA.
| | - B K Redel
- National Swine Resource and Research Center, University of Missouri, Columbia, MO, USA; USDA-ARS, Plant Genetics Unit, Columbia, MO, USA
| | - P R Chen
- Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - L D Spate
- Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - R S Prather
- National Swine Resource and Research Center, University of Missouri, Columbia, MO, USA; Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - K D Wells
- National Swine Resource and Research Center, University of Missouri, Columbia, MO, USA; Division of Animal Science, University of Missouri, Columbia, MO, USA
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Gabriel GC, Devine W, Redel BK, Whitworth KM, Samuel M, Spate LD, Cecil RF, Prather RS, Wu Y, Wells KD, Lo CW. Cardiovascular Development and Congenital Heart Disease Modeling in the Pig. J Am Heart Assoc 2021; 10:e021631. [PMID: 34219463 PMCID: PMC8483476 DOI: 10.1161/jaha.121.021631] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Modeling cardiovascular diseases in mice has provided invaluable insights into the cause of congenital heart disease. However, the small size of the mouse heart has precluded translational studies. Given current high‐efficiency gene editing, congenital heart disease modeling in other species is possible. The pig is advantageous given its cardiac anatomy, physiology, and size are similar to human infants. We profiled pig cardiovascular development and generated genetically edited pigs with congenital heart defects. Methods and Results Pig conceptuses and fetuses were collected spanning 7 stages (day 20 to birth at day 115), with at least 3 embryos analyzed per stage. A combination of magnetic resonance imaging and 3‐dimensional histological reconstructions with episcopic confocal microscopy were conducted. Gross dissections were performed in late‐stage or term fetuses by using sequential segmental analysis of the atrial, ventricular, and arterial segments. At day 20, the heart has looped, forming a common atria and ventricle and an undivided outflow tract. Cardiac morphogenesis progressed rapidly, with atrial and outflow septation evident by day 26 and ventricular septation completed by day 30. The outflow and atrioventricular cushions seen at day 20 undergo remodeling to form mature valves, a process continuing beyond day 42. Genetically edited pigs generated with mutation in chromatin modifier SAP130 exhibited tricuspid dysplasia, with tricuspid atresia associated with early embryonic lethality. Conclusions The major events in pig cardiac morphogenesis are largely complete by day 30. The developmental profile is similar to human and mouse, indicating gene edited pigs may provide new opportunities for preclinical studies focused on outcome improvements for congenital heart disease.
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Affiliation(s)
- George C Gabriel
- Department of Developmental Biology University of Pittsburgh School of Medicine Pittsburgh PA
| | - William Devine
- Department of Developmental Biology University of Pittsburgh School of Medicine Pittsburgh PA
| | - Bethany K Redel
- Division of Animal Sciences Animal Science Research CenterNational Swine Resource and Research CenterUniversity of Missouri Columbia MO
| | - Kristin M Whitworth
- Division of Animal Sciences Animal Science Research CenterNational Swine Resource and Research CenterUniversity of Missouri Columbia MO
| | - Melissa Samuel
- Division of Animal Sciences Animal Science Research CenterNational Swine Resource and Research CenterUniversity of Missouri Columbia MO
| | - Lee D Spate
- Division of Animal Sciences Animal Science Research CenterNational Swine Resource and Research CenterUniversity of Missouri Columbia MO
| | - Raissa F Cecil
- Division of Animal Sciences Animal Science Research CenterNational Swine Resource and Research CenterUniversity of Missouri Columbia MO
| | - Randall S Prather
- Division of Animal Sciences Animal Science Research CenterNational Swine Resource and Research CenterUniversity of Missouri Columbia MO
| | - Yijen Wu
- Department of Developmental Biology University of Pittsburgh School of Medicine Pittsburgh PA
| | - Kevin D Wells
- Division of Animal Sciences Animal Science Research CenterNational Swine Resource and Research CenterUniversity of Missouri Columbia MO
| | - Cecilia W Lo
- Department of Developmental Biology University of Pittsburgh School of Medicine Pittsburgh PA
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6
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Koppes EA, Redel BK, Johnson MA, Skvorak KJ, Ghaloul-Gonzalez L, Yates ME, Lewis DW, Gollin SM, Wu YL, Christ SE, Yerle M, Leshinski A, Spate LD, Benne JA, Murphy SL, Samuel MS, Walters EM, Hansen SA, Wells KD, Lichter-Konecki U, Wagner RA, Newsome JT, Dobrowolski SF, Vockley J, Prather RS, Nicholls RD. A porcine model of phenylketonuria generated by CRISPR/Cas9 genome editing. JCI Insight 2020; 5:141523. [PMID: 33055427 PMCID: PMC7605535 DOI: 10.1172/jci.insight.141523] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/17/2020] [Indexed: 12/17/2022] Open
Abstract
Phenylalanine hydroxylase-deficient (PAH-deficient) phenylketonuria (PKU) results in systemic hyperphenylalaninemia, leading to neurotoxicity with severe developmental disabilities. Dietary phenylalanine (Phe) restriction prevents the most deleterious effects of hyperphenylalaninemia, but adherence to diet is poor in adult and adolescent patients, resulting in characteristic neurobehavioral phenotypes. Thus, an urgent need exists for new treatments. Additionally, rodent models of PKU do not adequately reflect neurocognitive phenotypes, and thus there is a need for improved animal models. To this end, we have developed PAH-null pigs. After selection of optimal CRISPR/Cas9 genome-editing reagents by using an in vitro cell model, zygote injection of 2 sgRNAs and Cas9 mRNA demonstrated deletions in preimplantation embryos, with embryo transfer to a surrogate leading to 2 founder animals. One pig was heterozygous for a PAH exon 6 deletion allele, while the other was compound heterozygous for deletions of exon 6 and of exons 6-7. The affected pig exhibited hyperphenylalaninemia (2000-5000 μM) that was treatable by dietary Phe restriction, consistent with classical PKU, along with juvenile growth retardation, hypopigmentation, ventriculomegaly, and decreased brain gray matter volume. In conclusion, we have established a large-animal preclinical model of PKU to investigate pathophysiology and to assess new therapeutic interventions.
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Affiliation(s)
- Erik A. Koppes
- Division of Medical Genetics, Department of Pediatrics, University of Pittsburgh School of Medicine, and Universityof Pittsburgh Medical Center (UPMC) Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bethany K. Redel
- Division ofAnimal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
- National Swine Research and Resource Center (NSRRC), College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Marie A. Johnson
- Division of Medical Genetics, Department of Pediatrics, University of Pittsburgh School of Medicine, and Universityof Pittsburgh Medical Center (UPMC) Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kristen J. Skvorak
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lina Ghaloul-Gonzalez
- Division of Medical Genetics, Department of Pediatrics, University of Pittsburgh School of Medicine, and Universityof Pittsburgh Medical Center (UPMC) Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Megan E. Yates
- Division of Medical Genetics, Department of Pediatrics, University of Pittsburgh School of Medicine, and Universityof Pittsburgh Medical Center (UPMC) Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dale W. Lewis
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Susanne M. Gollin
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Yijen L. Wu
- Department of Developmental Biology, University of Pittsburgh, and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shawn E. Christ
- Department of Psychological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Martine Yerle
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Angela Leshinski
- Division of Medical Genetics, Department of Pediatrics, University of Pittsburgh School of Medicine, and Universityof Pittsburgh Medical Center (UPMC) Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lee D. Spate
- Division ofAnimal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
- National Swine Research and Resource Center (NSRRC), College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Joshua A. Benne
- National Swine Research and Resource Center (NSRRC), College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Stephanie L. Murphy
- National Swine Research and Resource Center (NSRRC), College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Melissa S. Samuel
- Division ofAnimal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
- National Swine Research and Resource Center (NSRRC), College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Eric M. Walters
- Division ofAnimal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
- National Swine Research and Resource Center (NSRRC), College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Sarah A. Hansen
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Kevin D. Wells
- Division ofAnimal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
- National Swine Research and Resource Center (NSRRC), College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Uta Lichter-Konecki
- Division of Medical Genetics, Department of Pediatrics, University of Pittsburgh School of Medicine, and Universityof Pittsburgh Medical Center (UPMC) Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Robert A. Wagner
- Division of Laboratory Animal Resources, Office of Research, Health Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph T. Newsome
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Division of Laboratory Animal Resources, Office of Research, Health Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven F. Dobrowolski
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jerry Vockley
- Division of Medical Genetics, Department of Pediatrics, University of Pittsburgh School of Medicine, and Universityof Pittsburgh Medical Center (UPMC) Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Randall S. Prather
- Division ofAnimal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
- National Swine Research and Resource Center (NSRRC), College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Robert D. Nicholls
- Division of Medical Genetics, Department of Pediatrics, University of Pittsburgh School of Medicine, and Universityof Pittsburgh Medical Center (UPMC) Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Pavlovic K, Tristán-Manzano M, Maldonado-Pérez N, Cortijo-Gutierrez M, Sánchez-Hernández S, Justicia-Lirio P, Carmona MD, Herrera C, Martin F, Benabdellah K. Using Gene Editing Approaches to Fine-Tune the Immune System. Front Immunol 2020; 11:570672. [PMID: 33117361 PMCID: PMC7553077 DOI: 10.3389/fimmu.2020.570672] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/20/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing technologies not only provide unprecedented opportunities to study basic cellular system functionality but also improve the outcomes of several clinical applications. In this review, we analyze various gene editing techniques used to fine-tune immune systems from a basic research and clinical perspective. We discuss recent advances in the development of programmable nucleases, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas-associated nucleases. We also discuss the use of programmable nucleases and their derivative reagents such as base editing tools to engineer immune cells via gene disruption, insertion, and rewriting of T cells and other immune components, such natural killers (NKs) and hematopoietic stem and progenitor cells (HSPCs). In addition, with regard to chimeric antigen receptors (CARs), we describe how different gene editing tools enable healthy donor cells to be used in CAR T therapy instead of autologous cells without risking graft-versus-host disease or rejection, leading to reduced adoptive cell therapy costs and instant treatment availability for patients. We pay particular attention to the delivery of therapeutic transgenes, such as CARs, to endogenous loci which prevents collateral damage and increases therapeutic effectiveness. Finally, we review creative innovations, including immune system repurposing, that facilitate safe and efficient genome surgery within the framework of clinical cancer immunotherapies.
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Affiliation(s)
- Kristina Pavlovic
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
- Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cellular Therapy Unit, Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - María Tristán-Manzano
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Noelia Maldonado-Pérez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Marina Cortijo-Gutierrez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Sabina Sánchez-Hernández
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Pedro Justicia-Lirio
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
- LentiStem Biotech, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - M. Dolores Carmona
- Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cellular Therapy Unit, Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
| | - Concha Herrera
- Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cellular Therapy Unit, Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain
- Department of Hematology, Reina Sofía University Hospital, Córdoba, Spain
| | - Francisco Martin
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Karim Benabdellah
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
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8
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Lucas CG, Spate AM, Samuel MS, Spate LD, Warren WC, Prather RS, Wells KD. A novel swine sex-linked marker and its application across different mammalian species. Transgenic Res 2020; 29:395-407. [PMID: 32607872 DOI: 10.1007/s11248-020-00204-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/18/2020] [Indexed: 01/25/2023]
Abstract
Advances in genome editing tools have reduced barriers to the creation of animal models. Due to their anatomical and physiological similarities to humans, there has been a growing need for pig models to study human diseases, for xenotransplantation and translational research. The ability to determine the sex of genetically modified embryos, cells or fetuses is beneficial for every project involving the production of transgenic animals. This strategy can improve the time-efficiency and lower the production costs. Additionally, sex assessment is very useful for wildlife studies to understand population behavior and structure. Thus, we developed a simple and fast PCR-based protocol for sex determination in pigs by using a unique primer set to amplify either the DDX3X or DDX3Y gene. The sex was 100% correctly assigned when tail genomic DNA, Day-35 fetus and hair samples from pigs were used. For both blastocysts and oocytes (84.6% and 96.5% of efficacy, respectively) the unidentified samples were potentially due to a limitation in sample size. Our assay also worked for domestic sheep (Ovis aries), American bison (Bison bison) and European cattle (Bos taurus) samples and by in silico analysis we confirmed X-Y amplicon length polymorphisms for the DDX3 gene in 12 other mammalian species. This PCR protocol for determining sex in pig tissues and cells showed to be simple, specific, highly reproducible and less time consuming as well as an important tool for other livestock species and wildlife studies.
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Affiliation(s)
- C G Lucas
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - A M Spate
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - M S Samuel
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - L D Spate
- Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - W C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - R S Prather
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - K D Wells
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA. .,Division of Animal Science, University of Missouri, Columbia, MO, USA.
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9
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Araldi RP, Khalil C, Grignet PH, Teixeira MR, de Melo TC, Módolo DG, Fernandes LGV, Ruiz J, de Souza EB. Medical applications of clustered regularly interspaced short palindromic repeats (CRISPR/Cas) tool: A comprehensive overview. Gene 2020; 745:144636. [PMID: 32244056 DOI: 10.1016/j.gene.2020.144636] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/30/2020] [Indexed: 12/22/2022]
Abstract
Since the discovery of the double helix and the introduction of genetic engineering, the possibility to develop new strategies to manipulate the genome has fascinated scientists around the world. Currently scientists have the knowledge andabilitytoedit the genomes. Several methodologies of gene editing have been established, all of them working like "scissor", creating double strand breaks at specific spots. The introduction of a new technology, which was adapted from the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas bacterial immune system, has revolutionized the genetic therapy field, as it allows a much more precise editing of gene than the previously described tools and, therefore, to prevent and treat disease in humans. This review aims to revisit the genome editing history that led to the rediscovery of the CRISPR/Cas technology and to explore the technical aspects, applications and perspectives of this fascinating, powerful, precise, simpler and cheaper technology in different fields.
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Affiliation(s)
- Rodrigo Pinheiro Araldi
- Genetic Bases of Thyroid Tumors Laboratory, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil; Programa de Pós-graduação em Biociências, Universidade Federal da Integração Latino-Americana (UNILA), Foz do Iguaçu, PR, Brazil.
| | - Charbel Khalil
- Reviva Research and Application Center- Lebanese University, Middle East Institute of Health University Hospital, Beirut, Lebanon
| | - Pedro Henrique Grignet
- Instituto Latino-Americano de Ciências da Vida e da Natureza (ILACVN), Universidade Federal da Integração Latino-Americana (UNILA), Foz do Iguaçu, PR, Brazil
| | - Michelli Ramires Teixeira
- Instituto Latino-Americano de Ciências da Vida e da Natureza (ILACVN), Universidade Federal da Integração Latino-Americana (UNILA), Foz do Iguaçu, PR, Brazil
| | - Thatiana Correa de Melo
- Instituto Latino-Americano de Ciências da Vida e da Natureza (ILACVN), Universidade Federal da Integração Latino-Americana (UNILA), Foz do Iguaçu, PR, Brazil
| | | | | | - Jorge Ruiz
- Programa de Pós-graduação em Biociências, Universidade Federal da Integração Latino-Americana (UNILA), Foz do Iguaçu, PR, Brazil; Instituto Latino-Americano de Ciências da Vida e da Natureza (ILACVN), Universidade Federal da Integração Latino-Americana (UNILA), Foz do Iguaçu, PR, Brazil
| | - Edislane Barreiros de Souza
- Laboratory of Genetics, Molecular Biology and Mutagenesis, Faculdade de Ciências e Letras de Assis, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Assis, SP, Brazil
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10
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Abstract
This chapter highlights the importance of reproductive technologies that are applied to porcine breeds. Nowadays the porcine industry, part of a high technological and specialized sector, offers high-quality protein food. The development of the swine industry is founded in the development of breeding/genetics, nutrition, animal husbandry, and animal health. The implementation of reproductive technologies in swine has conducted to levels of productivity never reached before. In addition, the pig is becoming an important species for biomedicine. The generation of pig models for human disease, xenotransplantation, or production of therapeutic proteins for human medicine has in fact generated a growing field of interest.
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11
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Redel BK, Spate LD, Prather RS. In Vitro Maturation, Fertilization, and Culture of Pig Oocytes and Embryos. Methods Mol Biol 2019; 2006:93-103. [PMID: 31230274 DOI: 10.1007/978-1-4939-9566-0_6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Assisted reproductive technologies in the pig are critical for the production of genetically modified pigs as models of human disease and to improve production agriculture. Methods of oocyte maturation, fertilization, and culture all play an extremely important role in how the embryo, fetus, and offspring will develop. In this chapter, we discuss the historical methods and recent advances that have been essential in promoting efficient and competent embryo development. Here we describe the procedures that can be used to mature, fertilize, and culture pig embryos to the blastocyst stage.
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Affiliation(s)
- Bethany K Redel
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA. .,National Swine Resource and Research Center, University of Missouri, Columbia, MO, USA.
| | - Lee D Spate
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA.,National Swine Resource and Research Center, University of Missouri, Columbia, MO, USA
| | - Randall S Prather
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA.,National Swine Resource and Research Center, University of Missouri, Columbia, MO, USA
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12
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Liu H, Sui T, Liu D, Liu T, Chen M, Deng J, Xu Y, Li Z. Multiple homologous genes knockout (KO) by CRISPR/Cas9 system in rabbit. Gene 2018; 647:261-267. [PMID: 29339069 DOI: 10.1016/j.gene.2018.01.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/30/2017] [Accepted: 01/11/2018] [Indexed: 01/06/2023]
Abstract
The CRISPR/Cas9 system is a highly efficient and convenient genome editing tool, which has been widely used for single or multiple gene mutation in a variety of organisms. Disruption of multiple homologous genes, which have similar DNA sequences and gene function, is required for the study of the desired phenotype. In this study, to test whether the CRISPR/Cas9 system works on the mutation of multiple homologous genes, a single guide RNA (sgRNA) targeting three fucosyltransferases encoding genes (FUT1, FUT2 and SEC1) was designed. As expected, triple gene mutation of FUT1, FUT2 and SEC1 could be achieved simultaneously via a sgRNA mediated CRISPR/Cas9 system. Besides, significantly reduced serum fucosyltransferases enzymes activity was also determined in those triple gene mutation rabbits. Thus, we provide the first evidence that multiple homologous genes knockout (KO) could be achieved efficiently by a sgRNA mediated CRISPR/Cas9 system in mammals, which could facilitate the genotype to phenotype studies of homologous genes in future.
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Affiliation(s)
- Huan Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Tingting Sui
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Di Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Tingjun Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Mao Chen
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Jichao Deng
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Yuanyuan Xu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China.
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China.
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13
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Zhang H, McCarty N. CRISPR Editing in Biological and Biomedical Investigation. J Cell Biochem 2017; 118:4152-4162. [PMID: 28467679 PMCID: PMC7166568 DOI: 10.1002/jcb.26111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 05/02/2017] [Indexed: 12/27/2022]
Abstract
The revolutionary technology for genome editing known as the clustered regularly interspaced short palindromic repeat (CRISPR)‐CRISPR‐associated protein 9 (Cas9) system has sparked advancements in biological and biomedical research. The scientific breakthrough of the development of CRISPR‐Cas9 technology has allowed us to recapitulate human diseases by generating animal models of interest ranging from zebrafish to non‐human primates. The CRISPR‐Cas9 system can also be used to delineate the mechanisms underlying the development of human disorders and to precisely correct disease‐causing mutations. Repurposing this technology enables wider applications in transcriptome and epigenome manipulation and holds promise to reach the clinic. In this review, we highlight the latest advances of the CRISPR‐Cas9 system in different platforms and discuss the hurdles and challenges this technology is facing. J. Cell. Biochem. 118: 4152–4162, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Han Zhang
- Center for Stem Cell and Regenerative Disease, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Center at Houston, Houston, Texas, 77030
| | - Nami McCarty
- Center for Stem Cell and Regenerative Disease, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Center at Houston, Houston, Texas, 77030
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14
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Genetic engineering alveolar macrophages for host resistance to PRRSV. Vet Microbiol 2017; 209:124-129. [PMID: 28215617 DOI: 10.1016/j.vetmic.2017.01.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/28/2016] [Accepted: 01/30/2017] [Indexed: 11/23/2022]
Abstract
Standard strategies for control of porcine reproductive and respiratory syndrome virus (PRRSV) have not been effective, as vaccines have not reduced the prevalence of disease and many producers depopulate after an outbreak. Another method of control would be to prevent the virus from infecting the pig. The virus was thought to infect alveolar macrophages by interaction with a variety of cell surface molecules. One popular model had PRRSV first interacting with heparin sulfate followed by binding to sialoadhesin and then being internalized into an endosome. Within the endosome, PRRSV was thought to interact with CD163 to uncoat the virus so the viral genome could be released into the cytosol and infect the cell. Other candidate receptors have included vimentin, CD151 and CD209. By using genetic engineering, it is possible to test the importance of individual entry mediators by knocking them out. Pigs engineered by knockout of sialoadhesin were still susceptible to infection, while CD163 knockout resulted in pigs that were resistant to infection. Genetic engineering is not only a valuable tool to determine the role of specific proteins in infection by PRRSV (in this case), but also provides a means to create animals resistant to disease. Genetic engineering of alveolar macrophages can also illuminate the role of other proteins in response to infection. We suggest that strategies to prevent infection be pursued to reduce the reservoir of virus.
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15
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Schomberg DT, Miranpuri GS, Chopra A, Patel K, Meudt JJ, Tellez A, Resnick DK, Shanmuganayagam D. Translational Relevance of Swine Models of Spinal Cord Injury. J Neurotrauma 2017; 34:541-551. [DOI: 10.1089/neu.2016.4567] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Dominic T. Schomberg
- Biomedical and Genomic Research Group, Department of Animal Sciences, University of Wisconsin–Madison, Wisconsin
| | - Gurwattan S. Miranpuri
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Abhishek Chopra
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Kush Patel
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Jennifer J. Meudt
- Biomedical and Genomic Research Group, Department of Animal Sciences, University of Wisconsin–Madison, Wisconsin
| | | | - Daniel K. Resnick
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Dhanansayan Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal Sciences, University of Wisconsin–Madison, Wisconsin
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16
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Legastelois I, Buffin S, Peubez I, Mignon C, Sodoyer R, Werle B. Non-conventional expression systems for the production of vaccine proteins and immunotherapeutic molecules. Hum Vaccin Immunother 2016; 13:947-961. [PMID: 27905833 DOI: 10.1080/21645515.2016.1260795] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The increasing demand for recombinant vaccine antigens or immunotherapeutic molecules calls into question the universality of current protein expression systems. Vaccine production can require relatively low amounts of expressed materials, but represents an extremely diverse category consisting of different target antigens with marked structural differences. In contrast, monoclonal antibodies, by definition share key molecular characteristics and require a production system capable of very large outputs, which drives the quest for highly efficient and cost-effective systems. In discussing expression systems, the primary assumption is that a universal production platform for vaccines and immunotherapeutics will unlikely exist. This review provides an overview of the evolution of traditional expression systems, including mammalian cells, yeast and E.coli, but also alternative systems such as other bacteria than E. coli, transgenic animals, insect cells, plants and microalgae, Tetrahymena thermophila, Leishmania tarentolae, filamentous fungi, cell free systems, and the incorporation of non-natural amino acids.
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Affiliation(s)
| | - Sophie Buffin
- a Research and Development, Sanofi Pasteur , Marcy L'Etoile , France
| | - Isabelle Peubez
- a Research and Development, Sanofi Pasteur , Marcy L'Etoile , France
| | | | - Régis Sodoyer
- b Technology Research Institute Bioaster , Lyon , France
| | - Bettina Werle
- b Technology Research Institute Bioaster , Lyon , France
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17
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Abstract
The recent advent of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated protein 9 (Cas9) system for precise genome editing has revolutionized methodologies in haematology and oncology studies. CRISPR-Cas9 technology can be used to remove and correct genes or mutations, and to introduce site-specific therapeutic genes in human cells. Inherited haematological disorders represent ideal targets for CRISPR-Cas9-mediated gene therapy. Correcting disease-causing mutations could alleviate disease-related symptoms in the near future. The CRISPR-Cas9 system is also a useful tool for delineating molecular mechanisms involving haematological malignancies. Prior to the use of CRISPR-Cas9-mediated gene correction in humans, appropriate delivery systems with higher efficiency and specificity must be identified, and ethical guidelines for applying the technology with controllable safety must be established. Here, the latest applications of CRISPR-Cas9 technology in haematological disorders, current challenges and future directions are reviewed and discussed.
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Affiliation(s)
- Han Zhang
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Centre at Houston, Houston, TX, USA
| | - Nami McCarty
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Centre at Houston, Houston, TX, USA.
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18
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Abstract
Animal models are an important resource for studying human diseases. Genetically engineered mice are the most commonly used species and have made significant contributions to our understanding of basic biology, disease mechanisms, and drug development. However, they often fail to recreate important aspects of human diseases and thus can have limited utility as translational research tools. Developing disease models in species more similar to humans may provide a better setting in which to study disease pathogenesis and test new treatments. This unit provides an overview of the history of genetically engineered large animals and the techniques that have made their development possible. Factors to consider when planning a large animal model, including choice of species, type of modification and methodology, characterization, production methods, and regulatory compliance, are also covered. © 2016 by John Wiley & Sons, Inc.
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