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Zhu J, Batra H, Ananthaswamy N, Mahalingam M, Tao P, Wu X, Guo W, Fokine A, Rao VB. Design of bacteriophage T4-based artificial viral vectors for human genome remodeling. Nat Commun 2023; 14:2928. [PMID: 37253769 PMCID: PMC10229621 DOI: 10.1038/s41467-023-38364-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/27/2023] [Indexed: 06/01/2023] Open
Abstract
Designing artificial viral vectors (AVVs) programmed with biomolecules that can enter human cells and carry out molecular repairs will have broad applications. Here, we describe an assembly-line approach to build AVVs by engineering the well-characterized structural components of bacteriophage T4. Starting with a 120 × 86 nm capsid shell that can accommodate 171-Kbp DNA and thousands of protein copies, various combinations of biomolecules, including DNAs, proteins, RNAs, and ribonucleoproteins, are externally and internally incorporated. The nanoparticles are then coated with cationic lipid to enable efficient entry into human cells. As proof of concept, we assemble a series of AVVs designed to deliver full-length dystrophin gene or perform various molecular operations to remodel human genome, including genome editing, gene recombination, gene replacement, gene expression, and gene silencing. These large capacity, customizable, multiplex, and all-in-one phage-based AVVs represent an additional category of nanomaterial that could potentially transform gene therapies and personalized medicine.
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Affiliation(s)
- Jingen Zhu
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Himanshu Batra
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Neeti Ananthaswamy
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Marthandan Mahalingam
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Pan Tao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Xiaorong Wu
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Wenzheng Guo
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Venigalla B Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA.
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2
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Blanch-Asensio A, Grandela C, Brandão KO, de Korte T, Mei H, Ariyurek Y, Yiangou L, Mol MP, van Meer BJ, Kloet SL, Mummery CL, Davis RP. STRAIGHT-IN enables high-throughput targeting of large DNA payloads in human pluripotent stem cells. CELL REPORTS METHODS 2022; 2:100300. [PMID: 36313798 PMCID: PMC9606106 DOI: 10.1016/j.crmeth.2022.100300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 07/12/2022] [Accepted: 08/31/2022] [Indexed: 04/20/2023]
Abstract
Inserting large DNA payloads (>10 kb) into specific genomic sites of mammalian cells remains challenging. Applications ranging from synthetic biology to evaluating the pathogenicity of disease-associated variants for precision medicine initiatives would greatly benefit from tools that facilitate this process. Here, we merge the strengths of different classes of site-specific recombinases and combine these with CRISPR-Cas9-mediated homologous recombination to develop a strategy for stringent site-specific replacement of genomic fragments at least 50 kb in size in human induced pluripotent stem cells (hiPSCs). We demonstrate the versatility of STRAIGHT-IN (serine and tyrosine recombinase-assisted integration of genes for high-throughput investigation) by (1) inserting various combinations of fluorescent reporters into hiPSCs to assess the excitation-contraction coupling cascade in derivative cardiomyocytes and (2) simultaneously targeting multiple variants associated with inherited cardiac arrhythmic disorders into a pool of hiPSCs. STRAIGHT-IN offers a precise approach to generate genetically matched panels of hiPSC lines efficiently and cost effectively.
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Affiliation(s)
- Albert Blanch-Asensio
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Catarina Grandela
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Karina O. Brandão
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Tessa de Korte
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Yavuz Ariyurek
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Loukia Yiangou
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Mervyn P.H. Mol
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Berend J. van Meer
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Susan L. Kloet
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Christine L. Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
- Department of Applied Stem Cell Technologies, University of Twente, 7500AE Enschede, the Netherlands
| | - Richard P. Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
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3
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Huang Y, Zhang W, Zhang C, Cui N, Xiao Z, Wang R, Su X. Rapid and reagent-free bioassay using autobioluminescent yeasts to detect agonistic and antagonistic activities of bisphenols against rat androgen receptor and progesterone receptor. J Steroid Biochem Mol Biol 2022; 222:106151. [PMID: 35787454 DOI: 10.1016/j.jsbmb.2022.106151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/20/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022]
Abstract
Bisphenol A (BPA) and its analogues have been classified as endocrine disruptors via binding to nuclear receptors. Two novel bioassays, BLYrARS and BLYrPRS, were developed for rapid detection of agonistic and antagonistic activities of BPA and five of its analogues binding rat androgen receptor (rAR) and rat progesterone receptor (rPR). The reporter bioassay was based on two autonomously bioluminescent strains of the yeast Saccharomyces cerevisiae, recombined with a bacterial luciferase reporter gene cassette (lux) that can produce autofluorescence, regulated by the corresponding hormone response element acting as the responsive promoter. The bioluminescent signal is autonomous and continuous without cell lysis or addition of exogenous reagents. The AR agonist R1881 could be detected at 4 h with a half-maximal effective concentration (EC50) of ~9.4 nM. The PR agonist progesterone could be determined at 4 h with an EC50 of ~2.74 nM. None of the sixteen bisphenols presented agonistic activities against rAR and rPR. However, thirteen BPs were rAR antagonists and eleven BPs acted as rPR antagonists with different potency. The BLYrARS and BLYrPRS bioassay characterized by automated signal acquisition without additional manipulations or cost can be applied for simple and rapid detection of agonistic and antagonistic activities of BPs and other compounds acting as agonists or antagonists of rAR and rPR. Based on data derived by use of this bioassay endocrine-disrupting activities of some BPA analogues are more potent than BPA.
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Affiliation(s)
- Yuan Huang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Wei Zhang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Chengdong Zhang
- Beijing Biorise Biotechnology Co., Ltd, Beijing 102206, China.
| | - Na Cui
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Zhiming Xiao
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Ruiguo Wang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Xiaoou Su
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
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4
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Zeng B, Zhou M, Liu B, Shen F, Xiao R, Su J, Hu Z, Zhang Y, Gu A, Wu L, Liu X, Liang D. Targeted addition of mini-dystrophin into rDNA locus of Duchenne muscular dystrophy patient-derived iPSCs. Biochem Biophys Res Commun 2021; 545:40-45. [PMID: 33540285 DOI: 10.1016/j.bbrc.2021.01.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 01/19/2021] [Indexed: 12/23/2022]
Abstract
Duchenne muscular dystrophy (DMD), the most common lethal muscular disorder, affects 1 in 5000 male births. It is caused by mutations in the X-linked dystrophin gene (DMD), and there is no effective treatment currently. Gene addition is a promising strategy owing to its universality for patients with all gene mutations types. In this study, we describe a site-specific gene addition strategy in induced pluripotent stem cells (iPSCs) derived from a DMD patient with exon 50 deletion. By using transcription activator-like effector nickases (TALENickases), the mini-dystrophin cassette was precisely targeted at the ribosomal RNA gene (rDNA) locus via homologous recombination with high targeting efficiency. The targeted clone retained the main pluripotent properties and was differentiated into cardiomyocytes. Significantly, the dystrophin expression and membrane localization were restored in the genetic corrected iPSCs and their derived cardiomyocytes. More importantly, the enhanced spontaneous contraction was observed in modified cardiomyocytes. These results provide a proof of principle for an efficient targeted gene addition for DMD gene therapy and represents a significant step toward precisely therapeutic for DMD.
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Affiliation(s)
- Baitao Zeng
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Miaojin Zhou
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Bo Liu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Fei Shen
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Rou Xiao
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Jiasun Su
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Zhiqing Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Yiti Zhang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Ao Gu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Lingqian Wu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China; Hunan Jiahui Genetics Hospital, Changsha, Hunan 410078, China
| | - Xionghao Liu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Desheng Liang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China; Hunan Jiahui Genetics Hospital, Changsha, Hunan 410078, China.
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5
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"Betwixt Mine Eye and Heart a League Is Took": The Progress of Induced Pluripotent Stem-Cell-Based Models of Dystrophin-Associated Cardiomyopathy. Int J Mol Sci 2020; 21:ijms21196997. [PMID: 32977524 PMCID: PMC7582534 DOI: 10.3390/ijms21196997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
The ultimate goal of precision disease modeling is to artificially recreate the disease of affected people in a highly controllable and adaptable external environment. This field has rapidly advanced which is evident from the application of patient-specific pluripotent stem-cell-derived precision therapies in numerous clinical trials aimed at a diverse set of diseases such as macular degeneration, heart disease, spinal cord injury, graft-versus-host disease, and muscular dystrophy. Despite the existence of semi-adequate treatments for tempering skeletal muscle degeneration in dystrophic patients, nonischemic cardiomyopathy remains one of the primary causes of death. Therefore, cardiovascular cells derived from muscular dystrophy patients' induced pluripotent stem cells are well suited to mimic dystrophin-associated cardiomyopathy and hold great promise for the development of future fully effective therapies. The purpose of this article is to convey the realities of employing precision disease models of dystrophin-associated cardiomyopathy. This is achieved by discussing, as suggested in the title echoing William Shakespeare's words, the settlements (or "leagues") made by researchers to manage the constraints ("betwixt mine eye and heart") distancing them from achieving a perfect precision disease model.
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Breuls N, Giacomazzi G, Sampaolesi M. (Epi)genetic Modifications in Myogenic Stem Cells: From Novel Insights to Therapeutic Perspectives. Cells 2019; 8:cells8050429. [PMID: 31075875 PMCID: PMC6562881 DOI: 10.3390/cells8050429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
The skeletal muscle is considered to be an ideal target for stem cell therapy as it has an inherent regenerative capacity. Upon injury, the satellite cells, muscle stem cells that reside under the basal lamina of the myofibres, start to differentiate in order to reconstitute the myofibres while maintaining the initial stem cell pool. In recent years, it has become more and more evident that epigenetic mechanisms such as histon modifications, DNA methylations and microRNA modulations play a pivatol role in this differentiation process. By understanding the mechanisms behind myogenesis, researchers are able to use this knowledge to enhance the differentiation and engraftment potential of different muscle stem cells. Besides manipulation on an epigenetic level, recent advances in the field of genome-engineering allow site-specific modifications in the genome of these stem cells. Combining epigenetic control of the stem cell fate with the ability to site-specifically correct mutations or add genes for further cell control, can increase the use of stem cells as treatment of muscular dystrophies drastically. In this review, we will discuss the advances that have been made in genome-engineering and the epigenetic regulation of muscle stem cells and how this knowledge can help to get stem cell therapy to its full potential.
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Affiliation(s)
- Natacha Breuls
- Translational Cardiomyology Lab, Department of Development and Regeneration, Stem Cell Institute Leuven, 3000 KU Leuven, Belgium.
| | - Giorgia Giacomazzi
- Translational Cardiomyology Lab, Department of Development and Regeneration, Stem Cell Institute Leuven, 3000 KU Leuven, Belgium.
| | - Maurilio Sampaolesi
- Translational Cardiomyology Lab, Department of Development and Regeneration, Stem Cell Institute Leuven, 3000 KU Leuven, Belgium.
- Human Anatomy Unit, Department of Public Health, Experimental and Forensic Medicine, and Interuniversity Institute of Myology, University of Pavia, 27100 Pavia, Italy.
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7
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Makhija H, Roy S, Hoon S, Ghadessy FJ, Wong D, Jaiswal R, Campana D, Dröge P. A novel λ integrase-mediated seamless vector transgenesis platform for therapeutic protein expression. Nucleic Acids Res 2018; 46:e99. [PMID: 29893931 PMCID: PMC6144826 DOI: 10.1093/nar/gky500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 05/22/2018] [Indexed: 02/06/2023] Open
Abstract
Advances in stem cell engineering, gene therapy and molecular medicine often involve genome engineering at a cellular level. However, functionally large or multi transgene cassette insertion into the human genome still remains a challenge. Current practices such as random transgene integration or targeted endonuclease-based genome editing are suboptimal and might pose safety concerns. Taking this into consideration, we previously developed a transgenesis tool derived from phage λ integrase (Int) that precisely recombines large plasmid DNA into an endogenous sequence found in human Long INterspersed Elements-1 (LINE-1). Despite this advancement, biosafety concerns associated with bacterial components of plasmids, enhanced uptake and efficient transgene expression remained problematic. We therefore further improved and herein report a more superior Int-based transgenesis tool. This novel Int platform allows efficient and easy derivation of sufficient amounts of seamless supercoiled transgene vectors from conventional plasmids via intramolecular recombination as well as subsequent intermolecular site-specific genome integration into LINE-1. Furthermore, we identified certain LINE-1 as preferred insertion sites for Int-mediated seamless vector transgenesis, and showed that targeted anti-CD19 chimeric antigen receptor gene integration achieves high-level sustained transgene expression in human embryonic stem cell clones for potential downstream therapeutic applications.
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Affiliation(s)
- Harshyaa Makhija
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Suki Roy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Shawn Hoon
- Molecular Engineering Lab, Biomedical Sciences Institute, Agency for Science Technology and Research, 61 Biopolis Drive, Singapore 138673
| | | | - Desmond Wong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Rahul Jaiswal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Dario Campana
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.,Nanyang Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building (EMB), 59 Nanyang Drive, Singapore 636921
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Cordova G, Negroni E, Cabello-Verrugio C, Mouly V, Trollet C. Combined Therapies for Duchenne Muscular Dystrophy to Optimize Treatment Efficacy. Front Genet 2018; 9:114. [PMID: 29692797 PMCID: PMC5902687 DOI: 10.3389/fgene.2018.00114] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/22/2018] [Indexed: 01/01/2023] Open
Abstract
Duchene Muscular Dystrophy (DMD) is the most frequent muscular dystrophy and one of the most severe due to the absence of the dystrophin protein. Typical pathological features include muscle weakness, muscle wasting, degeneration, and inflammation. At advanced stages DMD muscles present exacerbated extracellular matrix and fat accumulation. Recent progress in therapeutic approaches has allowed new strategies to be investigated, including pharmacological, gene-based and cell-based therapies. Gene and cell-based therapies are still limited by poor targeting and low efficiency in fibrotic dystrophic muscle, therefore it is increasingly evident that future treatments will have to include “combined therapies” to reach maximal efficiency. The scope of this mini-review is to provide an overview of the current literature on such combined therapies for DMD. By “combined therapies” we mean those that include both a therapy to correct the genetic defect and an additional one to address one of the secondary pathological features of the disease. In this mini-review, we will not provide a comprehensive view of the literature on therapies for DMD, since many such reviews already exist, but we will focus on the characteristics, efficiency, and potential of such combined therapeutic strategies that have been described so far for DMD.
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Affiliation(s)
- Gonzalo Cordova
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Association Institut de Myologie, Centre de Recherche en Myologie, UMRS974, Paris, France
| | - Elisa Negroni
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Association Institut de Myologie, Centre de Recherche en Myologie, UMRS974, Paris, France
| | - Claudio Cabello-Verrugio
- Laboratorio de Patologías Musculares, Fragilidad y Envejecimiento, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Vincent Mouly
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Association Institut de Myologie, Centre de Recherche en Myologie, UMRS974, Paris, France
| | - Capucine Trollet
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Association Institut de Myologie, Centre de Recherche en Myologie, UMRS974, Paris, France
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England J, Loughna S, Rutland CS. Multiple Species Comparison of Cardiac Troponin T and Dystrophin: Unravelling the DNA behind Dilated Cardiomyopathy. J Cardiovasc Dev Dis 2017; 4:E8. [PMID: 29367539 PMCID: PMC5715711 DOI: 10.3390/jcdd4030008] [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: 06/21/2017] [Revised: 07/01/2017] [Accepted: 07/05/2017] [Indexed: 12/14/2022] Open
Abstract
Animals have frequently been used as models for human disorders and mutations. Following advances in genetic testing and treatment options, and the decreasing cost of these technologies in the clinic, mutations in both companion and commercial animals are now being investigated. A recent review highlighted the genes associated with both human and non-human dilated cardiomyopathy. Cardiac troponin T and dystrophin were observed to be associated with both human and turkey (troponin T) and canine (dystrophin) dilated cardiomyopathies. This review gives an overview of the work carried out in cardiac troponin T and dystrophin to date in both human and animal dilated cardiomyopathy.
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Affiliation(s)
- Jennifer England
- School of Life Sciences, Medical School, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Siobhan Loughna
- School of Life Sciences, Medical School, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Catrin Sian Rutland
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK.
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