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Woodard LE, Galvan DL, Wilson MH. Site-Directed Genome Modification with Engineered Zinc Finger Proteins. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Lauren E. Woodard
- Department of Veterans Affairs; Nashville TN 37212 USA
- Vanderbilt University Medical Center; Department of Medicine, Department of Pharmacology; Nashville TN 37232 USA
| | - Daniel L. Galvan
- University of Texas at MD Anderson Cancer Center; Section of Nephrology; Houston TX 77030 USA
| | - Matthew H. Wilson
- Department of Veterans Affairs; Nashville TN 37212 USA
- Vanderbilt University Medical Center; Department of Medicine, Department of Pharmacology; Nashville TN 37232 USA
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Qi Z, Wilkinson MN, Chen X, Sankararaman S, Mayhew D, Mitra RD. An optimized, broadly applicable piggyBac transposon induction system. Nucleic Acids Res 2017; 45:e55. [PMID: 28082389 PMCID: PMC5397163 DOI: 10.1093/nar/gkw1290] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 01/01/2017] [Indexed: 11/29/2022] Open
Abstract
The piggyBac (PB) transposon has been used in a number of biological applications. The insertion of PB transposons into the genome can disrupt genes or regulatory regions, impacting cellular function, so for many experiments it is important that PB transposition is tightly controlled. Here, we systematically characterize three methods for the post-translational control of the PB transposon in four cell lines. We investigated fusions of the PB transposase with ERT2 and two degradation domains (FKBP-DD, DHFR-DD), in multiple orientations, and determined (i) the fold-induction achieved, (ii) the absolute transposition efficiency of the activated construct and (iii) the effects of two inducer molecules on cellular transcription and function. We found that the FKBP-DD confers the PB transposase with a higher transposition activity and better dynamic range than can be achieved with the other systems. In addition, we found that the FKBP-DD regulates transposon activity in a reversible and dose-dependent manner. Finally, we showed that Shld1, the chemical inducer of FKBP-DD, does not interfere with stem cell differentiation, whereas tamoxifen has significant effects. We believe the FKBP-based PB transposon induction will be useful for transposon-mediated genome engineering, insertional mutagenesis and the genome-wide mapping of transcription factor binding.
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Affiliation(s)
- Zongtai Qi
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, School of Medicine, St. Louis, MO 63108, USA
| | - Michael Nathaniel Wilkinson
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, School of Medicine, St. Louis, MO 63108, USA
| | - Xuhua Chen
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, School of Medicine, St. Louis, MO 63108, USA
| | - Sumithra Sankararaman
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, School of Medicine, St. Louis, MO 63108, USA
| | - David Mayhew
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, School of Medicine, St. Louis, MO 63108, USA
| | - Robi David Mitra
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, School of Medicine, St. Louis, MO 63108, USA
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Loperfido M, Jarmin S, Dastidar S, Di Matteo M, Perini I, Moore M, Nair N, Samara-Kuko E, Athanasopoulos T, Tedesco FS, Dickson G, Sampaolesi M, VandenDriessche T, Chuah MK. piggyBac transposons expressing full-length human dystrophin enable genetic correction of dystrophic mesoangioblasts. Nucleic Acids Res 2015; 44:744-60. [PMID: 26682797 PMCID: PMC4737162 DOI: 10.1093/nar/gkv1464] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/28/2015] [Indexed: 01/02/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a genetic neuromuscular disorder caused by the absence of dystrophin. We developed a novel gene therapy approach based on the use of the piggyBac (PB) transposon system to deliver the coding DNA sequence (CDS) of either full-length human dystrophin (DYS: 11.1 kb) or truncated microdystrophins (MD1: 3.6 kb; MD2: 4 kb). PB transposons encoding microdystrophins were transfected in C2C12 myoblasts, yielding 65±2% MD1 and 66±2% MD2 expression in differentiated multinucleated myotubes. A hyperactive PB (hyPB) transposase was then deployed to enable transposition of the large-size PB transposon (17 kb) encoding the full-length DYS and green fluorescence protein (GFP). Stable GFP expression attaining 78±3% could be achieved in the C2C12 myoblasts that had undergone transposition. Western blot analysis demonstrated expression of the full-length human DYS protein in myotubes. Subsequently, dystrophic mesoangioblasts from a Golden Retriever muscular dystrophy dog were transfected with the large-size PB transposon resulting in 50±5% GFP-expressing cells after stable transposition. This was consistent with correction of the differentiated dystrophic mesoangioblasts following expression of full-length human DYS. These results pave the way toward a novel non-viral gene therapy approach for DMD using PB transposons underscoring their potential to deliver large therapeutic genes.
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Affiliation(s)
- Mariana Loperfido
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Susan Jarmin
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Sumitava Dastidar
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium
| | - Mario Di Matteo
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Ilaria Perini
- Translational Cardiomyology Laboratory, Embryo and Stem Cell Biology Unit, Department of Development and Regeneration, University of Leuven, Leuven 3000, Belgium
| | - Marc Moore
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Nisha Nair
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium
| | - Ermira Samara-Kuko
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium
| | - Takis Athanasopoulos
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK Faculty of Science & Engineering, University of Wolverhampton, Wolverhampton, WV1 1LY, UK
| | | | - George Dickson
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Maurilio Sampaolesi
- Translational Cardiomyology Laboratory, Embryo and Stem Cell Biology Unit, Department of Development and Regeneration, University of Leuven, Leuven 3000, Belgium
| | - Thierry VandenDriessche
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Marinee K Chuah
- Department of Gene Therapy & Regenerative Medicine, Free University of Brussels, Brussels 1090, Belgium Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
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Abstract
DNA transposons offer an efficient nonviral method of permanently modifying the genomes of mammalian cells. The piggyBac transposon system has proven effective in genomic engineering of mammalian cells for preclinical applications, including gene discovery, simultaneous multiplexed genome modification, animal transgenesis, gene transfer in vivo achieving long-term gene expression in animals, and the genetic modification of clinically relevant cell types, such as induced pluripotent stem cells and human T lymphocytes. piggyBac has many desirable features, including seamless excision of transposons from the genomic DNA and the potential to target integration events to desired DNA sequences. In this review, we explore these recent applications and also highlight the unique advantages of using piggyBac for developing new molecular therapeutic strategies.
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Affiliation(s)
- Lauren E Woodard
- Department of Veterans Affairs, Tennessee Valley Health System, Nashville, TN, USA; Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew H Wilson
- Department of Veterans Affairs, Tennessee Valley Health System, Nashville, TN, USA; Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.
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Bire S, Rouleux-Bonnin F. Transgene Site-Specific Integration: Problems and Solutions. SITE-DIRECTED INSERTION OF TRANSGENES 2013. [DOI: 10.1007/978-94-007-4531-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Woodard LE, Li X, Malani N, Kaja A, Hice RH, Atkinson PW, Bushman FD, Craig NL, Wilson MH. Comparative analysis of the recently discovered hAT transposon TcBuster in human cells. PLoS One 2012; 7:e42666. [PMID: 23166581 PMCID: PMC3499496 DOI: 10.1371/journal.pone.0042666] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 07/10/2012] [Indexed: 11/30/2022] Open
Abstract
Background Transposons are useful tools for creating transgenic organisms, insertional mutagenesis, and genome engineering. TcBuster, a novel hAT-family transposon system derived from the red flour beetle Tribolium castaneum, was shown to be highly active in previous studies in insect embryoes. Methodology/Principal Findings We tested TcBuster for its activity in human embryonic kidney 293 (HEK-293) cells. Excision footprints obtained from HEK-293 cells contained small insertions and deletions consistent with a hAT-type repair mechanism of hairpin formation and non-homologous end-joining. Genome-wide analysis of 23,417 piggyBac, 30,303 Sleeping Beauty, and 27,985 TcBuster integrations in HEK-293 cells revealed a uniquely different integration pattern when compared to other transposon systems with regards to genomic elements. TcBuster experimental conditions were optimized to assay TcBuster activity in HEK-293 cells by colony assay selection for a neomycin-containing transposon. Increasing transposon plasmid increased the number of colonies, whereas gene transfer activity dependent on codon-optimized transposase plasmid peaked at 100 ng with decreased colonies at the highest doses of transposase DNA. Expression of the related human proteins Buster1, Buster3, and SCAND3 in HEK-293 cells did not result in genomic integration of the TcBuster transposon. TcBuster, Tol2, and piggyBac were compared directly at different ratios of transposon to transposase and found to be approximately comparable while having their own ratio preferences. Conclusions/Significance TcBuster was found to be highly active in mammalian HEK-293 cells and represents a promising tool for mammalian genome engineering.
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Affiliation(s)
- Lauren E. Woodard
- Department of Medicine, Division of Nephrology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xianghong Li
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Nirav Malani
- Department of Microbiology, Perlman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Aparna Kaja
- Department of Medicine, Division of Nephrology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Robert H. Hice
- Department of Entomology & Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Peter W. Atkinson
- Department of Entomology & Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, Perlman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nancy L. Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew H. Wilson
- Department of Medicine, Division of Nephrology, Baylor College of Medicine, Houston, Texas, United States of America
- Michael E. DeBakey Veteran's Administration Medical Center, Houston, Texas, United States of America
- * E-mail:
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Di Matteo M, Belay E, Chuah MK, Vandendriessche T. Recent developments in transposon-mediated gene therapy. Expert Opin Biol Ther 2012; 12:841-58. [PMID: 22679910 DOI: 10.1517/14712598.2012.684875] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION The continuous improvement of gene transfer technologies has broad implications for stem cell biology, gene discovery, and gene therapy. Although viral vectors are efficient gene delivery vehicles, their safety, immunogenicity and manufacturing challenges hamper clinical progress. In contrast, non-viral gene delivery systems are less immunogenic and easier to manufacture. AREAS COVERED In this review, we explore the emerging potential of transposons in gene and cell therapy. The safety, efficiency, and biology of novel hyperactive Sleeping Beauty (SB) and piggyBac (PB) transposon systems will be highlighted for ex vivo gene therapy in clinically relevant adult stem/progenitor cells, particularly hematopoietic stem cells (HSCs), mesenchymal stem cells (MSCs), myoblasts, and induced pluripotent stem (iPS) cells. Moreover, efforts toward in vivo transposon-based gene therapy will be discussed. EXPERT OPINION The latest generation SB and PB transposons currently represent some of the most attractive systems for stable non-viral genetic modification of primary cells, particularly adult stem cells. This paves the way toward the use of transposons as a non-viral gene therapy approach to correct hereditary disorders including those that affect the hematopoietic system. The development of targeted integration into "safe harbor" genetic loci may further improve their safety profile.
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Affiliation(s)
- Mario Di Matteo
- Free University of Brussels, Division of Gene Therapy & Regenerative Medicine, Laarbeeklaan 103, B-1090 Brussels, Belgium
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Towards artificial metallonucleases for gene therapy: recent advances and new perspectives. Future Med Chem 2011; 3:1935-66. [DOI: 10.4155/fmc.11.139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.
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Abstract
Until recently, progress in ex vivo gene therapy (GT) for human immunodeficiency virus-1 (HIV-1) treatment has been incremental. Long-term HIV-1 remission in a patient who received a heterologous stem cell transplant for acquired immunodeficiency syndrome-related lymphoma from a CCR5(-/-) donor, even after discontinuation of conventional therapy, has energized the field. We review the status of current approaches as well as future directions in the areas of therapeutic targets, combinatorial strategies, vector design, introduction of therapeutics into stem cells and enrichment/expansion of gene-modified cells. Finally, we discuss recent advances towards clinical application of HIV-1 GT.
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Affiliation(s)
- Lisa J Scherer
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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