Meganucleases and DNA double-strand break-induced recombination : Perspectives for gene therapy
TL;DR: Current systems based on redesigned endonucleases will be presented, with a special emphasis on the recent advances in homing endonuclease engineering, and the main issues that will need to be addressed in order to bring this promising technology to the patient.
Abstract: Meganucleases are sequence-specific endonucleases recognizing large (>12 bp) sequence sites and several laboratories have used these proteins to induce highly efficient gene targeting in mammalian cells. The recent development of artificial endonucleases with tailored specificities has opened the door for a wide range of new applications, including therapeutic ones: redesigned endonucleases cleaving chosen sequences could be used to in gene therapy to correct mutated genes or introduce transgenes in chosen loci. Such "targeted" approaches markedly differ from current gene therapy strategies based on the random insertion of a complementing virus-borne transgene. As a consequence, they should bypass the odds of random insertion. Artificial fusion proteins including Zinc-Finger binding domains have provided important proofs of concept, however the toxicity of these proteins is still an issue. Today custom-designed homing endonucleases, the natural meganucleases, could represent an efficient alternative. After a brief description of the origin of the technology, current systems based on redesigned endonucleases will be presented, with a special emphasis on the recent advances in homing endonuclease engineering. Finally, we will discuss the main issues that will need to be addressed in order to bring this promising technology to the patient.
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TL;DR: The history of ZFN development is reviewed, considerable progress has been made in methods for deriving zinc-finger sets for new genomic targets, but approaches to design and selection are still being perfected.
Abstract: Zinc-finger nucleases (ZFNs) are targetable DNA cleavage reagents that have been adopted as gene-targeting tools. ZFN-induced double-strand breaks are subject to cellular DNA repair processes that lead to both targeted mutagenesis and targeted gene replacement at remarkably high frequencies. This article briefly reviews the history of ZFN development and summarizes applications that have been made to genome editing in many different organisms and situations. Considerable progress has been made in methods for deriving zinc-finger sets for new genomic targets, but approaches to design and selection are still being perfected. An issue that needs more attention is the extent to which available mechanisms of double-strand break repair limit the scope and utility of ZFN-initiated events. The bright prospects for future applications of ZFNs, including human gene therapy, are discussed.
852 citations
Cites background from "Meganucleases and DNA double-strand..."
...Another approach has been to modify the recognition specificity of enzymes such as I-SceI (homing endonucleases, also called meganucleases) (Ashworth et al. 2006; Pâques and Duchateau 2007)....
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TL;DR: 'genomic safe harbours' are discussed — chromosomal locations where therapeutic transgenes can integrate and function in a predictable manner without perturbing endogenous gene activity and promoting cancer.
Abstract: Interactions between newly integrated DNA and the host genome limit the reliability and safety of transgene integration for therapeutic cell engineering and other applications. Although targeted gene delivery has made considerable progress, the question of where to insert foreign sequences in the human genome to maximize safety and efficacy has received little attention. In this Opinion article, we discuss 'genomic safe harbours' - chromosomal locations where therapeutic transgenes can integrate and function in a predictable manner without perturbing endogenous gene activity and promoting cancer.
429 citations
Patent•
10 Dec 2010TL;DR: In this paper, the authors present a method for gene targeting with transcription activator-like effector nucleases (TALENS) and discuss its application in the field of bioinformatics.
Abstract: Materials and Methods related to gene targeting (e.g., gene targeting with transcription activator-like effector nucleases; “TALENS”) are provided.
427 citations
TL;DR: Genome engineering promises to advance basic plant research by linking DNA sequences to biological function and will enable plants' biosynthetic capacity to be harnessed to produce the many agricultural products required by an expanding world population.
Abstract: Recent advances in genome engineering provide newfound control over a plant's genetic material. It is now possible for most bench scientists to alter DNA in living plant cells in a variety of ways, including introducing specific nucleotide substitutions in a gene that change a protein's amino acid sequence, deleting genes or chromosomal segments, and inserting foreign DNA at precise genomic locations. Such targeted DNA sequence modifications are enabled by sequence-specific nucleases that create double-strand breaks in the genomic loci to be altered. The repair of the breaks, through either homologous recombination or nonhomologous end joining, can be controlled to achieve the desired sequence modification. Genome engineering promises to advance basic plant research by linking DNA sequences to biological function. Further, genome engineering will enable plants' biosynthetic capacity to be harnessed to produce the many agricultural products required by an expanding world population.
403 citations
Cites background from "Meganucleases and DNA double-strand..."
...The third class of sequence-specific nucleases used for genome engineering—the homing endonucleases or meganucleases—derive from naturally occurring proteins encoded by mobile introns (82, 108)....
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TL;DR: These alternative approaches based on non-viral vectorization and/or targeted insertion aimed at achieving safer gene transfer are reviewed, with a special emphasis on megan nucleases, a family of naturally occurring rare-cutting endonucleases, and speculate on their current and future potential.
Abstract: The importance of safer approaches for gene therapy has been underscored by a series of severe adverse events (SAEs) observed in patients involved in clinical trials for Severe Combined Immune Deficiency Disease (SCID) and Chromic Granulomatous Disease (CGD). While a new generation of viral vectors is in the process of replacing the classical gamma-retrovirus – based approach, a number of strategies have emerged based on non-viral vectorization and/or targeted insertion aimed at achieving safer gene transfer. Currently, these methods display lower efficacies than viral transduction although many of them can yield more than 1% engineered cells in vitro. Nuclease-based approaches, wherein an endonuclease is used to trigger site-specific genome editing, can significantly increase the percentage of targeted cells. These methods therefore provide a real alternative to classical gene transfer as well as gene editing. However, the first endonuclease to be in clinic today is not used for gene transfer, but to inactivate a gene (CCR5) required for HIV infection. Here, we review these alternative approaches, with a special emphasis on meganucleases, a family of naturally occurring rare-cutting endonucleases, and speculate on their current and future potential.
372 citations
Cites background from "Meganucleases and DNA double-strand..."
...Since then, this simple system has been widely adopted by the scientific community and has allowed for a better understanding of the DNA repair mechanism in a variety of cell types and experimental conditions [89]....
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...SCID diseases), a low frequency of repair should be enough to provide a therapeutic effect [89]....
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...Since the first reports of using the I-SceI meganuclease in mammalian cells, the practice of stimulating HR via nucleases has become standard in many fields [88, 89]....
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References
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Book•
01 Jan 2006
TL;DR: Animal Models and Therapy, Directed Differentiation and Characterization of Genetically Modified Embryonic Stem Cells for Therapy, and Use of Differentiating Embryonics Stem cells in the Parkinsonian Mouse Model are reviewed.
Abstract: Isolation and Maintenance.- Isolation and Differentiation of Medaka Embryonic Stem Cells.- Maintenance of Chicken Embryonic Stem Cells In Vitro.- Derivation and Culture of Mouse Trophoblast Stem Cells In Vitro.- Derivation, Maintenance, and Characterization of Rat Embryonic Stem Cells In Vitro.- Derivation, Maintenance, and Induction of the Differentiation In Vitro of Equine Embryonic Stem Cells.- Generation and Characterization of Monkey Embryonic Stem Cells.- Derivation and Propagation of Embryonic Stem Cells in Serum- and Feeder-Free Culture.- Signaling in Embryonic Stem Cell Differentiation.- Internal Standards in Differentiating Embryonic Stem Cells In Vitro.- Matrix Assembly, Cell Polarization, and Cell Survival.- Phosphoinositides, Inositol Phosphates, and Phospholipase C in Embryonic Stem Cells.- Cripto Signaling in Differentiating Embryonic Stem Cells.- The Use of Embryonic Stem Cells to Study Hedgehog Signaling.- Transfection and Promoter Analysis in Embryonic Stem Cells.- SAGE Analysis to Identify Embryonic Stem Cell-Predominant Transcripts.- Utilization of Digital Differential Display to Identify Novel Targets of Oct3/4.- Gene Silencing Using RNA Interference in Embryonic Stem Cells.- Genetic Manipulation of Embryonic Stem Cells.- Efficient Transfer of HSV-1 Amplicon Vectors Into Embryonic Stem Cells and Their Derivatives.- Lentiviral Vector-Mediated Gene Transfer in Embryonic Stem Cells.- Use of the Cytomegalovirus Promoter for Transient and Stable Transgene Expression in Mouse Embryonic Stem Cells.- Use of Simian Immunodeficiency Virus Vectors for Simian Embryonic Stem Cells.- Generation of Green Fluorescent Protein-Expressing Monkey Embryonic Stem Cells.- DNA Damage Response and Mutagenesis in Mouse Embryonic Stem Cells.- Ultraviolet-Induced Apoptosis in Embryonic Stem Cells In Vitro.- Use of Embryonic Stem Cells in Pharmacological and Toxicological Screens.- Use of Differentiating Embryonic Stem Cells in Pharmacological Studies.- Embryonic Stem Cells as a Source of Differentiated Neural Cells for Pharmacological Screens.- Use of Murine Embryonic Stem Cells in Embryotoxicity Assays.- Use of Chemical Mutagenesis in Mouse Embryonic Stem Cells.- Epigenetic Analysis of Embryonic Stem Cells.- Nuclear Reprogramming of Somatic Nucleus Hybridized With Embryonic Stem Cells by Electrofusion.- Methylation in Embryonic Stem Cells In Vitro.- Tumor-Like Properties.- Identification of Genes Involved in Tumor-Like Properties of Embryonic Stem Cells.- In Vivo Tumor Formation From Primate Embryonic Stem Cells.- Animal Models and Therapy.- Directed Differentiation and Characterization of Genetically Modified Embryonic Stem Cells for Therapy.- Use of Differentiating Embryonic Stem Cells in the Parkinsonian Mouse Model.
3,665 citations
French Institute of Health and Medical Research1, University of Freiburg2, Hospital Research Foundation3, Medical Research Council4, Utrecht University5, Harvard University6, Pasteur Institute7, Babraham Institute8, University of Paris9, Curie Institute10, National Institutes of Health11, University of Sydney12, Ludwig Maximilian University of Munich13, LSU Health Sciences Center New Orleans14
TL;DR: Retrovirus vector insertion can trigger deregulated premalignant cell proliferation with unexpected frequency, most likely driven by retrovirus enhancer activity on the LMO2 gene promoter.
Abstract: We have previously shown correction of X-linked severe combined immunodeficiency [SCID-X1, also known as gamma chain (gamma(c)) deficiency] in 9 out of 10 patients by retrovirus-mediated gamma(c) gene transfer into autologous CD34 bone marrow cells. However, almost 3 years after gene therapy, uncontrolled exponential clonal proliferation of mature T cells (with gammadelta+ or alphabeta+ T cell receptors) has occurred in the two youngest patients. Both patients' clones showed retrovirus vector integration in proximity to the LMO2 proto-oncogene promoter, leading to aberrant transcription and expression of LMO2. Thus, retrovirus vector insertion can trigger deregulated premalignant cell proliferation with unexpected frequency, most likely driven by retrovirus enhancer activity on the LMO2 gene promoter.
3,514 citations
TL;DR: The one-step gene disruption techniques described here are versatile in that a disruption can be made simply by the appropriate cloning experiment and the resultant chromosomal insertion is nonreverting and contains a genetically linked marker.
Abstract: The one-step gene disruption techniques described here are versatile in that a disruption can be made simply by the appropriate cloning experiment. The resultant chromosomal insertion is nonreverting and contains a genetically linked marker. Detailed knowledge of the restriction map of a fragment is not necessary. It is even possible to "probe" a fragment that is unmapped for genetic functions by constructing a series of insertions and testing each one for its phenotype.
2,848 citations
"Meganucleases and DNA double-strand..." refers background or methods in this paper
...In the late seventies the first gene targeting (GT) experiments in the yeast Saccharomyces cerevisiae opened new perspectives for genome engineering [Hinnen et al., 1978; Orr-Weaver et al., 1981; Orr-Weaver et al., 1983; Rothstein, 1983; Szostak et al., 1983]....
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...(b) In another design, described by Rothstein [Rothstein, 1983], the linear sequence contains a marker surrounded by...
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TL;DR: This work mutated, by gene targeting, the endogenous hypoxanthine phosphoribosyl transferase (HPRT) gene in mouse embryo-derived stem (ES) cells and compared the gene-targeting efficiencies of two classes of neor-Hprt recombinant vectors.
2,512 citations
"Meganucleases and DNA double-strand..." refers background in this paper
...It took only a few years before the same basic strategies were successfully implemented in mammalian cells [Doetschman et al., 1987; Koller and Smithies, 1989; Mansour et al., 1988; Mansour et al., 1990; Thomas and Capecchi, 1987; Thomas and Capecchi, 1990]....
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...Whereas in yeast, targeted events represented 100% of the stably transformed cells, they accounted for only 1/100 to 1/1000 of the transformants in mouse ES cells [Doetschman et al., 1987; Koller and Smithies, 1989; Mansour et al., 1988; Mansour et al., 1990; Thomas and Capecchi, 1987; Thomas and Capecchi, 1990]....
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TL;DR: This work proposes a new mechanism for meiotic recombination, in which events are initiated by double-strand breaks that are enlarged to double- Strand gaps, and postmeiotic segregation can result from heteroduplex DNA formed at the boundaries of the gap-repair region.
2,387 citations
"Meganucleases and DNA double-strand..." refers background in this paper
...In the late seventies the first gene targeting (GT) experiments in the yeast Saccharomyces cerevisiae opened new perspectives for genome engineering [Hinnen et al., 1978; Orr-Weaver et al., 1981; Orr-Weaver et al., 1983; Rothstein, 1983; Szostak et al., 1983]....
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..., 1978], and was significantly stimulated by free DNA ends in the construct [Orr-Weaver et al., 1981; Orr-Weaver et al., 1983; Szostak et al., 1983]....
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...The recombinogenic properties of DSBs had been established shortly before [Szostak et al., 1983], but the novelty was that nature had evolved sequence-specific endonucleases to actively trigger recombination....
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