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Ahmadi M, Damavandi N, Akbari Eidgahi MR, Davami F. Utilization of Site-Specific Recombination in Biopharmaceutical Production. IRANIAN BIOMEDICAL JOURNAL 2015; 20:68-76. [PMID: 26602035 PMCID: PMC4726886 DOI: 10.7508/ibj.2016.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mammalian expression systems, due to their capacity in post-translational modification, are preferred systems for biopharmaceutical protein production. Several recombinant protein systems have been introduced to the market, most of which are under clinical development. In spite of significant improvements such as cell line engineering, introducing novel expression methods, gene silencing and process development, expression level is unpredictable and unstable because of the random location of integration in the genome. Site-specific recombination techniques are capable of producing stable and high producer clonal cells; therefore, they are gaining more importance in the biopharmaceutical production. Site-specific recombination methods increase the recombinant protein production by specifically inserting a vector at a locus with specific expression trait. The present review focused on the latest developments in site-specific recombination techniques, their specific features and comparisons.
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Affiliation(s)
- Maryam Ahmadi
- Dept. of Medical Biotechnology, Semnan University of Medical Sciences, Semnan, Iran.,Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Narges Damavandi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Dept. of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Fatemeh Davami
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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52
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Mouse embryonic stem cells with a multi-integrase mouse artificial chromosome for transchromosomic mouse generation. Transgenic Res 2015; 24:717-27. [PMID: 26055730 PMCID: PMC4504986 DOI: 10.1007/s11248-015-9884-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/28/2015] [Indexed: 01/25/2023]
Abstract
The mouse artificial chromosome (MAC) has several advantages as a gene delivery vector, including stable episomal maintenance of the exogenous genetic material and the ability to carry large and/or multiple gene inserts including their regulatory elements. Previously, a MAC containing multi-integration site (MI-MAC) was generated to facilitate transfer of multiple genes into desired cells. To generate transchromosomic (Tc) mice containing a MI-MAC with genes of interest, the desired genes were inserted into MI-MAC in CHO cells, and then the MI-MAC was transferred to mouse embryonic stem (mES) cells via microcell-mediated chromosome transfer (MMCT). However, the efficiency of MMCT from CHO to mES cells is very low (<10−6). In this study, we constructed mES cell lines containing a MI-MAC vector to directly insert a gene of interest into the MI-MAC in mES cells via a simple transfection method for Tc mouse generation. The recombination rate of the GFP gene at each attachment site (FRT, PhiC31attP, R4attP, TP901-1attP and Bxb1attP) on MI-MAC was greater than 50 % in MI-MAC mES cells. Chimeric mice with high coat colour chimerism were generated from the MI-MAC mES cell lines and germline transmission from the chimera was observed. As an example for the generation of Tc mice with a desired gene by the MI-MAC mES approach, a Tc mouse strain ubiquitously expressing Emerald luciferase was efficiently established. Thus, the findings suggest that this new Tc strategy employing mES cells and a MI-MAC vector is efficient and useful for animal transgenesis.
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53
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Nakayama Y, Uno N, Uno K, Mizoguchi Y, Komoto S, Kazuki Y, Nanba E, Inoue T, Oshimura M. Recurrent micronucleation through cell cycle progression in the presence of microtubule inhibitors. Cell Struct Funct 2015; 40:51-9. [PMID: 25736016 DOI: 10.1247/csf.14005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Although most cell lines undergo mitotic arrest after prolonged exposure to microtubule inhibitors, some cells subsequently exit this state and become tetraploid. Among these cells, limited numbers of rodent cells are known to undergo multinucleation to generate multiple small independent nuclei, or micronuclei by prolonged colcemid treatment. Micronuclei are thought to be formed when cells shift to a pseudo G1 phase, during which the onset of chromosomal decondensation allows individual chromosomes distributed throughout the cell to serve as sites for the reassembly of nuclear membranes. To better define this process, we used long-term live cell imaging to observe micronucleation induced in mouse A9 cells by treating with the microtubule inhibitor colcemid. Our observations confirm that nuclear envelope formation occurs when mitotic-arrested cells shift to a pseudo G1 phase and adopt a tetraploid state, accompanied by chromosome decondensation. Unexpectedly, only a small number of cells containing large micronuclei were formed. We found that tetraploid micronucleated cells proceeded through an additional cell cycle, shifting to a pseudo G1 phase and forming octoploid micronucleated cells that were smaller and more numerous compared with the tetraploid micronucleated cells. Our data suggest that micronucleation occur when cells shift from mitotic arrest to a pseudo G1 phase, and demonstrate that, rather than being a single event, micronucleation is an inducible recurrent process that leads to the formation of progressively smaller and more numerous micronuclei.
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Affiliation(s)
- Yuji Nakayama
- Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University
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54
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Takiguchi M, Kazuki Y, Hiramatsu K, Abe S, Iida Y, Takehara S, Nishida T, Ohbayashi T, Wakayama T, Oshimura M. A novel and stable mouse artificial chromosome vector. ACS Synth Biol 2014; 3:903-14. [PMID: 23654256 DOI: 10.1021/sb3000723] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human chromosome fragments (hCFs) and human artificial chromosomes (HACs) can be transferred into mouse ES cells to produce trans-chromosomic (Tc) mice. Although hCFs and HACs containing large genomic DNAs can be autonomously maintained in Tc mice, their retention rate is variable in mouse ES cell lines and Tc mouse tissues, possibly because of centromere differences between the species. To improve the retention rate of artificial chromosomes in mouse cells, we constructed novel mouse artificial chromosome (MAC) vectors by truncating a natural mouse chromosome at a site adjacent to the centromeric region. We obtained cell clones containing the MAC vectors that were stably maintained in mouse ES cells and various tissues in Tc mice. The MACs possess acceptor sites into which a desired gene or genes can be inserted. Thus, Tc mice harboring the MAC vectors may be valuable tools for functional analyses of desired genes, producing humanized model mice, and synthetic biology.
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Affiliation(s)
- Masato Takiguchi
- Department
of Biomedical Science,
Institute of Regenerative Medicine and Biofunction, Graduate School
of Medical Science, Tottori University,
86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Yasuhiro Kazuki
- Department
of Biomedical Science,
Institute of Regenerative Medicine and Biofunction, Graduate School
of Medical Science, Tottori University,
86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Chromosome Engineering Research
Center, Tottori University, Tottori, Japan
| | - Kei Hiramatsu
- Department
of Biomedical Science,
Institute of Regenerative Medicine and Biofunction, Graduate School
of Medical Science, Tottori University,
86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Satoshi Abe
- Department
of Biomedical Science,
Institute of Regenerative Medicine and Biofunction, Graduate School
of Medical Science, Tottori University,
86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Yuichi Iida
- Department
of Biomedical Science,
Institute of Regenerative Medicine and Biofunction, Graduate School
of Medical Science, Tottori University,
86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Shoko Takehara
- Chromosome Engineering Research
Center, Tottori University, Tottori, Japan
| | - Tadashi Nishida
- Division of Laboratory Animal
Science, Research Center for Bioscience and Technology, Tottori University, Tottori, Japan
| | - Tetsuya Ohbayashi
- Division of Laboratory Animal
Science, Research Center for Bioscience and Technology, Tottori University, Tottori, Japan
| | - Teruhiko Wakayama
- RIKEN Center for Developmental Biology, 2-2-3 minatojima Minamimachi
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Mitsuo Oshimura
- Department
of Biomedical Science,
Institute of Regenerative Medicine and Biofunction, Graduate School
of Medical Science, Tottori University,
86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Chromosome Engineering Research
Center, Tottori University, Tottori, Japan
- JST, CREST, 5, Sanbancho, Tokyo, Japan
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55
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Yasunaga M, Murotomi K, Abe H, Yamazaki T, Nishii S, Ohbayashi T, Oshimura M, Noguchi T, Niwa K, Ohmiya Y, Nakajima Y. Highly sensitive luciferase reporter assay using a potent destabilization sequence of calpain 3. J Biotechnol 2014; 194:115-23. [PMID: 25528501 DOI: 10.1016/j.jbiotec.2014.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 11/18/2014] [Accepted: 12/10/2014] [Indexed: 11/17/2022]
Abstract
Reporter assays that use luciferases are widely employed for monitoring cellular events associated with gene expression in vitro and in vivo. To improve the response of the luciferase reporter to acute changes of gene expression, a destabilization sequence is frequently used to reduce the stability of luciferase protein in the cells, which results in an increase of sensitivity of the luciferase reporter assay. In this study, we identified a potent destabilization sequence (referred to as the C9 fragment) consisting of 42 amino acid residues from human calpain 3 (CAPN3). Whereas the half-life of Emerald Luc (ELuc) from the Brazilian click beetle Pyrearinus termitilluminans was reduced by fusing PEST (t1/2=9.8 to 2.8h), the half-life of C9-fused ELuc was significantly shorter (t1/2=1.0h) than that of PEST-fused ELuc when measurements were conducted at 37°C. In addition, firefly luciferase (luc2) was also markedly destabilized by the C9 fragment compared with the humanized PEST sequence. These results indicate that the C9 fragment from CAPN3 is a much more potent destabilization sequence than the PEST sequence. Furthermore, real-time bioluminescence recording of the activation kinetics of nuclear factor-κB after transient treatment with tumor necrosis factor α revealed that the response of C9-fused ELuc is significantly greater than that of PEST-fused ELuc, demonstrating that the use of the C9 fragment realizes a luciferase reporter assay that has faster response speed compared with that provided by the PEST sequence.
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Affiliation(s)
- Mayu Yasunaga
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan
| | - Kazutoshi Murotomi
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan
| | - Hiroko Abe
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan
| | - Tomomi Yamazaki
- Tsuruga Institute of Biotechnology, TOYOBO Corporation Ltd., Tsuruga, Fukui 914-0047, Japan
| | - Shigeaki Nishii
- Tsuruga Institute of Biotechnology, TOYOBO Corporation Ltd., Tsuruga, Fukui 914-0047, Japan
| | - Tetsuya Ohbayashi
- Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University, Yonago, Tottori 683-8503, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori 683-8503, Japan; Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Sciences, Tottori University, Yonago, Tottori 683-8503, Japan
| | - Takako Noguchi
- Department of Psychiatry and Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093-0603, USA
| | - Kazuki Niwa
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8063, Japan
| | - Yoshihiro Ohmiya
- DAILAB, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8063, Japan
| | - Yoshihiro Nakajima
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan.
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56
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Suzuki T, Kazuki Y, Oshimura M, Hara T. A novel system for simultaneous or sequential integration of multiple gene-loading vectors into a defined site of a human artificial chromosome. PLoS One 2014; 9:e110404. [PMID: 25303219 PMCID: PMC4193884 DOI: 10.1371/journal.pone.0110404] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/15/2014] [Indexed: 11/19/2022] Open
Abstract
Human artificial chromosomes (HACs) are gene-delivery vectors suitable for introducing large DNA fragments into mammalian cells. Although a HAC theoretically incorporates multiple gene expression cassettes of unlimited DNA size, its application has been limited because the conventional gene-loading system accepts only one gene-loading vector (GLV) into a HAC. We report a novel method for the simultaneous or sequential integration of multiple GLVs into a HAC vector (designated as the SIM system) via combined usage of Cre, FLP, Bxb1, and φC31 recombinase/integrase. As a proof of principle, we first attempted simultaneous integration of three GLVs encoding EGFP, Venus, and TdTomato into a gene-loading site of a HAC in CHO cells. These cells successfully expressed all three fluorescent proteins. Furthermore, microcell-mediated transfer of HACs enabled the expression of those fluorescent proteins in recipient cells. We next demonstrated that GLVs could be introduced into a HAC one-by-one via reciprocal usage of recombinase/integrase. Lastly, we introduced a fourth GLV into a HAC after simultaneous integration of three GLVs by FLP-mediated DNA recombination. The SIM system expands the applicability of HAC vectors and is useful for various biomedical studies, including cell reprogramming.
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Affiliation(s)
- Teruhiko Suzuki
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
- * E-mail:
| | - Yasuhiro Kazuki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Tottori, Japan
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori, Japan
| | - Takahiko Hara
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo, Japan
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57
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Abstract
In recent years, application of serine integrases for genomic engineering has increased in popularity. The factor-independence and unidirectionality of these large serine recombinases makes them well suited for reactions such as site-directed vector integration and cassette exchange in a wide variety of organisms. In order to generate information that might be useful for altering the specificity of serine integrases and to improve their efficiency, we tested a hybridization strategy that has been successful with several small serine recombinases. We created chimeras derived from three characterized members of the serine integrase family, phiC31, phiBT1, and TG1 integrases, by joining their amino- and carboxy-terminal portions. We found that several phiBT1-phiC31 (BC) and phiC31-TG1 (CT) hybrid integrases are active in E. coli. BC chimeras function on native att-sites and on att-sites that are hybrids between those of the two donor enzymes, while CT chimeras only act on the latter att-sites. A BC hybrid, BC{−1}, was also active in human HeLa cells. Our work is the first to demonstrate chimeric serine integrase activity. This analysis sheds light on integrase structure and function, and establishes a potentially tractable means to probe the specificity of the thousands of putative large serine recombinases that have been revealed by bioinformatics studies.
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Affiliation(s)
- Alfonso P Farruggio
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5120, USA
| | - Michele P Calos
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5120, USA
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58
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Tsuji S, Kawamura F, Kubiura M, Hayashi A, Ohbayashi T, Kazuki Y, Chesné C, Oshimura M, Tada M. Dual-color fluorescence imaging to monitor CYP3A4 and CYP3A7 expression in human hepatic carcinoma HepG2 and HepaRG cells. PLoS One 2014; 9:e104123. [PMID: 25101946 PMCID: PMC4125183 DOI: 10.1371/journal.pone.0104123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 07/11/2014] [Indexed: 12/31/2022] Open
Abstract
Human adult hepatocytes expressing CYP3A4, a major cytochrome P450 enzyme, are required for cell-based assays to evaluate the potential risk of drug-drug interactions caused by transcriptional induction of P450 enzymes in early-phase drug discovery and development. However, CYP3A7 is preferentially expressed in premature hepatoblasts and major hepatic carcinoma cell lines. The human hepatocellular carcinoma cell line HepaRG possesses a high self-renewal capacity and can differentiate into hepatic cells similar to human adult hepatocytes in vitro. Transgenic HepaRG cells, in which the expression of fluorescent reporters is regulated by 35 kb regulatory elements of CYP3A4, have a distinct advantage over human hepatocytes isolated by collagenase perfusion, which are unstable in culture. Thus, we created transgenic HepaRG and HepG2 cells by replacing the protein-coding regions of human CYP3A4 and CYP3A7 with enhanced green fluorescent protein (EGFP) and DsRed reporters, respectively, in a bacterial artificial chromosome vector that included whole regulatory elements. The intensity of DsRed fluorescence was initially high during the proliferation of transgenic HepaRG cells. However, most EGFP-positive cells were derived from those in which DsRed fluorescence was extinguished. Comparative analyses in these transgenic clones showed that changes in the total fluorescence intensity of EGFP reflected fold changes in the mRNA level of endogenous CYP3A4. Moreover, CYP3A4 induction was monitored by the increase in EGFP fluorescence. Thus, this assay provides a real-time evaluation system for quality assurance of hepatic differentiation into CYP3A4-expressing cells, unfavourable CYP3A4 induction, and fluorescence-activated cell sorting-mediated enrichment of CYP3A4-expressing hepatocytes based on the total fluorescence intensities of fluorescent reporters, without the need for many time-consuming steps.
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Affiliation(s)
- Saori Tsuji
- Bio Frontier Project Promotion Section, Organization for Tottori Industrial Promotion, Yonago, Japan
| | - Fumihiko Kawamura
- Division of Molecular Genetics and Biofunction, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Musashi Kubiura
- Division of Molecular Genetics and Biofunction, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Ayaka Hayashi
- Division of Molecular Genetics and Biofunction, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Tetsuya Ohbayashi
- Division of Laboratory Animal Science, Research Center for Bioscience and Technology, Tottori University, Yonago, Japan
| | - Yasuhiro Kazuki
- Division of Molecular Genetics and Biofunction, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
- Chromosome Engineering Research Center, Tottori University, Yonago, Japan
| | | | - Mitsuo Oshimura
- Chromosome Engineering Research Center, Tottori University, Yonago, Japan
| | - Masako Tada
- Chromosome Engineering Research Center, Tottori University, Yonago, Japan
- * E-mail:
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59
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Kouprina N, Tomilin AN, Masumoto H, Earnshaw WC, Larionov V. Human artificial chromosome-based gene delivery vectors for biomedicine and biotechnology. Expert Opin Drug Deliv 2014; 11:517-35. [DOI: 10.1517/17425247.2014.882314] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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60
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Tóth A, Fodor K, Praznovszky T, Tubak V, Udvardy A, Hadlaczky G, Katona RL. Novel method to load multiple genes onto a mammalian artificial chromosome. PLoS One 2014; 9:e85565. [PMID: 24454889 PMCID: PMC3893256 DOI: 10.1371/journal.pone.0085565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/03/2013] [Indexed: 01/05/2023] Open
Abstract
Mammalian artificial chromosomes are natural chromosome-based vectors that may carry a vast amount of genetic material in terms of both size and number. They are reasonably stable and segregate well in both mitosis and meiosis. A platform artificial chromosome expression system (ACEs) was earlier described with multiple loading sites for a modified lambda-integrase enzyme. It has been shown that this ACEs is suitable for high-level industrial protein production and the treatment of a mouse model for a devastating human disorder, Krabbe's disease. ACEs-treated mutant mice carrying a therapeutic gene lived more than four times longer than untreated counterparts. This novel gene therapy method is called combined mammalian artificial chromosome-stem cell therapy. At present, this method suffers from the limitation that a new selection marker gene should be present for each therapeutic gene loaded onto the ACEs. Complex diseases require the cooperative action of several genes for treatment, but only a limited number of selection marker genes are available and there is also a risk of serious side-effects caused by the unwanted expression of these marker genes in mammalian cells, organs and organisms. We describe here a novel method to load multiple genes onto the ACEs by using only two selectable marker genes. These markers may be removed from the ACEs before therapeutic application. This novel technology could revolutionize gene therapeutic applications targeting the treatment of complex disorders and cancers. It could also speed up cell therapy by allowing researchers to engineer a chromosome with a predetermined set of genetic factors to differentiate adult stem cells, embryonic stem cells and induced pluripotent stem (iPS) cells into cell types of therapeutic value. It is also a suitable tool for the investigation of complex biochemical pathways in basic science by producing an ACEs with several genes from a signal transduction pathway of interest.
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Affiliation(s)
- Anna Tóth
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Katalin Fodor
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Tünde Praznovszky
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Vilmos Tubak
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Andor Udvardy
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gyula Hadlaczky
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Robert L. Katona
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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Zhu F, Gamboa M, Farruggio AP, Hippenmeyer S, Tasic B, Schüle B, Chen-Tsai Y, Calos MP. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Res 2013; 42:e34. [PMID: 24304893 PMCID: PMC3950688 DOI: 10.1093/nar/gkt1290] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.
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Affiliation(s)
- Fangfang Zhu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA, Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, CA 94305, USA, Parkinson's Institute and Clinical Center, Sunnyvale, CA 94085, USA and Stanford Transgenic Research Facility, Stanford University, Stanford, CA 94305, USA
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62
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Xu Z, Thomas L, Davies B, Chalmers R, Smith M, Brown W. Accuracy and efficiency define Bxb1 integrase as the best of fifteen candidate serine recombinases for the integration of DNA into the human genome. BMC Biotechnol 2013; 13:87. [PMID: 24139482 PMCID: PMC4015280 DOI: 10.1186/1472-6750-13-87] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/09/2013] [Indexed: 11/18/2022] Open
Abstract
Background Phage-encoded serine integrases, such as φC31 integrase, are widely used for genome engineering. Fifteen such integrases have been described but their utility for genome engineering has not been compared in uniform assays. Results We have compared fifteen serine integrases for their utility for DNA manipulations in mammalian cells after first demonstrating that all were functional in E. coli. Chromosomal recombination reporters were used to show that seven integrases were active on chromosomally integrated DNA in human fibroblasts and mouse embryonic stem cells. Five of the remaining eight enzymes were active on extra-chromosomal substrates thereby demonstrating that the ability to mediate extra-chromosomal recombination is no guide to ability to mediate site-specific recombination on integrated DNA. All the integrases that were active on integrated DNA also promoted DNA integration reactions that were not mediated through conservative site-specific recombination or damaged the recombination sites but the extent of these aberrant reactions varied over at least an order of magnitude. Bxb1 integrase yielded approximately two-fold more recombinants and displayed about two fold less damage to the recombination sites than the next best recombinase; φC31 integrase. Conclusions We conclude that the Bxb1 and φC31 integrases are the reagents of choice for genome engineering in vertebrate cells and that DNA damage repair is a major limitation upon the utility of this class of site-specific recombinase.
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Affiliation(s)
| | | | | | | | | | - William Brown
- Queens Medical Centre, School of Life Sciences, Nottingham University, Nottingham NG7 2UH, UK.
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63
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Bigda JJ, Koszałka P. Wacław Szybalski's contribution to immunotherapy: HGPRT mutation & HAT selection as first steps to gene therapy and hybrid techniques in mammalian cells. Gene 2013; 525:158-61. [DOI: 10.1016/j.gene.2013.03.099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 02/27/2013] [Accepted: 03/07/2013] [Indexed: 01/04/2023]
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Lee NCO, Kononenko AV, Lee HS, Tolkunova EN, Liskovykh MA, Masumoto H, Earnshaw WC, Tomilin AN, Larionov V, Kouprina N. Protecting a transgene expression from the HAC-based vector by different chromatin insulators. Cell Mol Life Sci 2013; 70:3723-37. [PMID: 23677492 PMCID: PMC3771377 DOI: 10.1007/s00018-013-1362-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/25/2013] [Accepted: 04/30/2013] [Indexed: 01/07/2023]
Abstract
Human artificial chromosomes (HACs) are vectors that offer advantages of capacity and stability for gene delivery and expression. Several studies have even demonstrated their use for gene complementation in gene-deficient recipient cell lines and animal transgenesis. Recently, we constructed an advance HAC-based vector, alphoidtetO-HAC, with a conditional centromere. In this HAC, a gene-loading site was inserted into a centrochromatin domain critical for kinetochore assembly and maintenance. While by definition this domain is permissive for transcription, there have been no long-term studies on transgene expression within centrochromatin. In this study, we compared the effects of three chromatin insulators, cHS4, gamma-satellite DNA, and tDNA, on the expression of an EGFP transgene inserted into the alphoidtetO-HAC vector. Insulator function was essential for stable expression of the transgene in centrochromatin. In two analyzed host cell lines, a tDNA insulator composed of two functional copies of tRNA genes showed the highest barrier activity. We infer that proximity to centrochromatin does not protect genes lacking chromatin insulators from epigenetic silencing. Barrier elements that prevent gene silencing in centrochromatin would thus help to optimize transgenesis using HAC vectors.
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Affiliation(s)
- Nicholas C O Lee
- Laboratories of Molecular Pharmacology, National Cancer Institute, Bethesda, MD, 20892, USA
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65
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Yau YY, Stewart CN. Less is more: strategies to remove marker genes from transgenic plants. BMC Biotechnol 2013; 13:36. [PMID: 23617583 PMCID: PMC3689633 DOI: 10.1186/1472-6750-13-36] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Selectable marker genes (SMGs) and selection agents are useful tools in the production of transgenic plants by selecting transformed cells from a matrix consisting of mostly untransformed cells. Most SMGs express protein products that confer antibiotic- or herbicide resistance traits, and typically reside in the end product of genetically-modified (GM) plants. The presence of these genes in GM plants, and subsequently in food, feed and the environment, are of concern and subject to special government regulation in many countries. The presence of SMGs in GM plants might also, in some cases, result in a metabolic burden for the host plants. Their use also prevents the re-use of the same SMG when a second transformation scheme is needed to be performed on the transgenic host. In recent years, several strategies have been developed to remove SMGs from GM products while retaining the transgenes of interest. This review describes the existing strategies for SMG removal, including the implementation of site specific recombination systems, TALENs and ZFNs. This review discusses the advantages and disadvantages of existing SMG-removal strategies and explores possible future research directions for SMG removal including emerging technologies for increased precision for genome modification.
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Affiliation(s)
- Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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66
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Kouprina N, Earnshaw WC, Masumoto H, Larionov V. A new generation of human artificial chromosomes for functional genomics and gene therapy. Cell Mol Life Sci 2013; 70:1135-48. [PMID: 22907415 PMCID: PMC3522797 DOI: 10.1007/s00018-012-1113-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 07/25/2012] [Accepted: 07/30/2012] [Indexed: 12/30/2022]
Abstract
Since their description in the late 1990s, human artificial chromosomes (HACs) carrying a functional kinetochore were considered as a promising system for gene delivery and expression with a potential to overcome many problems caused by the use of viral-based gene transfer systems. Indeed, HACs avoid the limited cloning capacity, lack of copy number control and insertional mutagenesis due to integration into host chromosomes that plague viral vectors. Nevertheless, until recently, HACs have not been widely recognized because of uncertainties of their structure and the absence of a unique gene acceptor site. The situation changed a few years ago after engineering of HACs with a single loxP gene adopter site and a defined structure. In this review, we summarize recent progress made in HAC technology and concentrate on details of two of the most advanced HACs, 21HAC generated by truncation of human chromosome 21 and alphoid(tetO)-HAC generated de novo using a synthetic tetO-alphoid DNA array. Multiple potential applications of the HAC vectors are discussed, specifically the unique features of two of the most advanced HAC cloning systems.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Chromosomes, Artificial, Human/classification
- Chromosomes, Artificial, Human/genetics
- Chromosomes, Artificial, Human/physiology
- Disease Models, Animal
- Gene Transfer Techniques
- Genetic Diseases, Inborn/genetics
- Genetic Diseases, Inborn/pathology
- Genetic Diseases, Inborn/therapy
- Genetic Therapy/methods
- Genomics/methods
- Humans
- Models, Biological
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Affiliation(s)
- Natalay Kouprina
- Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, MD, USA.
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67
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Uno N, Uno K, Zatti S, Ueda K, Hiratsuka M, Katoh M, Oshimura M. The transfer of human artificial chromosomes via cryopreserved microcells. Cytotechnology 2013; 65:803-9. [PMID: 23494082 DOI: 10.1007/s10616-013-9548-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/18/2013] [Indexed: 12/27/2022] Open
Abstract
Microcell-mediated chromosome transfer (MMCT) technology enables a single and intact mammalian chromosome or megabase-sized chromosome fragments to be transferred from donor to recipient cells. The conventional MMCT method is performed immediately after the purification of microcells. The timing of the isolation of microcells and the preparation of recipient cells is very important. Thus, ready-made microcells can improve and simplify the process of MMCT. Here, we established a cryopreservation method to store microcells at -80 °C, and compared these cells with conventionally- (immediately-) prepared cells with respect to the efficiency of MMCT and the stability of a human artificial chromosome (HAC) transferred to human HT1080 cells. The HAC transfer in microcell hybrids was confirmed by FISH analysis. There was no significant difference between the two methods regarding chromosome transfer efficiency and the retention rate of HAC. Thus, cryopreservation of ready-to-use microcells provides an improved and simplified protocol for MMCT.
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Affiliation(s)
- Narumi Uno
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
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68
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Lanza AM, Cheng JK, Alper HS. Emerging synthetic biology tools for engineering mammalian cell systems and expediting cell line development. Curr Opin Chem Eng 2012. [DOI: 10.1016/j.coche.2012.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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69
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Baltz RH. Streptomyces temperate bacteriophage integration systems for stable genetic engineering of actinomycetes (and other organisms). ACTA ACUST UNITED AC 2012; 39:661-72. [DOI: 10.1007/s10295-011-1069-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/23/2011] [Indexed: 12/21/2022]
Abstract
Abstract
ϕC31, ϕBT1, R4, and TG1 are temperate bacteriophages with broad host specificity for species of the genus Streptomyces. They form lysogens by integrating site-specifically into diverse attB sites located within individual structural genes that map to the conserved core region of streptomycete linear chromosomes. The target genes containing the ϕC31, ϕBT1, R4, and TG1 attB sites encode a pirin-like protein, an integral membrane protein, an acyl-CoA synthetase, and an aminotransferase, respectively. These genes are highly conserved within the genus Streptomyces, and somewhat conserved within other actinomycetes. In each case, integration is mediated by a large serine recombinase that catalyzes unidirectional recombination between the bacteriophage attP and chromosomal attB sites. The unidirectional nature of the integration mechanism has been exploited in genetic engineering to produce stable recombinants of streptomycetes, other actinomycetes, eucaryotes, and archaea. The ϕC31 attachment/integration (Att/Int) system has been the most widely used, and it has been coupled with the ϕBT1 Att/Int system to facilitate combinatorial biosynthesis of novel lipopeptide antibiotics in Streptomyces fradiae.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting 6438 North Olney Street 46220 Indianapolis IN USA
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70
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Devoy A, Bunton-Stasyshyn RKA, Tybulewicz VL, Smith AJ, Fisher EM. Genomically humanized mice: technologies and promises. Nat Rev Genet 2011; 13:14-20. [PMID: 22179716 PMCID: PMC4782217 DOI: 10.1038/nrg3116] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mouse models have become an invaluable tool for understanding human health and disease owing to our ability to manipulate the mouse genome exquisitely. Recent progress in genomic analysis has led to an increase in the number and type of disease-causing mutations detected and has also highlighted the importance of non-coding regions. As a result, there is increasing interest in creating 'genomically' humanized mouse models, in which entire human genomic loci are transferred into the mouse genome. The technical challenges towards achieving this aim are large but are starting to be tackled with success.
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Affiliation(s)
- Anny Devoy
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK , +44 203 456 7890
| | - Rosie KA Bunton-Stasyshyn
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK, , +44 203 456 7890
| | - Victor L.J. Tybulewicz
- MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK, ; +44 20 8816 2184
| | - Andrew J.H. Smith
- Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH9 3JQ, UK; and the MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, ; +44 131 651 7244
| | - Elizabeth M.C. Fisher
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK, ; +44 203 456 7890
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Waldner C, Rempel O, Schütte F, Yanik M, Solomentsew N, Ryffel GU. Double conditional human embryonic kidney cell line based on FLP and ΦC31 mediated transgene integration. BMC Res Notes 2011; 4:420. [PMID: 22008483 PMCID: PMC3208510 DOI: 10.1186/1756-0500-4-420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 10/18/2011] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND FLP recombinase mediated integration into a pre-integrated FRT site is routinely used to generate highly reproducible stable transgenic cell lines. In this study, we broaden the system of site specific integration by introducing ΦC31 integrase mediated integration into attP sites. RESULTS We generated a HEK293 host cell line with a single copy FRT as well as an attP site allowing site specific integration of two distinct transgenes. To achieve conditional control, we used the tetracycline and Shld1 inducible systems. By introducing fluorescent reporters we show that integration and induction of two transgenes are completely independent. We applied this new technique to investigate the effect of HNF4α on proliferation of HEK293 cells by introducing HNF4α into each integration site. We obtained in two independent cell lines highly reproducible results that prove the usefulness of this novel HEK-attP/FRT cell line. CONCLUSIONS In this study we have established and applied a HEK-attP/FRT cell line that allows site specific integration of two conditional transgenes using the FLP recombinase as well as the ΦC31 integrase.
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Affiliation(s)
- Christoph Waldner
- Institut für Zellbiologie (Tumorforschung), Universität Duisburg-Essen, Hufelandstr, 55, D-45122 Essen, Germany.
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Kazuki Y, Oshimura M. Human artificial chromosomes for gene delivery and the development of animal models. Mol Ther 2011; 19:1591-601. [PMID: 21750534 DOI: 10.1038/mt.2011.136] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Random integration of conventional gene delivery vectors such as viruses, plasmids, P1 phage-derived artificial chromosomes, bacterial artificial chromosomes and yeast artificial chromosomes can be associated with transgene silencing. Furthermore, integrated viral sequences can activate oncogenes adjacent to the insertion site resulting in cancer. Various human artificial chromosomes (HACs) exhibit several potential characteristics desired for an ideal gene delivery vector, including stable episomal maintenance and the capacity to carry large genomic loci with their regulatory elements, thus allowing the physiological regulation of the introduced gene in a manner similar to that of native chromosomes. HACs have been generated mainly using either a "top-down approach" (engineered chromosomes), or a "bottom-up approach" (de novo artificial chromosomes). The recent emergence of stem cell-based tissue engineering has opened up new avenues for gene and cell therapies. This review describes the lessons learned and prospects identified mainly from studies in the construction of HACs and HAC-mediated gene expression systems in cultured cells, as well as in animals.
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Affiliation(s)
- Yasuhiro Kazuki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
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