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Sam Im Y, Hoon Yoo D, Kim HE, Young Oh J, Kim YO. Generation of integration-free induced pluripotent stem cell line (KSCBi017-A) from peripheral blood mononuclear cells of a healthy male individual. Stem Cell Res 2022; 65:102965. [PMID: 36403547 DOI: 10.1016/j.scr.2022.102965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022] Open
Abstract
A human induced pluripotent stem cell (hiPSC) line, KSCBi017-A, was generated from a 50-year-old male individual using non-integrating episomal vectors expressing reprogramming factors. The generated hiPSCs were integration-free, expressed pluripotency markers, exhibited the potential for differentiation into three germ layers in vivo, and maintained the normal karyotype. This cell line can be used as a control for a disease model and is available from Korea National Stem Cell Bank.
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Affiliation(s)
- Young Sam Im
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju-si, South Korea
| | - Dae Hoon Yoo
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju-si, South Korea
| | - Hyung-Eun Kim
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju-si, South Korea
| | - Ji Young Oh
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju-si, South Korea
| | - Yong-Ou Kim
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju-si, South Korea.
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2
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Episomes and Transposases-Utilities to Maintain Transgene Expression from Nonviral Vectors. Genes (Basel) 2022; 13:genes13101872. [PMID: 36292757 PMCID: PMC9601623 DOI: 10.3390/genes13101872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
The efficient delivery and stable transgene expression are critical for applications in gene therapy. While carefully selected and engineered viral vectors allowed for remarkable clinical successes, they still bear significant safety risks. Thus, nonviral vectors are a sound alternative and avoid genotoxicity and adverse immunological reactions. Nonviral vector systems have been extensively studied and refined during the last decades. Emerging knowledge of the epigenetic regulation of replication and spatial chromatin organisation, as well as new technologies, such as Crispr/Cas, were employed to enhance the performance of different nonviral vector systems. Thus, nonviral vectors are in focus and hold some promising perspectives for future applications in gene therapy. This review addresses three prominent nonviral vector systems: the Sleeping Beauty transposase, S/MAR-based episomes, and viral plasmid replicon-based EBV vectors. Exemplarily, we review different utilities, modifications, and new concepts that were pursued to overcome limitations regarding stable transgene expression and mitotic stability. New insights into the nuclear localisation of nonviral vector molecules and the potential consequences thereof are highlighted. Finally, we discuss the remaining limitations and provide an outlook on possible future developments in nonviral vector technology.
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3
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Im YS, Yoo DH, Kim HE, Oh JY, Kim YO. Generation of integration-free induced pluripotent stem cell line (KSCBi012-A) from urinary epithelial cells of a healthy male individual. Stem Cell Res 2022; 63:102841. [PMID: 35700632 DOI: 10.1016/j.scr.2022.102841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/12/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
A human induced pluripotent cell (hiPSC) line, KSCBi012-A, was generated from a 40-year-old male individual using non-integrating episomal vectors expressing reprogramming factors. The generated hiPSCs were integration-free, expressed pluripotency markers, exhibited the potential for differentiation into three germ layers in vivo, and maintained the normal karyotype. This cell line can be used as a control for a disease model and is available from Korea National Stem Cell Bank.
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Affiliation(s)
- Young Sam Im
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju, Republic of Korea
| | - Dae Hoon Yoo
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju, Republic of Korea
| | - Hyung-Eun Kim
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju, Republic of Korea
| | - Ji Young Oh
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju, Republic of Korea
| | - Yong-Ou Kim
- Division of Intractable Diseases Research, Korea National Institute of Health, Osong, Cheongju, Republic of Korea.
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4
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Roig-Merino A, Urban M, Bozza M, Peterson JD, Bullen L, Büchler-Schäff M, Stäble S, van der Hoeven F, Müller-Decker K, McKay TR, Milsom MD, Harbottle RP. An episomal DNA vector platform for the persistent genetic modification of pluripotent stem cells and their differentiated progeny. Stem Cell Reports 2021; 17:143-158. [PMID: 34942088 PMCID: PMC8758943 DOI: 10.1016/j.stemcr.2021.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/14/2022] Open
Abstract
The genetic modification of stem cells (SCs) is typically achieved using integrating vectors, whose potential integrative genotoxicity and propensity for epigenetic silencing during differentiation limit their application. The genetic modification of cells should provide sustainable levels of transgene expression, without compromising the viability of a cell or its progeny. We developed nonviral, nonintegrating, and autonomously replicating minimally sized DNA nanovectors to persistently genetically modify SCs and their differentiated progeny without causing any molecular or genetic damage. These DNA vectors are capable of efficiently modifying murine and human pluripotent SCs with minimal impact and without differentiation-mediated transgene silencing or vector loss. We demonstrate that these vectors remain episomal and provide robust and sustained transgene expression during self-renewal and targeted differentiation of SCs both in vitro and in vivo through embryogenesis and differentiation into adult tissues, without damaging their phenotypic characteristics. Nanovectors are used to engineer SCs efficiently, safely, and persistently Isogenic SC lines retain their capacity for self-renewal and pluripotency Nanovectors survive reprogramming and differentiation without loss or silencing Nanovectors are a universal genetic tool for the modification of any cell
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Affiliation(s)
- Alicia Roig-Merino
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Manuela Urban
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Matthias Bozza
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Julia D Peterson
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Louise Bullen
- Stem Cell Biology, Manchester Metropolitan University (MMU), Manchester M1 5GD, UK
| | - Marleen Büchler-Schäff
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (Hi-STEM), Heidelberg 69120, Germany; Division of Experimental Hematology, DKFZ, Heidelberg 69120, Germany
| | - Sina Stäble
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (Hi-STEM), Heidelberg 69120, Germany; Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, Heidelberg 69120, Germany
| | | | | | - Tristan R McKay
- Stem Cell Biology, Manchester Metropolitan University (MMU), Manchester M1 5GD, UK
| | - Michael D Milsom
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (Hi-STEM), Heidelberg 69120, Germany; Division of Experimental Hematology, DKFZ, Heidelberg 69120, Germany
| | - Richard P Harbottle
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
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5
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Yang J, Lee J, Land MA, Lai S, Igoshin OA, St-Pierre F. A synthetic circuit for buffering gene dosage variation between individual mammalian cells. Nat Commun 2021; 12:4132. [PMID: 34226556 PMCID: PMC8257781 DOI: 10.1038/s41467-021-23889-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Precise control of gene expression is critical for biological research and biotechnology. However, transient plasmid transfections in mammalian cells produce a wide distribution of copy numbers per cell, and consequently, high expression heterogeneity. Here, we report plasmid-based synthetic circuits - Equalizers - that buffer copy-number variation at the single-cell level. Equalizers couple a transcriptional negative feedback loop with post-transcriptional incoherent feedforward control. Computational modeling suggests that the combination of these two topologies enables Equalizers to operate over a wide range of plasmid copy numbers. We demonstrate experimentally that Equalizers outperform other gene dosage compensation topologies and produce as low cell-to-cell variation as chromosomally integrated genes. We also show that episome-encoded Equalizers enable the rapid generation of extrachromosomal cell lines with stable and uniform expression. Overall, Equalizers are simple and versatile devices for homogeneous gene expression and can facilitate the engineering of synthetic circuits that function reliably in every cell.
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Affiliation(s)
- Jin Yang
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jihwan Lee
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - Michelle A Land
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shujuan Lai
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, TX, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - François St-Pierre
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA.
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
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6
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Nassor F, Jarray R, Biard DSF, Maïza A, Papy-Garcia D, Pavoni S, Deslys JP, Yates F. Long Term Gene Expression in Human Induced Pluripotent Stem Cells and Cerebral Organoids to Model a Neurodegenerative Disease. Front Cell Neurosci 2020; 14:14. [PMID: 32116560 PMCID: PMC7026130 DOI: 10.3389/fncel.2020.00014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/20/2020] [Indexed: 11/19/2022] Open
Abstract
Human brain organoids (mini-brains) consist of self-organized three-dimensional (3D) neural tissue which can be derived from reprogrammed adult cells and maintained for months in culture. These 3D structures manifest substantial potential for the modeling of neurodegenerative diseases and pave the way for personalized medicine. However, as these 3D brain models can express the whole human genetic complexity, it is critical to have access to isogenic mini-brains that only differ in specific and controlled genetic variables. Genetic engineering based on retroviral vectors is incompatible with the long-term modeling needed here and implies a risk of random integration while methods using CRISPR-Cas9 are still too complex to adapt to stem cells. We demonstrate in this study that our strategy which relies on an episomal plasmid vector derived from the Epstein-Barr virus (EBV) offers a simple and robust approach, avoiding the remaining caveats of mini-brain models. For this proof-of-concept, we used a normal tau protein with a fluorescent tag and a mutant genetic form (P301S) leading to Fronto-Temporal Dementia. Isogenic cell lines were obtained which were stable for more than 30 passages expressing either form. We show that the presence of the plasmid in the cells does not interfere with the mini-brain differentiation protocol and obtain the development of a pathologically relevant phenotype in cerebral organoids, with pathological hyperphosphorylation of the tau protein. Such a simple and versatile genetic strategy opens up the full potential of human organoids to contribute to disease modeling, personalized medicine and testing of therapeutics.
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Affiliation(s)
- Ferid Nassor
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France.,CellTechs Laboratory, Sup'Biotech, Villejuif, France
| | - Rafika Jarray
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France.,CellTechs Laboratory, Sup'Biotech, Villejuif, France
| | - Denis S F Biard
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Auriane Maïza
- Glycobiology, Cell Growth, Tissue Repair and Regeneration (Gly-CRRET), UPEC 4397, Université Paris Est Créteil, Créteil, France
| | - Dulce Papy-Garcia
- Glycobiology, Cell Growth, Tissue Repair and Regeneration (Gly-CRRET), UPEC 4397, Université Paris Est Créteil, Créteil, France
| | - Serena Pavoni
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Jean-Philippe Deslys
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Frank Yates
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France.,CellTechs Laboratory, Sup'Biotech, Villejuif, France
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7
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Survivin Improves Reprogramming Efficiency of Human Neural Progenitors by Single Molecule OCT4. Stem Cells Int 2016; 2016:4729535. [PMID: 27974895 PMCID: PMC5128714 DOI: 10.1155/2016/4729535] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/01/2016] [Indexed: 12/11/2022] Open
Abstract
Induced pluripotent stem (iPS) cells have been generated from human somatic cells by ectopic expression of four Yamanaka factors. Here, we report that Survivin, an apoptosis inhibitor, can enhance iPS cells generation from human neural progenitor cells (NPCs) together with one factor OCT4 (1F-OCT4-Survivin). Compared with 1F-OCT4, Survivin accelerates the process of reprogramming from human NPCs. The neurocyte-originated induced pluripotent stem (NiPS) cells generated from 1F-OCT4-Survivin resemble human embryonic stem (hES) cells in morphology, surface markers, global gene expression profiling, and epigenetic status. Survivin keeps high expression in both iPS and ES cells. During the process of NiPS cell to neural cell differentiation, the expression of Survivin is rapidly decreased in protein level. The mechanism of Survivin promotion of reprogramming efficiency from NPCs may be associated with stabilization of β-catenin in WNT signaling pathway. This hypothesis is supported by experiments of RT-PCR, chromatin immune-precipitation, and Western blot in human ES cells. Our results showed overexpression of Survivin could improve the efficiency of reprogramming from NPCs to iPS cells by one factor OCT4 through stabilization of the key molecule, β-catenin.
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Ali Hosseini Rad SM, Bamdad T, Arefian E, Mossahebi-Mohammadi M, Sadeghizadeh M. An EBV-based plasmid can replicate and maintain in stem cells. Biotechnol Prog 2015; 31:1579-85. [PMID: 26260294 DOI: 10.1002/btpr.2153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/28/2015] [Indexed: 11/10/2022]
Abstract
Viral vectors have a wide range of applications in biology, particularly in gene therapy. Based on their integration capacity, viral vectors are classified as either integrating or non-integrating vectors. Although integrating vectors, such as lentivectors, have the ability to direct prolonged expression of exogenous genes, manipulation of the host genome is an inappropriate feature of these gene delivery tools. Non-integrating vectors, such as episomal replicating plasmids, can replicate and persist in host cells for long periods without any chromosomal interruption. These advantages made them good tools for gene induction purposes in gene therapy and basic studies. Due to the necessity of gene induction in stem cells for study of mammalian development and targeted differentiation, the use of integrating vectors for prolonged expression of genes of interest has been developed. Application of replicating plasmids can overcome some drawbacks associated with integrating vectors, although replication and maintenance of these plasmids can differ between cell types. Previously, it has been shown that such plasmids can be maintained in human embryonic stem cells for more than one month, but the rate of the plasmid replication during the host cell cycle has not been elucidated. In the present study, we showed that an EBV-based plasmid can replicate simultaneously with host in pluripotent and multipotent human and mouse stem cells and can be sustained for long time periods in dividing cells.
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Affiliation(s)
- Seyed Mohammad Ali Hosseini Rad
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, 14115-331, Iran.,Department of Molecular Biology and Genetic Engineering, Stem Cell Technology Research Center, Tehran, 1997775555, Iran
| | - Taravat Bamdad
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, 14115-331, Iran
| | - Ehsan Arefian
- Department of Molecular Biology and Genetic Engineering, Stem Cell Technology Research Center, Tehran, 1997775555, Iran.,Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, 14155-6455, Iran
| | - Majid Mossahebi-Mohammadi
- Department of Hematology and Blood Banking, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-175, Iran
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Fontes A, Lakshmipathy U. Advances in genetic modification of pluripotent stem cells. Biotechnol Adv 2013; 31:994-1001. [PMID: 23856320 DOI: 10.1016/j.biotechadv.2013.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 05/24/2013] [Accepted: 07/04/2013] [Indexed: 12/20/2022]
Abstract
Genetically engineered stem cells aid in dissecting basic cell function and are valuable tools for drug discovery, in vivo cell tracking, and gene therapy. Gene transfer into pluripotent stem cells has been a challenge due to their intrinsic feature of growing in clusters and hence not amenable to common gene delivery methods. Several advances have been made in the rapid assembly of DNA elements, optimization of culture conditions, and DNA delivery methods. This has lead to the development of viral and non-viral methods for transient or stable modification of cells, albeit with varying efficiencies. Most methods require selection and clonal expansion that demand prolonged culture and are not suited for cells with limited proliferative potential. Choosing the right platform based on preferred length, strength, and context of transgene expression is a critical step. Random integration of the transgene into the genome can be complicated due to silencing or altered regulation of expression due to genomic effects. An alternative to this are site-specific methods that target transgenes followed by screening to identify the genomic loci that support long-term expression with stem cell proliferation and differentiation. A highly precise and accurate editing of the genome driven by homology can be achieved using traditional methods as well as the newer technologies such as zinc finger nuclease, TAL effector nucleases and CRISPR. In this review, we summarize the different genetic engineering methods that have been successfully used to create modified embryonic and induced pluripotent stem cells.
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Affiliation(s)
- Andrew Fontes
- Primary and Stem Cell Systems, Life Technologies, 5781 Van Allen Way, Carlsbad, CA 92008, USA
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10
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Stable transfection using episomal vectors to create modified human embryonic stem cells. Methods Mol Biol 2013. [PMID: 23546763 DOI: 10.1007/978-1-62703-348-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Gene delivery into stem cells can be achieved using viral and nonviral methods. Nonviral methods are more appealing and the use of episomal vectors that do not integrate into the genome enables expression of transgene that are not subject to genomic loci effects that could affect expression levels. Here we describe in detail transfection and stable pooled clone creation of human embryonic stem cells with episomal vectors.
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