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Hartley A, Burger L, Wincek CL, Dons L, Li T, Grewenig A, Taşgın T, Urban M, Roig-Merino A, Ghazvini M, Harbottle RP. A Simple Nonviral Method to Generate Human Induced Pluripotent Stem Cells Using SMAR DNA Vectors. Genes (Basel) 2024; 15:575. [PMID: 38790204 PMCID: PMC11121542 DOI: 10.3390/genes15050575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) are a powerful tool for biomedical research, but their production presents challenges and safety concerns. Yamanaka and Takahashi revolutionised the field by demonstrating that somatic cells could be reprogrammed into pluripotent cells by overexpressing four key factors for a sufficient time. iPSCs are typically generated using viruses or virus-based methods, which have drawbacks such as vector persistence, risk of insertional mutagenesis, and oncogenesis. The application of less harmful nonviral vectors is limited as conventional plasmids cannot deliver the levels or duration of the factors necessary from a single transfection. Hence, plasmids that are most often used for reprogramming employ the potentially oncogenic Epstein-Barr nuclear antigen 1 (EBNA-1) system to ensure adequate levels and persistence of expression. In this study, we explored the use of nonviral SMAR DNA vectors to reprogram human fibroblasts into iPSCs. We show for the first time that iPSCs can be generated using nonviral plasmids without the use of EBNA-1 and that these DNA vectors can provide sufficient expression to induce pluripotency. We describe an optimised reprogramming protocol using these vectors that can produce high-quality iPSCs with comparable pluripotency and cellular function to those generated with viruses or EBNA-1 vectors.
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Affiliation(s)
- Anna Hartley
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Luisa Burger
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Cornelia L. Wincek
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
| | - Lieke Dons
- Erasmus MC iPS Core Facility, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands (M.G.)
| | - Tracy Li
- Erasmus MC iPS Core Facility, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands (M.G.)
| | - Annabel Grewenig
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
| | - Toros Taşgın
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Manuela Urban
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Alicia Roig-Merino
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Mehrnaz Ghazvini
- Erasmus MC iPS Core Facility, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands (M.G.)
| | - Richard P. Harbottle
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
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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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Xu ZJ, Jia YL, Wang M, Yi DD, Zhang WL, Wang XY, Zhang JH. Effect of promoter, promoter mutation and enhancer on transgene expression mediated by episomal vectors in transfected HEK293, Chang liver and primary cells. Bioengineered 2020; 10:548-560. [PMID: 31668126 PMCID: PMC6844389 DOI: 10.1080/21655979.2019.1684863] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The episomal vector cannot integrate into the host cell chromosome, which has no potential risk in gene therapy. However, the low level of transgene expression driven by episomal vectors needs to be solved. In this study, we investigated the effects of enhancers, promoters and promoter variants on transgene expression levels driven by episomal vectors in HEK293, Chang liver and primary cells. Results showed that all eight cis-acting elements used could increase transfection efficiency and transient eGFP expression in transfected HEK293 and Chang liver cells. In stably transfected mammalian cells, the elongation factor-1 alpha (EF-1α) promoter and mutant-404 showed high and stable transgene expression. The mechanisms might be related to the type and quantity of transcription factor regulatory elements. Moreover, quantitative reverse transcription polymerase chain reaction analysis showed that mRNA expression levels were not directly proportional to protein expression levels. Furthermore, the EF-1α promoter conferred high transgene expression levels in primary cells, and the plasmid was also present in the episomal state. Taken together, these results provided valuable information for improving transgene expression with episomal vectors in mammalian cells.
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Affiliation(s)
- Zhong-Jie Xu
- Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yan-Long Jia
- Pharmacy collage, Xinxiang Medical University, Xinxiang, Henan, China
| | - Meng Wang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Dan-Dan Yi
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China.,Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Wei-Li Zhang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China.,Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiao-Yin Wang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China.,Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Jun-He Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
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4
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Stavrou EF, Simantirakis E, Verras M, Barbas C, Vassilopoulos G, Peterson KR, Athanassiadou A. Episomal vectors based on S/MAR and the β-globin Replicator, encoding a synthetic transcriptional activator, mediate efficient γ-globin activation in haematopoietic cells. Sci Rep 2019; 9:19765. [PMID: 31874995 PMCID: PMC6930265 DOI: 10.1038/s41598-019-56056-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 11/30/2019] [Indexed: 12/19/2022] Open
Abstract
We report the development of episomal vectors for the specific γ-globin transcription activation in its native position by activator Zif-VP64, based on the Scaffold/Matrix Attachment Region (S/MAR) for episomal retention and the β-globin Replicator, the DNA replication-Initiation Region from the β-globin locus. Vector Zif-VP64-Ep1 containing transcription cassettes CMV- Zif-VP64 and CMV-eGFP-S/MAR transfected a)K562 cells; b)murine β-YAC bone marrow cells (BMC); c)human haematopoietic progenitor CD34+ cells, with transfection efficiencies of 46.3 ± 5.2%, 23.0 ± 2.1% and 24.2 ± 2.4% respectively. K562 transfections generated stable cell lines running for 28 weeks with and without selection, with increased levels of γ-globin mRNA by 3.3 ± 0.13, of γ-globin protein by 6.75 ± 3.25 and HbF protein by 2 ± 0.2 fold, while the vector remained episomal and non integrated. In murine β-YAC BMCs the vector mediated the activation of the silent human γ-globin gene and in CD34+ cells, increased γ-globin mRNA, albeit only transiently. A second vector Zif-VP64-Ep2, with both transcription cassettes carrying promoter SFFV instead of CMV and the addition of β-globin Replicator, transferred into CD34+ cells, produced CD34+ eGFP+ cells, that generated colonies in colony forming cell cultures. Importantly, these were 100% fluorescent, with 2.11 ± 0.13 fold increased γ-globin mRNA, compared to non-transfected cells. We consider these episomal vectors valid, safer alternatives to viral vectors.
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Affiliation(s)
- Eleana F Stavrou
- Department of General Biology, School of Medicine, University of Patras, Patras, Greece.
| | - Emannuouil Simantirakis
- Hematology Clinic, Medical School, University of Thessaly and Gene and Cell Therapy Laboratory, BRFAA, Athens, Greece
| | - Meletios Verras
- Department of General Biology, School of Medicine, University of Patras, Patras, Greece
| | - Carlos Barbas
- Skaggs Institute for Chemical Biology, Department of Molecular Biology, Scripps Research Institute, La Jolla, California, USA
| | - George Vassilopoulos
- Hematology Clinic, Medical School, University of Thessaly and Gene and Cell Therapy Laboratory, BRFAA, Athens, Greece
| | - Kenneth R Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aglaia Athanassiadou
- Department of General Biology, School of Medicine, University of Patras, Patras, Greece.
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5
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Wang XY, Zhang X, Wang TY, Jia YL, Xu DH, Yi DD. Shortened nuclear matrix attachment regions are sufficient for replication and maintenance of episomes in mammalian cells. Mol Biol Cell 2019; 30:2761-2770. [PMID: 31509492 PMCID: PMC6789156 DOI: 10.1091/mbc.e19-02-0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Matrix attachment regions (MARs) can mediate the replication of vector episomes in mammalian cells; however, the molecular mode of action remains unclear. Here, we assessed the characteristics of MARs and the mechanism that mediates episomal vector replication in mammalian cells. Five shortened subfragments of β-interferon MAR fragments were cloned and transferred into CHO cells, and transgene expression levels, presence of the gene, and the episomal maintenance mechanism were determined. Three shortened MAR derivatives (position 781–1320, 1201–1740, and 1621–2201) retained full MAR activity and mediated episomal vector replication. Moreover, the three shortened MARs showed higher transgene expression levels, greater efficiency in colony formation, and more persistent transgene expression compared with those of the original pEPI-1 plasmid, and three functional truncated MARs can bind to SAF-A MAR-binding protein. These results suggest that shortened MARs are sufficient for replication and maintenance of episomes in CHO cells.
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Affiliation(s)
- Xiao-Yin Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang 453003, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Xi Zhang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang 453003, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Yan-Long Jia
- Pharmacy Collage, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Dan-Hua Xu
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang 453003, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Dan-Dan Yi
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang 453003, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
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Sánchez-Hernández S, Gutierrez-Guerrero A, Martín-Guerra R, Cortijo-Gutierrez M, Tristán-Manzano M, Rodriguez-Perales S, Sanchez L, Garcia-Perez JL, Chato-Astrain J, Fernandez-Valades R, Carrillo-Galvez AB, Anderson P, Montes R, Real PJ, Martin F, Benabdellah K. The IS2 Element Improves Transcription Efficiency of Integration-Deficient Lentiviral Vector Episomes. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:16-28. [PMID: 30227274 PMCID: PMC6141704 DOI: 10.1016/j.omtn.2018.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 07/02/2018] [Accepted: 08/14/2018] [Indexed: 02/06/2023]
Abstract
Integration-defective lentiviral vectors (IDLVs) have become an important alternative tool for gene therapy applications and basic research. Unfortunately, IDLVs show lower transgene expression as compared to their integrating counterparts. In this study, we aimed to improve the expression levels of IDLVs by inserting the IS2 element, which harbors SARs and HS4 sequences, into their LTRs (SE-IS2-IDLVs). Contrary to our expectations, the presence of the IS2 element did not abrogate epigenetic silencing by histone deacetylases. In addition, the IS2 element reduced episome levels in IDLV-transduced cells. Interestingly, despite these negative effects, SE-IS2-IDLVs outperformed SE-IDLVs in terms of percentage and expression levels of the transgene in several cell lines, including neurons, neuronal progenitor cells, and induced pluripotent stem cells. We estimated that the IS2 element enhances the transcriptional activity of IDLV LTR circles 6- to 7-fold. The final effect the IS2 element in IDLVs will greatly depend on the target cell and the balance between the negative versus the positive effects of the IS2 element in each cell type. The better performance of SE-IS2-IDLVs was not due to improved stability or differences in the proportions of 1-LTR versus 2-LTR circles but probably to a re-positioning of IS2-episomes into transcriptionally active regions.
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Affiliation(s)
- Sabina Sánchez-Hernández
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Alejandra Gutierrez-Guerrero
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Rocío Martín-Guerra
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Marina Cortijo-Gutierrez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - María Tristán-Manzano
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Department, CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - Laura Sanchez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Jose Luis Garcia-Perez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Jesus Chato-Astrain
- Department of Histology, Tissue Engineering Group, University of Granada, Granada, Spain
| | - Ricardo Fernandez-Valades
- Pediatric Surgery Department, University Hospital "Virgen de las Nieves," Avda. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Ana Belén Carrillo-Galvez
- Oncology Department, GENYO, Centre for Genomics and Oncology, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Per Anderson
- LentiStem Biotech, GENYO, Avda. de la Ilustración 114, 18016 PTS Granada, Spain; Oncology Department, GENYO, Centre for Genomics and Oncology, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Rosa Montes
- Oncology Department, GENYO, Centre for Genomics and Oncology, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Pedro J Real
- Oncology Department, GENYO, Centre for Genomics and Oncology, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; Departament of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Francisco Martin
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; LentiStem Biotech, GENYO, Avda. de la Ilustración 114, 18016 PTS Granada, Spain.
| | - Karim Benabdellah
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; LentiStem Biotech, GENYO, Avda. de la Ilustración 114, 18016 PTS Granada, Spain.
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7
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Assembly and Functional Analysis of an S/MAR Based Episome with the Cystic Fibrosis Transmembrane Conductance Regulator Gene. Int J Mol Sci 2018; 19:ijms19041220. [PMID: 29673202 PMCID: PMC5979583 DOI: 10.3390/ijms19041220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 12/24/2022] Open
Abstract
Improving the efficacy of gene therapy vectors is still an important goal toward the development of safe and efficient gene therapy treatments. S/MAR (scaffold/matrix attached region)-based vectors are maintained extra-chromosomally in numerous cell types, which is similar to viral-based vectors. Additionally, when established as an episome, they show a very high mitotic stability. In the present study we tested the idea that addition of an S/MAR element to a CFTR (cystic fibrosis transmembrane conductance regulator) expression vector, may allow the establishment of a CFTR episome in bronchial epithelial cells. Starting from the observation that the S/MAR vector pEPI-EGFP (enhanced green fluorescence protein) is maintained as an episome in human bronchial epithelial cells, we assembled the CFTR vector pBQ-S/MAR. This vector, transfected in bronchial epithelial cells with mutated CFTR, supported long term wt CFTR expression and activity, which in turn positively impacted on the assembly of tight junctions in polarized epithelial cells. Additionally, the recovery of intact pBQ-S/MAR, but not the parental vector lacking the S/MAR element, from transfected cells after extensive proliferation, strongly suggested that pBQ-S/MAR was established as an episome. These results add a new element, the S/MAR, that can be considered to improve the persistence and safety of gene therapy vectors for cystic fibrosis pulmonary disease.
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8
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Chen F, Qi X, Zhang R, Wu ZY, Yan CE, Li J, Liu QY, Qi J. Episomal lentiviral vectors confer erythropoietin expression in dividing cells. Plasmid 2017; 90:15-19. [PMID: 28189631 DOI: 10.1016/j.plasmid.2017.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 02/05/2017] [Accepted: 02/07/2017] [Indexed: 01/07/2023]
Abstract
Lentiviral vectors are now widely considered as one of the most common gene delivery tools for dividing and non-dividing cells. However, insertional mutagenesis has been found in clinical trials with retroviral vectors, which poses a safety risk. The use of non-integrating lentiviral (NIL) vectors, which avoid integration, eliminates the insertional mutagenesis problem. These NIL vectors are unable to mediate stable gene delivery into dividing cells, which makes them of limited use in the clinical practice of gene therapy. In this study, we constructed a NIL vector which harbors the scaffold/matrix attachment region (S/MAR) sequence and a therapeutic gene. NIL retained episomal erythropoietin (EPO) gene expression for 74days in dividing cells both with and without selection. Furthermore, Southern blot analysis showed that the NIL vector was retained extrachromosomally in CHO cells. In conclusion, the NIL vector based on an S/MAR sequence retained the extrachromosomal expression of a therapeutic gene in dividing cells. Our results show that NIL vectors maybe a safe and effective means of gene delivery, which is of potential clinical significance.
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Affiliation(s)
- Feng Chen
- Department of Clinical Laboratory, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 10021, PR China.
| | - Xin Qi
- Department of Clinical Laboratory, China-Japan Union Hospital of Jilin University, Changchun 130031, Jilin, PR China
| | - Rong Zhang
- Department of Clinical Laboratory, Central Hospital of Qingdao, Qingdao 266042, Shandong, PR China
| | - Zong-Yong Wu
- Department of Clinical Laboratory, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 10021, PR China
| | - Cui-E Yan
- Department of Clinical Laboratory, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 10021, PR China
| | - Jia Li
- Department of Clinical Laboratory, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 10021, PR China
| | - Qiu-Ying Liu
- Department of Clinical Laboratory, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 10021, PR China
| | - Jun Qi
- Department of Clinical Laboratory, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 10021, PR China
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9
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Šimčíková M, Prather KLJ, Prazeres DMF, Monteiro GA. Towards effective non-viral gene delivery vector. Biotechnol Genet Eng Rev 2017; 31:82-107. [PMID: 27160661 DOI: 10.1080/02648725.2016.1178011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Despite very good safety records, clinical trials using plasmid DNA failed due to low transfection efficiency and brief transgene expression. Although this failure is both due to poor plasmid design and to inefficient delivery methods, here we will focus on the former. The DNA elements like CpG motifs, selection markers, origins of replication, cryptic eukaryotic signals or nuclease-susceptible regions and inverted repeats showed detrimental effects on plasmids' performance as biopharmaceuticals. On the other hand, careful selection of promoter, polyadenylation signal, codon optimization and/or insertion of introns or nuclear-targeting sequences for therapeutic protein expression can enhance the clinical efficacy. Minimal vectors, which are devoid of the bacterial backbone and consist exclusively of the eukaryotic expression cassette, demonstrate better performance in terms of expression levels, bioavailability, transfection rates and increased therapeutic effects. Although the results are promising, minimal vectors have not taken over the conventional plasmids in clinical trials due to challenging manufacturing issues.
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Affiliation(s)
- Michaela Šimčíková
- a MIT-Portugal Program.,b iBB-Institute for Bioengineering and Biosciences , Lisbon , Portugal
| | - Kristala L J Prather
- a MIT-Portugal Program.,c Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Duarte M F Prazeres
- a MIT-Portugal Program.,c Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Department of Bioengineering , Instituto Superior Técnico , Lisbon , Portugal
| | - Gabriel A Monteiro
- a MIT-Portugal Program.,c Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Department of Bioengineering , Instituto Superior Técnico , Lisbon , Portugal
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10
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Xu Z, Chen F, Zhang L, Lu J, Xu P, Liu G, Xie X, Mu W, Wang Y, Liu D. Non-integrating lentiviral vectors based on the minimal S/MAR sequence retain transgene expression in dividing cells. SCIENCE CHINA-LIFE SCIENCES 2016; 59:1024-1033. [PMID: 27614752 DOI: 10.1007/s11427-016-0067-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/21/2016] [Indexed: 01/10/2023]
Abstract
Safe and efficient gene transfer systems are the basis of gene therapy applications. Non-integrating lentiviral (NIL) vectors are among the most promising candidates for gene transfer tools, because they exhibit high transfer efficiency in both dividing and non-dividing cells and do not present a risk of insertional mutagenesis. However, non-integrating lentiviral vectors cannot introduce stable exogenous gene expression to dividing cells, thereby limiting their application. Here, we report the design of a non-integrating lentiviral vector that contains the minimal scaffold/matrix attachment region (S/MAR) sequence (SNIL), and this SNIL vector is able to retain episomal transgene expression in dividing cells. Using SNIL vectors, we detected the expression of the eGFP gene for 61 days in SNIL-transduced stable CHO cells, either with selection or not. In the NIL group without the S/MAR sequence, however, the transduced cells died under selection for the transient expression of NIL vectors. Furthermore, Southern blot assays demonstrated that the SNIL vectors were retained extrachromosomally in the CHO cells. In conclusion, the minimal S/MAR sequence retained the non-integrating lentiviral vectors in dividing cells, which indicates that SNIL vectors have the potential for use as a gene transfer tool.
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Affiliation(s)
- Zhen Xu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Feng Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Lingling Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Jing Lu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Peng Xu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Guang Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Xuemin Xie
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Wenli Mu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Yajun Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Depei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
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Harraghy N, Calabrese D, Fisch I, Girod PA, LeFourn V, Regamey A, Mermod N. Epigenetic regulatory elements: Recent advances in understanding their mode of action and use for recombinant protein production in mammalian cells. Biotechnol J 2015; 10:967-78. [DOI: 10.1002/biot.201400649] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/20/2015] [Accepted: 05/20/2015] [Indexed: 12/18/2022]
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12
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Lin Y, Li Z, Wang T, Wang X, Wang L, Dong W, Jing C, Yang X. MAR characteristic motifs mediate episomal vector in CHO cells. Gene 2015; 559:137-43. [DOI: 10.1016/j.gene.2015.01.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/05/2015] [Accepted: 01/13/2015] [Indexed: 01/24/2023]
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13
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Verghese SC, Goloviznina NA, Skinner AM, Lipps HJ, Kurre P. S/MAR sequence confers long-term mitotic stability on non-integrating lentiviral vector episomes without selection. Nucleic Acids Res 2014; 42:e53. [PMID: 24474068 PMCID: PMC3985655 DOI: 10.1093/nar/gku082] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/27/2013] [Accepted: 01/06/2014] [Indexed: 01/11/2023] Open
Abstract
Insertional oncogene activation and aberrant splicing have proved to be major setbacks for retroviral stem cell gene therapy. Integrase-deficient human immunodeficiency virus-1-derived vectors provide a potentially safer approach, but their circular genomes are rapidly lost during cell division. Here we describe a novel lentiviral vector (LV) that incorporates human ß-interferon scaffold/matrix-associated region sequences to provide an origin of replication for long-term mitotic maintenance of the episomal LTR circles. The resulting 'anchoring' non-integrating lentiviral vector (aniLV) achieved initial transduction rates comparable with integrating vector followed by progressive establishment of long-term episomal expression in a subset of cells. Analysis of aniLV-transduced single cell-derived clones maintained without selective pressure for >100 rounds of cell division showed sustained transgene expression from episomes and provided molecular evidence for long-term episome maintenance. To evaluate aniLV performance in primary cells, we transduced lineage-depleted murine hematopoietic progenitor cells, observing GFP expression in clonogenic progenitor colonies and peripheral blood leukocyte chimerism following transplantation into conditioned hosts. In aggregate, our studies suggest that scaffold/matrix-associated region elements can serve as molecular anchors for non-integrating lentivector episomes, providing sustained gene expression through successive rounds of cell division and progenitor differentiation in vitro and in vivo.
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Affiliation(s)
- Santhosh Chakkaramakkil Verghese
- Department of Pediatrics, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR 97239, USA, Department of Surgery/Surgical Oncology, Oregon Health & Science University, Portland, OR 97239, USA, Center for Biomedical Education and Research, Institute of Cell Biology, University of Witten/Herdecke, Witten 58453, Germany, Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA and Department of Cell & Developmental Biology Oregon Health & Science University, Portland, OR 97239, USA
| | - Natalya A. Goloviznina
- Department of Pediatrics, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR 97239, USA, Department of Surgery/Surgical Oncology, Oregon Health & Science University, Portland, OR 97239, USA, Center for Biomedical Education and Research, Institute of Cell Biology, University of Witten/Herdecke, Witten 58453, Germany, Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA and Department of Cell & Developmental Biology Oregon Health & Science University, Portland, OR 97239, USA
| | - Amy M. Skinner
- Department of Pediatrics, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR 97239, USA, Department of Surgery/Surgical Oncology, Oregon Health & Science University, Portland, OR 97239, USA, Center for Biomedical Education and Research, Institute of Cell Biology, University of Witten/Herdecke, Witten 58453, Germany, Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA and Department of Cell & Developmental Biology Oregon Health & Science University, Portland, OR 97239, USA
| | - Hans J. Lipps
- Department of Pediatrics, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR 97239, USA, Department of Surgery/Surgical Oncology, Oregon Health & Science University, Portland, OR 97239, USA, Center for Biomedical Education and Research, Institute of Cell Biology, University of Witten/Herdecke, Witten 58453, Germany, Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA and Department of Cell & Developmental Biology Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter Kurre
- Department of Pediatrics, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR 97239, USA, Department of Surgery/Surgical Oncology, Oregon Health & Science University, Portland, OR 97239, USA, Center for Biomedical Education and Research, Institute of Cell Biology, University of Witten/Herdecke, Witten 58453, Germany, Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR 97239, USA and Department of Cell & Developmental Biology Oregon Health & Science University, Portland, OR 97239, USA
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Hagedorn C, Baiker A, Postberg J, Ehrhardt A, Lipps HJ. Handling S/MAR vectors. Cold Spring Harb Protoc 2012; 2012:657-63. [PMID: 22661441 DOI: 10.1101/pdb.top068262] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nonviral episomal vectors represent attractive alternatives to currently used virus-based expression systems. In the late 1990s, it was shown that a plasmid containing an expression cassette linked to a scaffold/matrix attached region (S/MAR) replicates as a low copy number episome in all cell lines tested, as well as primary cells, and can be used for the genetic modification of higher animals. Once established in the cell, the S/MAR vector replicates early during S-phase and, in the absence of selection, is stably retained in the cells for an unlimited period of time. This vector can therefore be regarded as a minimal model system for studying the epigenetic regulation of replication and functional nuclear architecture. In theory, this construct represents an almost "ideal" expression system for gene therapy. In practice, S/MAR-based vectors stably modify mammalian cells with efficiencies far below those of virus-based constructs. Consequently, they have not yet found application in gene therapy trials. Furthermore, S/MAR vector systems are not trivial to handle and several critical technical issues have to be considered when modifying these vectors for various applications.
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Affiliation(s)
- Claudia Hagedorn
- Centre for Biomedical Education and Research, Institute of Cell Biology, University of Witten/Herdecke, 58453 Witten, Germany
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15
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Ivics Z, Izsvák Z. Nonviral gene delivery with the sleeping beauty transposon system. Hum Gene Ther 2012; 22:1043-51. [PMID: 21867398 DOI: 10.1089/hum.2011.143] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Effective gene therapy requires robust delivery of therapeutic genes into relevant target cells, long-term gene expression, and minimal risks of secondary effects. Nonviral gene transfer approaches typically result in only short-lived transgene expression in primary cells, because of the lack of nuclear maintenance of the vector over several rounds of cell division. The development of efficient and safe nonviral vectors armed with an integrating feature would thus greatly facilitate clinical gene therapy studies. The latest generation transposon technology based on the Sleeping Beauty (SB) transposon may potentially overcome some of these limitations. SB was shown to provide efficient stable gene transfer and sustained transgene expression in primary cell types, including human hematopoietic progenitors, mesenchymal stem cells, muscle stem/progenitor cells (myoblasts), induced pluripotent stem cells, and T cells. These cells are relevant targets for stem cell biology, regenerative medicine, and gene- and cell-based therapies of complex genetic diseases. Moreover, the first-in-human clinical trial has been launched to use redirected T cells engineered with SB for gene therapy of B cell lymphoma. We discuss aspects of cellular delivery of the SB transposon system, transgene expression provided by integrated transposon vectors, target site selection of the transposon vectors, and potential risks associated with random genomic insertion.
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Affiliation(s)
- Zoltán Ivics
- Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany.
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Coutelle C, Waddington SN. Vector systems for prenatal gene therapy: choosing vectors for different applications. Methods Mol Biol 2012; 891:41-53. [PMID: 22648767 DOI: 10.1007/978-1-61779-873-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This chapter gives a comparative review of the different vector systems applied to date in prenatal gene therapy experiments highlighting the need for versatility and choice for application in accordance with the actual aim of the study. It reviews the key characteristics of the four main gene therapy vector systems and gives examples for their successful application in prenatal gene therapy experiments.
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Affiliation(s)
- Charles Coutelle
- National Heart and Lung Institute, Molecular and Cellular Medicine Section, Imperial College London, London, UK.
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