1
|
Wang F, Huang Y, Li J, Zhou W, Wang W. Targeted gene delivery systems for T-cell engineering. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00954-6. [PMID: 38753155 DOI: 10.1007/s13402-024-00954-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2024] [Indexed: 06/27/2024] Open
Abstract
T lymphocytes are indispensable for the host systems of defense against pathogens, tumors, and environmental threats. The therapeutic potential of harnessing the cytotoxic properties of T lymphocytes for antigen-specific cell elimination is both evident and efficacious. Genetically engineered T-cells, such as those employed in CAR-T and TCR-T cell therapies, have demonstrated significant clinical benefits in treating cancer and autoimmune disorders. However, the current landscape of T-cell genetic engineering is dominated by strategies that necessitate in vitro T-cell isolation and modification, which introduce complexity and prolong the development timeline of T-cell based immunotherapies. This review explores the complexities of gene delivery systems designed for T cells, covering both viral and nonviral vectors. Viral vectors are known for their high transduction efficiency, yet they face significant limitations, such as potential immunogenicity and the complexities involved in large-scale production. Nonviral vectors, conversely, offer a safer profile and the potential for scalable manufacturing, yet they often struggle with lower transduction efficiency. The pursuit of gene delivery systems that can achieve targeted gene transfer to T cell without the need for isolation represents a significant advancement in the field. This review assesses the design principles and current research progress of such systems, highlighting the potential for in vivo gene modification therapies that could revolutionize T-cell based treatments. By providing a comprehensive analysis of these systems, we aim to contribute valuable insights into the future development of T-cell immunotherapy.
Collapse
Affiliation(s)
- Fengling Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Yong Huang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - JiaQian Li
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Weilin Zhou
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Wei Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| |
Collapse
|
2
|
Kovač A, Miskey C, Ivics Z. Sleeping Beauty Transposon Insertions into Nucleolar DNA by an Engineered Transposase Localized in the Nucleolus. Int J Mol Sci 2023; 24:14978. [PMID: 37834425 PMCID: PMC10573994 DOI: 10.3390/ijms241914978] [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: 06/06/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Transposons are nature's gene delivery vehicles that can be harnessed for experimental and therapeutic purposes. The Sleeping Beauty (SB) transposon shows efficient transposition and long-term transgene expression in human cells, and is currently under clinical development for gene therapy. SB transposition occurs into the human genome in a random manner, which carries a risk of potential genotoxic effects associated with transposon integration. Here, we evaluated an experimental strategy to manipulate SB's target site distribution by preferentially compartmentalizing the SB transposase to the nucleolus, which contains repetitive ribosomal RNA (rRNA) genes. We generated a fusion protein composed of the nucleolar protein nucleophosmin (B23) and the SB100X transposase, which was found to retain almost full transposition activity as compared to unfused transposase and to be predominantly localized to nucleoli in transfected human cells. Analysis of transposon integration sites generated by B23-SB100X revealed a significant enrichment into the p-arms of chromosomes containing nucleolus organizing regions (NORs), with preferential integration into the p13 and p11.2 cytobands directly neighboring the NORs. This bias in the integration pattern was accompanied by an enrichment of insertions into nucleolus-associated chromatin domains (NADs) at the periphery of nucleolar DNA and into lamina-associated domains (LADs). Finally, sub-nuclear targeting of the transposase resulted in preferential integration into chromosomal domains associated with the Upstream Binding Transcription Factor (UBTF) that plays a critical role in the transcription of 47S rDNA gene repeats of the NORs by RNA Pol I. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.
Collapse
Affiliation(s)
| | | | - Zoltán Ivics
- Transposition and Genome Engineering, Research Centre of the Division of Hematology, Gene and Cell Therapy, Paul Ehrlich Institute, Paul Ehrlich Str. 51–59, D-63225 Langen, Germany; (A.K.); (C.M.)
| |
Collapse
|
3
|
Harmening N, Johnen S, Izsvák Z, Ivics Z, Kropp M, Bascuas T, Walter P, Kreis A, Pajic B, Thumann G. Enhanced Biosafety of the Sleeping Beauty Transposon System by Using mRNA as Source of Transposase to Efficiently and Stably Transfect Retinal Pigment Epithelial Cells. Biomolecules 2023; 13:biom13040658. [PMID: 37189405 DOI: 10.3390/biom13040658] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
Neovascular age-related macular degeneration (nvAMD) is characterized by choroidal neovascularization (CNV), which leads to retinal pigment epithelial (RPE) cell and photoreceptor degeneration and blindness if untreated. Since blood vessel growth is mediated by endothelial cell growth factors, including vascular endothelial growth factor (VEGF), treatment consists of repeated, often monthly, intravitreal injections of anti-angiogenic biopharmaceuticals. Frequent injections are costly and present logistic difficulties; therefore, our laboratories are developing a cell-based gene therapy based on autologous RPE cells transfected ex vivo with the pigment epithelium derived factor (PEDF), which is the most potent natural antagonist of VEGF. Gene delivery and long-term expression of the transgene are enabled by the use of the non-viral Sleeping Beauty (SB100X) transposon system that is introduced into the cells by electroporation. The transposase may have a cytotoxic effect and a low risk of remobilization of the transposon if supplied in the form of DNA. Here, we investigated the use of the SB100X transposase delivered as mRNA and showed that ARPE-19 cells as well as primary human RPE cells were successfully transfected with the Venus or the PEDF gene, followed by stable transgene expression. In human RPE cells, secretion of recombinant PEDF could be detected in cell culture up to one year. Non-viral ex vivo transfection using SB100X-mRNA in combination with electroporation increases the biosafety of our gene therapeutic approach to treat nvAMD while ensuring high transfection efficiency and long-term transgene expression in RPE cells.
Collapse
Affiliation(s)
- Nina Harmening
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Zoltan Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Martina Kropp
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Thais Bascuas
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Peter Walter
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Andreas Kreis
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Bojan Pajic
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
- Eye Clinic ORASIS, Swiss Eye Research Foundation, 5734 Reinach, Switzerland
- Faculty of Sciences, Department of Physics, University of Novi Sad, Trg Dositeja Obradovica 4, 21000 Novi Sad, Serbia
- Faculty of Medicine of the Military Medical Academy, University of Defense, 11000 Belgrade, Serbia
| | - Gabriele Thumann
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| |
Collapse
|
4
|
Tsai HC, Pietrobon V, Peng M, Wang S, Zhao L, Marincola FM, Cai Q. Current strategies employed in the manipulation of gene expression for clinical purposes. J Transl Med 2022; 20:535. [PMID: 36401279 PMCID: PMC9673226 DOI: 10.1186/s12967-022-03747-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
Abnormal gene expression level or expression of genes containing deleterious mutations are two of the main determinants which lead to genetic disease. To obtain a therapeutic effect and thus to cure genetic diseases, it is crucial to regulate the host's gene expression and restore it to physiological conditions. With this purpose, several molecular tools have been developed and are currently tested in clinical trials. Genome editing nucleases are a class of molecular tools routinely used in laboratories to rewire host's gene expression. Genome editing nucleases include different categories of enzymes: meganucleses (MNs), zinc finger nucleases (ZFNs), clustered regularly interspaced short palindromic repeats (CRISPR)- CRISPR associated protein (Cas) and transcription activator-like effector nuclease (TALENs). Transposable elements are also a category of molecular tools which includes different members, for example Sleeping Beauty (SB), PiggyBac (PB), Tol2 and TcBuster. Transposons have been used for genetic studies and can serve as gene delivery tools. Molecular tools to rewire host's gene expression also include episomes, which are divided into different categories depending on their molecular structure. Finally, RNA interference is commonly used to regulate gene expression through the administration of small interfering RNA (siRNA), short hairpin RNA (shRNA) and bi-functional shRNA molecules. In this review, we will describe the different molecular tools that can be used to regulate gene expression and discuss their potential for clinical applications. These molecular tools are delivered into the host's cells in the form of DNA, RNA or protein using vectors that can be grouped into physical or biochemical categories. In this review we will also illustrate the different types of payloads that can be used, and we will discuss recent developments in viral and non-viral vector technology.
Collapse
Affiliation(s)
| | | | - Maoyu Peng
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | - Suning Wang
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | - Lihong Zhao
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | | | - Qi Cai
- Kite Pharma Inc, Santa Monica, CA, 90404, USA.
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Miskey C, Kesselring L, Querques I, Abrusán G, Barabas O, Ivics Z. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2807-2825. [PMID: 35188569 PMCID: PMC8934666 DOI: 10.1093/nar/gkac092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/14/2022] Open
Abstract
The Sleeping Beauty (SB) transposon system is a popular tool for genome engineering, but random integration into the genome carries a certain genotoxic risk in therapeutic applications. Here we investigate the role of amino acids H187, P247 and K248 in target site selection of the SB transposase. Structural modeling implicates these three amino acids located in positions analogous to amino acids with established functions in target site selection in retroviral integrases and transposases. Saturation mutagenesis of these residues in the SB transposase yielded variants with altered target site selection properties. Transposon integration profiling of several mutants reveals increased specificity of integrations into palindromic AT repeat target sequences in genomic regions characterized by high DNA bendability. The H187V and K248R mutants redirect integrations away from exons, transcriptional regulatory elements and nucleosomal DNA in the human genome, suggesting enhanced safety and thus utility of these SB variants in gene therapy applications.
Collapse
Affiliation(s)
| | | | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - György Abrusán
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Zoltán Ivics
- To whom correspondence should be addressed. Tel: +49 6103 77 6000; Fax: +49 6103 77 1280;
| |
Collapse
|
7
|
Goshayeshi L, Yousefi Taemeh S, Dehdilani N, Nasiri M, Ghahramani Seno MM, Dehghani H. CRISPR/dCas9-mediated transposition with specificity and efficiency of site-directed genomic insertions. FASEB J 2021; 35:e21359. [PMID: 33496003 DOI: 10.1096/fj.202001830rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/28/2022]
Abstract
The ability and efficiency of targeted nucleases to perform sequence replacements or insertions into the genome are limited. This limited efficiency for sequence replacements or insertions can be explained by the dependency on DNA repair pathways, the possibility of cellular toxicity, and unwanted activation of proto-oncogenes. The piggyBac (PB) transposase uses a very efficient enzymatic mechanism to integrate DNA fragments into the genome in a random manner. In this study, we fused an RNA-guided catalytically inactive Cas9 (dCas9) to the PB transposase and used dual sgRNAs to localize this molecule to specific genomic targets. We designed and used a promoter/reporter complementation assay to register and recover cells harboring-specific integrations, where only by complementation upon correct genomic integration, the reporter can be activated. Using an RNA-guided piggyBac transposase and dual sgRNAs, we were able to achieve site-directed integrations in the human ROSA26 safe harbor region in 0.32% of cells. These findings show that the methodology used in this study can be used for targeting genomic regions. An application for this finding could be in cancer cells to insert sequences into specific target regions that are intended to be destroyed, or to place promoter cargos behind the tumor suppressor genes to activate them.
Collapse
Affiliation(s)
- Lena Goshayeshi
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sara Yousefi Taemeh
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Nima Dehdilani
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammadreza Nasiri
- Recombinant Proteins Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad M Ghahramani Seno
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hesam Dehghani
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| |
Collapse
|
8
|
Ochmann MT, Ivics Z. Jumping Ahead with Sleeping Beauty: Mechanistic Insights into Cut-and-Paste Transposition. Viruses 2021; 13:76. [PMID: 33429848 PMCID: PMC7827188 DOI: 10.3390/v13010076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/16/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Sleeping Beauty (SB) is a transposon system that has been widely used as a genetic engineering tool. Central to the development of any transposon as a research tool is the ability to integrate a foreign piece of DNA into the cellular genome. Driven by the need for efficient transposon-based gene vector systems, extensive studies have largely elucidated the molecular actors and actions taking place during SB transposition. Close transposon relatives and other recombination enzymes, including retroviral integrases, have served as useful models to infer functional information relevant to SB. Recently obtained structural data on the SB transposase enable a direct insight into the workings of this enzyme. These efforts cumulatively allowed the development of novel variants of SB that offer advanced possibilities for genetic engineering due to their hyperactivity, integration deficiency, or targeting capacity. However, many aspects of the process of transposition remain poorly understood and require further investigation. We anticipate that continued investigations into the structure-function relationships of SB transposition will enable the development of new generations of transposition-based vector systems, thereby facilitating the use of SB in preclinical studies and clinical trials.
Collapse
Affiliation(s)
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany;
| |
Collapse
|
9
|
Blattner G, Cavazza A, Thrasher AJ, Turchiano G. Gene Editing and Genotoxicity: Targeting the Off-Targets. Front Genome Ed 2020; 2:613252. [PMID: 34713236 PMCID: PMC8525370 DOI: 10.3389/fgeed.2020.613252] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/20/2020] [Indexed: 12/26/2022] Open
Abstract
Gene editing technologies show great promise for application to human disease as a result of rapid developments in targeting tools notably based on ZFN, TALEN, and CRISPR-Cas systems. Precise modification of a DNA sequence is now possible in mature human somatic cells including stem and progenitor cells with increasing degrees of efficiency. At the same time new technologies are required to evaluate their safety and genotoxicity before widespread clinical application can be confidently implemented. A number of methodologies have now been developed in an attempt to predict expected and unexpected modifications occurring during gene editing. This review surveys the techniques currently available as state of the art, highlighting benefits and limitations, and discusses approaches that may achieve sufficient accuracy and predictability for application in clinical settings.
Collapse
Affiliation(s)
| | | | | | - Giandomenico Turchiano
- Infection, Immunity and Inflammation Research and Teaching Department, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| |
Collapse
|
10
|
Amberger M, Ivics Z. Latest Advances for the Sleeping Beauty Transposon System: 23 Years of Insomnia but Prettier than Ever: Refinement and Recent Innovations of the Sleeping Beauty Transposon System Enabling Novel, Nonviral Genetic Engineering Applications. Bioessays 2020; 42:e2000136. [PMID: 32939778 DOI: 10.1002/bies.202000136] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/29/2020] [Indexed: 12/13/2022]
Abstract
The Sleeping Beauty transposon system is a nonviral DNA transfer tool capable of efficiently mediating transposition-based, stable integration of DNA sequences of choice into eukaryotic genomes. Continuous refinements of the system, including the emergence of hyperactive transposase mutants and novel approaches in vectorology, greatly improve upon transposition efficiency rivaling viral-vector-based methods for stable gene insertion. Current developments, such as reversible transgenesis and proof-of-concept RNA-guided transposition, further expand on possible applications in the future. In addition, innate advantages such as lack of preferential integration into genes reduce insertional mutagenesis-related safety concerns while comparably low manufacturing costs enable widespread implementation. Accordingly, the system is recognized as a powerful and versatile tool for genetic engineering and is playing a central role in an ever-expanding number of gene and cell therapy clinical trials with the potential to become a key technology to meet the growing demand for advanced therapy medicinal products.
Collapse
Affiliation(s)
- Maximilian Amberger
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, D-63225, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, D-63225, Germany
| |
Collapse
|
11
|
Kovač A, Miskey C, Menzel M, Grueso E, Gogol-Döring A, Ivics Z. RNA-guided retargeting of S leeping Beauty transposition in human cells. eLife 2020; 9:e53868. [PMID: 32142408 PMCID: PMC7077980 DOI: 10.7554/elife.53868] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
An ideal tool for gene therapy would enable efficient gene integration at predetermined sites in the human genome. Here we demonstrate biased genome-wide integration of the Sleeping Beauty (SB) transposon by combining it with components of the CRISPR/Cas9 system. We provide proof-of-concept that it is possible to influence the target site selection of SB by fusing it to a catalytically inactive Cas9 (dCas9) and by providing a single guide RNA (sgRNA) against the human Alu retrotransposon. Enrichment of transposon integrations was dependent on the sgRNA, and occurred in an asymmetric pattern with a bias towards sites in a relatively narrow, 300 bp window downstream of the sgRNA targets. Our data indicate that the targeting mechanism specified by CRISPR/Cas9 forces integration into genomic regions that are otherwise poor targets for SB transposition. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.
Collapse
Affiliation(s)
- Adrian Kovač
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Esther Grueso
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| |
Collapse
|
12
|
Abstract
Since Barbara McClintock’s groundbreaking discovery of mobile DNA sequences some 70 years ago, transposable elements have come to be recognized as important mutagenic agents impacting genome composition, genome evolution, and human health. Transposable elements are a major constituent of prokaryotic and eukaryotic genomes, and the transposition mechanisms enabling transposon proliferation over evolutionary time remain engaging topics for study, suggesting complex interactions with the host, both antagonistic and mutualistic. The impact of transposition is profound, as over 100 human heritable diseases have been attributed to transposon insertions. Transposition can be highly mutagenic, perturbing genome integrity and gene expression in a wide range of organisms. This mutagenic potential has been exploited in the laboratory, where transposons have long been utilized for phenotypic screening and the generation of defined mutant libraries. More recently, barcoding applications and methods for RNA-directed transposition are being used towards new phenotypic screens and studies relevant for gene therapy. Thus, transposable elements are significant in affecting biology both
in vivo and in the laboratory, and this review will survey advances in understanding the biological role of transposons and relevant laboratory applications of these powerful molecular tools.
Collapse
Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
13
|
Hernandez M, Recalde S, Garcia-Garcia L, Bezunartea J, Miskey C, Johnen S, Diarra S, Sebe A, Rodriguez-Madoz JR, Pouillot S, Marie C, Izsvák Z, Scherman D, Kropp M, Prosper F, Thumann G, Ivics Z, Garcia-Layana A, Fernandez-Robredo P. Preclinical Evaluation of a Cell-Based Gene Therapy Using the Sleeping Beauty Transposon System in Choroidal Neovascularization. Mol Ther Methods Clin Dev 2019; 15:403-417. [PMID: 31890733 PMCID: PMC6909167 DOI: 10.1016/j.omtm.2019.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/30/2019] [Indexed: 01/05/2023]
Abstract
Age-related macular degeneration (AMD) is a progressive retinal disorder characterized by imbalanced pro- and antiangiogenic signals. The aim of this study was to evaluate the effect of ex vivo cell-based gene therapy with stable expression of human pigment epithelium-derived factor (PEDF) release using the non-viral Sleeping Beauty (SB100X) transposon system delivered by miniplasmids free of antibiotic resistance markers (pFAR4). Retinal pigment epithelial (RPE) cells and iris pigment epithelial (IPE) cells were co-transfected with pFAR4-inverted terminal repeats (ITRs) CMV-PEDF-BGH and pFAR4-CMV-SB100X-SV40 plasmids. Laser-induced choroidal neovascularization (CNV) was performed in rats, and transfected primary cells (transfected RPE [tRPE] and transfected IPE [tIPE] cells) were injected into the subretinal space. The leakage and CNV areas, vascular endothelial growth factor (VEGF), PEDF protein expression, metalloproteinases 2 and 9 (MMP-2/9), and microglial/macrophage markers were measured. Injection with tRPE/IPE cells significantly reduced the leakage area at 7 and 14 days and the CNV area at 7 days. There was a significant increase in PEDF and the PEDF/VEGF ratio with tRPE cells and a reduction in the MMP-2 activity. Our data demonstrated that ex vivo non-viral gene therapy reduces CNV and could be an effective and safe therapeutic option for angiogenic retinal diseases.
Collapse
Affiliation(s)
- Maria Hernandez
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Sergio Recalde
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Laura Garcia-Garcia
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Jaione Bezunartea
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich-Institut, 63225 Langen, Germany
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Sabine Diarra
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Attila Sebe
- Division of Medical Biotechnology, Paul Ehrlich-Institut, 63225 Langen, Germany
| | - Juan Roberto Rodriguez-Madoz
- Regenerative Medicine Program, Center for Applied Medical Research (CIMA), University of Navarra, IdiSNA, Pamplona 31008, Spain
| | | | - Corinne Marie
- Université de Paris, UTCBS, CNRS, INSERM, F-75006 Paris, France
- Chimie ParisTech, PSL Research University, F-75005 Paris, France
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Daniel Scherman
- Université de Paris, UTCBS, CNRS, INSERM, F-75006 Paris, France
| | - Martina Kropp
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Felipe Prosper
- Regenerative Medicine Program, Center for Applied Medical Research (CIMA), University of Navarra, IdiSNA, Pamplona 31008, Spain
- Area of Cell Therapy, Clínica Universidad de Navarra, University of Navarra, IdiSNA, Pamplona 31008, Spain
| | - Gabriele Thumann
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich-Institut, 63225 Langen, Germany
| | - Alfredo Garcia-Layana
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Patricia Fernandez-Robredo
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| |
Collapse
|
14
|
Querques I, Mades A, Zuliani C, Miskey C, Alb M, Grueso E, Machwirth M, Rausch T, Einsele H, Ivics Z, Hudecek M, Barabas O. A highly soluble Sleeping Beauty transposase improves control of gene insertion. Nat Biotechnol 2019; 37:1502-1512. [PMID: 31685959 PMCID: PMC6894935 DOI: 10.1038/s41587-019-0291-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/13/2019] [Indexed: 12/21/2022]
Abstract
The Sleeping Beauty (SB) transposon system is an efficient non-viral gene transfer tool in mammalian cells but its broad use has been hampered by uncontrolled transposase gene activity from DNA vectors, posing a risk for genome instability, and by the inability to use transposase protein directly. Here, we used rational protein design based on the crystal structure of the hyperactive SB100X variant to create an SB transposase (hsSB) with enhanced solubility and stability. We demonstrate that hsSB can be delivered with transposon DNA to genetically modify cell lines and embryonic, hematopoietic and induced pluripotent stem cells (iPSCs), overcoming uncontrolled transposase activity. We used hsSB to generate chimeric antigen receptor (CAR) T-cells, which exhibit potent anti-tumor activity in vitro and in xenograft mice. We found that hsSB spontaneously penetrates cells, enabling modification of iPSCs and generation of CAR-T cells without the use of transfection reagents. Titration of hsSB to modulate genomic integration frequency achieved as few as two integrations per genome.
Collapse
Affiliation(s)
- Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Mades
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Miriam Alb
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Esther Grueso
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Markus Machwirth
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Tobias Rausch
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Michael Hudecek
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany.
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| |
Collapse
|
15
|
Kuroki-Kami A, Nichuguti N, Yatabe H, Mizuno S, Kawamura S, Fujiwara H. Targeted gene knockin in zebrafish using the 28S rDNA-specific non-LTR-retrotransposon R2Ol. Mob DNA 2019; 10:23. [PMID: 31139267 PMCID: PMC6530143 DOI: 10.1186/s13100-019-0167-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/13/2019] [Indexed: 02/07/2023] Open
Abstract
Background Although most of long interspersed elements (LINEs), one class of non-LTR-retrotransposons, are integrated into the host genome randomely, some elements are retrotransposed into the specific sequences of the genomic regions, such as rRNA gene (rDNA) clusters, telomeric repeats and other repetitive sequenes. Most of the sequence-specific LINEs have been reported mainly among invertebrate species and shown to retrotranspose into the specific sequences in vivo and in vitro systems. Recenlty, 28S rDNA-specific LINE R2 elements are shown to be distributed among widespread vertebrate species, but the sequence-specific retrotransposition of R2 has never been demonstrated in vertebrates. Results Here we cloned a full length unit of R2 from medaka fish Oryzias latipes, named R2Ol, and engineered it to a targeted gene integration tool in zebrafish. By injecting R2Ol-encoding mRNA into zebrafish embryos, R2Ol retrotransposed precisely into the target site at high efficiency (98%) and was transmitted to the next generation at high frequency (50%). We also generated transgenic zebrafish carrying the enhanced green fluorescent protein (EGFP) reporter gene in 28S rDNA target by the R2Ol retrotransposition system. Conclusions Sequence-specific LINE retrotransposes into the precise sequence using target primed reverse transcription (TPRT), possibly providing an alternative and effective targeted gene knockin method in vertebrates. Electronic supplementary material The online version of this article (10.1186/s13100-019-0167-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Azusa Kuroki-Kami
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Bldg., Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8562 Japan
| | - Narisu Nichuguti
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Bldg., Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8562 Japan
| | - Haruka Yatabe
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Bldg., Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8562 Japan
| | - Sayaka Mizuno
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Bldg., Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8562 Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Bldg., Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8562 Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Bldg., Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8562 Japan
| |
Collapse
|
16
|
Guan S, Munder A, Hedtfeld S, Braubach P, Glage S, Zhang L, Lienenklaus S, Schultze A, Hasenpusch G, Garrels W, Stanke F, Miskey C, Johler SM, Kumar Y, Tümmler B, Rudolph C, Ivics Z, Rosenecker J. Self-assembled peptide-poloxamine nanoparticles enable in vitro and in vivo genome restoration for cystic fibrosis. NATURE NANOTECHNOLOGY 2019; 14:287-297. [PMID: 30692673 DOI: 10.1038/s41565-018-0358-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Developing safe and efficient non-viral delivery systems remains a major challenge for in vivo applications of gene therapy, especially in cystic fibrosis. Unlike conventional cationic polymers or lipids, the emerging poloxamine-based copolymers display promising in vivo gene delivery capabilities. However, poloxamines are invalid for in vitro applications and their in vivo transfection efficiency is still low compared with viral vectors. Here, we show that peptides developed by modular design approaches can spontaneously form compact and monodisperse nanoparticles with poloxamines and nucleic acids via self-assembly. Both messenger RNA and plasmid DNA expression mediated by peptide-poloxamine nanoparticles are greatly boosted in vitro and in the lungs of cystic fibrosis mice with negligible toxicity. Peptide-poloxamine nanoparticles containing integrating vectors enable successful in vitro and in vivo long-term restoration of cystic fibrosis transmembrane conductance regulator deficiency with a safe integration profile. Our dataset provides a new framework for designing non-viral gene delivery systems qualified for in vivo genetic modifications.
Collapse
Affiliation(s)
- Shan Guan
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Antje Munder
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, German Center for Lung Research, Hannover, Germany
| | - Silke Hedtfeld
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Peter Braubach
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, German Center for Lung Research, Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Silke Glage
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Longgui Zhang
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Stefan Lienenklaus
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Anja Schultze
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Wiebke Garrels
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Frauke Stanke
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, German Center for Lung Research, Hannover, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Sarah M Johler
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Burkhard Tümmler
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, German Center for Lung Research, Hannover, Germany
| | - Carsten Rudolph
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
- Ethris, Planegg, Germany
| | - Zoltan Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Joseph Rosenecker
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany.
| |
Collapse
|
17
|
Rydzek J, Nerreter T, Peng H, Jutz S, Leitner J, Steinberger P, Einsele H, Rader C, Hudecek M. Chimeric Antigen Receptor Library Screening Using a Novel NF-κB/NFAT Reporter Cell Platform. Mol Ther 2019; 27:287-299. [PMID: 30573301 PMCID: PMC6369451 DOI: 10.1016/j.ymthe.2018.11.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/16/2022] Open
Abstract
Chimeric antigen receptor (CAR)-T cell immunotherapy is under intense preclinical and clinical investigation, and it involves a rapidly increasing portfolio of novel target antigens and CAR designs. We established a platform that enables rapid and high-throughput CAR-screening campaigns with reporter cells derived from the T cell lymphoma line Jurkat. Reporter cells were equipped with nuclear factor κB (NF-κB) and nuclear factor of activated T cells (NFAT) reporter genes that generate a duplex output of enhanced CFP (ECFP) and EGFP, respectively. As a proof of concept, we modified reporter cells with CD19-specific and ROR1-specific CARs, and we detected high-level reporter signals that allowed distinguishing functional from non-functional CAR constructs. The reporter data were highly reproducible, and the time required for completing each testing campaign was substantially shorter with reporter cells (6 days) compared to primary CAR-T cells (21 days). We challenged the reporter platform to a large-scale screening campaign on a ROR1-CAR library, and we showed that reporter cells retrieved a functional CAR variant that was present with a frequency of only 6 in 1.05 × 106. The data illustrate the potential to implement this reporter platform into the preclinical development path of novel CAR-T cell products and to inform and accelerate the selection of lead CAR candidates for clinical translation.
Collapse
Affiliation(s)
- Julian Rydzek
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Thomas Nerreter
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Sabrina Jutz
- Institut für Immunologie, Medizinische Universität Wien, Wien, Austria
| | - Judith Leitner
- Institut für Immunologie, Medizinische Universität Wien, Wien, Austria
| | - Peter Steinberger
- Institut für Immunologie, Medizinische Universität Wien, Wien, Austria
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael Hudecek
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany.
| |
Collapse
|
18
|
Portier I, Vanhoorelbeke K, Verhenne S, Pareyn I, Vandeputte N, Deckmyn H, Goldenberg DS, Samal HB, Singh M, Ivics Z, Izsvák Z, De Meyer SF. High and long-term von Willebrand factor expression after Sleeping Beauty transposon-mediated gene therapy in a mouse model of severe von Willebrand disease. J Thromb Haemost 2018; 16:592-604. [PMID: 29288565 DOI: 10.1111/jth.13938] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Indexed: 01/08/2023]
Abstract
Essentials von Willebrand disease (VWD) is the most common inherited bleeding disorder. Gene therapy for VWD offers long-term therapy for VWD patients. Transposons efficiently integrate the large von Willebrand factor (VWF) cDNA in mice. Liver-directed transposons support sustained VWF expression with suboptimal multimerization. SUMMARY Background Type 3 von Willebrand disease (VWD) is characterized by complete absence of von Willebrand factor (VWF). Current therapy is limited to treatment with exogenous VWF/FVIII products, which only provide a short-term solution. Gene therapy offers the potential for a long-term treatment for VWD. Objectives To develop an integrative Sleeping Beauty (SB) transposon-mediated VWF gene transfer approach in a preclinical mouse model of severe VWD. Methods We established a robust platform for sustained transgene murine VWF (mVWF) expression in the liver of Vwf-/- mice by combining a liver-specific promoter with a sandwich transposon design and the SB100X transposase via hydrodynamic gene delivery. Results The sandwich SB transposon was suitable to deliver the full-length mVWF cDNA (8.4 kb) and supported supra-physiological expression that remained stable for up to 1.5 years after gene transfer. The sandwich vector stayed episomal (~60 weeks) or integrated in the host genome, respectively, in the absence or presence of the transposase. Transgene integration was confirmed using carbon tetrachloride-induced liver regeneration. Analysis of integration sites by high-throughput analysis revealed random integration of the sandwich vector. Although the SB vector supported long-term expression of supra-physiological VWF levels, the bleeding phenotype was not corrected in all mice. Long-term expression of VWF by hepatocytes resulted in relatively reduced amounts of high-molecular-weight multimers, potentially limiting its hemostatic efficacy. Conclusions Although this integrative platform for VWF gene transfer is an important milestone of VWD gene therapy, cell type-specific targeting is yet to be achieved.
Collapse
Affiliation(s)
- I Portier
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| | - K Vanhoorelbeke
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| | - S Verhenne
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| | - I Pareyn
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| | - N Vandeputte
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| | - H Deckmyn
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| | - D S Goldenberg
- The Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - H B Samal
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - M Singh
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Z Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Z Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - S F De Meyer
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| |
Collapse
|
19
|
Holstein M, Mesa-Nuñez C, Miskey C, Almarza E, Poletti V, Schmeer M, Grueso E, Ordóñez Flores JC, Kobelt D, Walther W, Aneja MK, Geiger J, Bonig HB, Izsvák Z, Schleef M, Rudolph C, Mavilio F, Bueren JA, Guenechea G, Ivics Z. Efficient Non-viral Gene Delivery into Human Hematopoietic Stem Cells by Minicircle Sleeping Beauty Transposon Vectors. Mol Ther 2018; 26:1137-1153. [PMID: 29503198 PMCID: PMC6079369 DOI: 10.1016/j.ymthe.2018.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 01/08/2018] [Accepted: 01/12/2018] [Indexed: 12/26/2022] Open
Abstract
The Sleeping Beauty (SB) transposon system is a non-viral gene delivery platform that combines simplicity, inexpensive manufacture, and favorable safety features in the context of human applications. However, efficient correction of hematopoietic stem and progenitor cells (HSPCs) with non-viral vector systems, including SB, demands further refinement of gene delivery techniques. We set out to improve SB gene transfer into hard-to-transfect human CD34+ cells by vectorizing the SB system components in the form of minicircles that are devoid of plasmid backbone sequences and are, therefore, significantly reduced in size. As compared to conventional plasmids, delivery of the SB transposon system as minicircle DNA is ∼20 times more efficient, and it is associated with up to a 50% reduction in cellular toxicity in human CD34+ cells. Moreover, providing the SB transposase in the form of synthetic mRNA enabled us to further increase the efficacy and biosafety of stable gene delivery into hematopoietic progenitors ex vivo. Genome-wide insertion site profiling revealed a close-to-random distribution of SB transposon integrants, which is characteristically different from gammaretroviral and lentiviral integrations in HSPCs. Transplantation of gene-marked CD34+ cells in immunodeficient mice resulted in long-term engraftment and hematopoietic reconstitution, which was most efficient when the SB transposase was supplied as mRNA and nucleofected cells were maintained for 4–8 days in culture before transplantation. Collectively, implementation of minicircle and mRNA technologies allowed us to further refine the SB transposon system in the context of HSPC gene delivery to ultimately meet clinical demands of an efficient and safe non-viral gene therapy protocol.
Collapse
Affiliation(s)
- Marta Holstein
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Cristina Mesa-Nuñez
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain; Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM) Madrid, Spain
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Elena Almarza
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain; Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM) Madrid, Spain
| | | | | | - Esther Grueso
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Juan Carlos Ordóñez Flores
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Dennis Kobelt
- Translational Oncology, Experimental and Clinical Research Center, Charité University Medicine, Berlin, Germany
| | - Wolfgang Walther
- Translational Oncology, Experimental and Clinical Research Center, Charité University Medicine, Berlin, Germany
| | | | | | - Halvard B Bonig
- Department of Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - Zsuzsanna Izsvák
- Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | | | - Carsten Rudolph
- ethris GmbH, Planegg, Germany; Department of Pediatrics, Ludwig Maximilian University, Munich, Germany
| | - Fulvio Mavilio
- Genethon, Evry, France; Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Juan A Bueren
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain; Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM) Madrid, Spain
| | - Guillermo Guenechea
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain; Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM) Madrid, Spain
| | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany.
| |
Collapse
|
20
|
Abstract
With the advent of next-generation sequencing (NGS) and the demand for a personalized healthcare system, the fields of precision medicine and gene therapy are advancing in new directions. There is a push to identify genes that contribute to disease development, either alone or in conjunction with other genes or environmental factors, and then design targeted therapies based on this knowledge, rather than the traditional approach of treating generalized symptoms with pharmaceuticals in a one-size-fits-all manner. Identification of genes that contribute to disease pathogenesis and progression is critical for the maturation of the precision medicine field. Concomitant with a better understanding of disease pathology, precision medicine approaches can be adopted with greater confidence and are expected to lead to a new standard for clinical practice. In this chapter, we provide a brief introduction to precision medicine, discuss the importance of identifying genes and genetic variants that contribute to disease development and progression, offer examples of approaches that can be applied to treat specific diseases, and present some of the current challenges and limitations of precision medicine.
Collapse
Affiliation(s)
- Taylor M Benson
- Department of Biomedical Research, Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Fatjon Leti
- Department of Biomedical Research, Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Johanna K DiStefano
- Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ, 85004, USA.
| |
Collapse
|
21
|
Ade CM, Derbes RS, Wagstaff BJ, Linker SB, White TB, Deharo D, Belancio VP, Ivics Z, Roy-Engel AM. Evaluating different DNA binding domains to modulate L1 ORF2p-driven site-specific retrotransposition events in human cells. Gene 2017; 642:188-198. [PMID: 29154869 DOI: 10.1016/j.gene.2017.11.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/11/2017] [Indexed: 12/28/2022]
Abstract
DNA binding domains (DBDs) have been used with great success to impart targeting capabilities to a variety of proteins creating highly useful genomic tools. We evaluated the ability of five types of DBDs and strategies (AAV Rep proteins, Cre, TAL effectors, zinc finger proteins, and Cas9/gRNA system) to target the L1 ORF2 protein to drive retrotransposition of Alu inserts to specific sequences in the human genome. First, we find that the L1 ORF2 protein tolerates the addition of protein domains both at the amino- and carboxy-terminus. Although in some instances retrotransposition efficiencies slightly diminished, all fusion proteins containing an intact ORF2 were capable of driving retrotransposition. Second, the stability of individual ORF2 fusion proteins varies and difficult to predict. Third, DBDs that require the formation of multimers for target recognition are unlikely to modify targeting of ORF2p-driven insertions. Fourth, the more components needed to assemble into a complex to drive targeted retrotransposition, the less likely the strategy will increase targeted insertions. Fifth, abundance of target sequences present in the genome will likely dictate the effectiveness and efficiency of targeted insertions. Lastly, the cleavage capabilities of Cas9 (or a Cas9 nickase variant) are unable to substitute for the L1 ORF2 endonuclease domain functions, suggestive that the endonuclease domain has alternate functions needed for retrotransposition. From these studies, we conclude that the most critical component for the modification of the human L1 ORF2 protein to drive targeted insertions is the selection of the DBD due to the varying functional requirements and impacts on protein stability.
Collapse
Affiliation(s)
- Catherine M Ade
- Department of Cellular and Molecular Biology, Tulane University, USA
| | - Rebecca S Derbes
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center and LCRC, 1700 Tulane Ave., New Orleans, LA 70112, USA
| | - Bradley J Wagstaff
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center and LCRC, 1700 Tulane Ave., New Orleans, LA 70112, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA 92037-1002, USA
| | - Travis B White
- Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Dawn Deharo
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Astrid M Roy-Engel
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center and LCRC, 1700 Tulane Ave., New Orleans, LA 70112, USA.
| |
Collapse
|
22
|
Kawakami K, Largaespada DA, Ivics Z. Transposons As Tools for Functional Genomics in Vertebrate Models. Trends Genet 2017; 33:784-801. [PMID: 28888423 DOI: 10.1016/j.tig.2017.07.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023]
Abstract
Genetic tools and mutagenesis strategies based on transposable elements are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of their inherent capacity to insert into DNA, transposons can be developed into powerful tools for chromosomal manipulations. Transposon-based forward mutagenesis screens have numerous advantages including high throughput, easy identification of mutated alleles, and providing insight into genetic networks and pathways based on phenotypes. For example, the Sleeping Beauty transposon has become highly instrumental to induce tumors in experimental animals in a tissue-specific manner with the aim of uncovering the genetic basis of diverse cancers. Here, we describe a battery of mutagenic cassettes that can be applied in conjunction with transposon vectors to mutagenize genes, and highlight versatile experimental strategies for the generation of engineered chromosomes for loss-of-function as well as gain-of-function mutagenesis for functional gene annotation in vertebrate models, including zebrafish, mice, and rats.
Collapse
Affiliation(s)
- Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan; These authors contributed equally to this work
| | - David A Largaespada
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN, USA; These authors contributed equally to this work
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany; These authors contributed equally to this work..
| |
Collapse
|
23
|
Liu N, Bechinger B, Süss R. The histidine-rich peptide LAH4-L1 strongly promotes PAMAM-mediated transfection at low nitrogen to phosphorus ratios in the presence of serum. Sci Rep 2017; 7:9585. [PMID: 28852016 PMCID: PMC5575053 DOI: 10.1038/s41598-017-10049-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/02/2017] [Indexed: 11/09/2022] Open
Abstract
Non-viral vectors are widely used and investigated for the delivery of genetic material into cells. However, gene delivery barriers like lysosomal degradation, serum inhibition and transient gene expression so far still limit their clinical applications. Aiming to overcome these limitations, a pH-sensitive hybrid gene vector (PSL complex) was designed by self-assembly of poly(amidoamine) (PAMAM) dendrimers, the histidine-rich peptide LAH4-L1 and the sleeping beauty transposon system (SB transposon system, a plasmid system capable of efficient and precise genomic insertion). Transfection studies revealed that PSL complexes achieved excellent efficiency in all investigated cell lines (higher than 90% in HeLa cells and over 30% in MDCK cells, a difficult-to-transfect cell line). Additionally, the PSL complexes showed high serum tolerance and exhibited outstanding transfection efficiency even in medium containing 50% serum (higher than 90% in HeLa cells). Moreover, a high level of long-term gene expression (over 30% in HeLa cells) was observed. Furthermore, PSL complexes not only resulted in high endocytosis, but also showed enhanced ability of endosomal escape compared to PAMAM/DNA complexes. These results demonstrate that simple association of PAMAM dendrimers, LAH4-L1 peptides and the SB transposon system by self-assembly is a general and promising strategy for efficient and safe gene delivery.
Collapse
Affiliation(s)
- Nan Liu
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology and Biopharmacy and Freiburger Materialforschungszentrum (FMF), Albert Ludwig University Freiburg, Sonnenstr. 5, 79104, Freiburg, Germany.
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, Membrane Biophysics and NMR, Chemistry Institute UMR7177, rue Blaise Pascal 1, 67008, Strasbourg, France
| | - Regine Süss
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology and Biopharmacy and Freiburger Materialforschungszentrum (FMF), Albert Ludwig University Freiburg, Sonnenstr. 5, 79104, Freiburg, Germany.
| |
Collapse
|
24
|
Kim MS, Kini AG. Engineering and Application of Zinc Finger Proteins and TALEs for Biomedical Research. Mol Cells 2017; 40:533-541. [PMID: 28835021 PMCID: PMC5582299 DOI: 10.14348/molcells.2017.0139] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Engineered DNA-binding domains provide a powerful technology for numerous biomedical studies due to their ability to recognize specific DNA sequences. Zinc fingers (ZF) are one of the most common DNA-binding domains and have been extensively studied for a variety of applications, such as gene regulation, genome engineering and diagnostics. Another novel DNA-binding domain known as a transcriptional activator-like effector (TALE) has been more recently discovered, which has a previously undescribed DNA-binding mode. Due to their modular architecture and flexibility, TALEs have been rapidly developed into artificial gene targeting reagents. Here, we describe the methods used to design these DNA-binding proteins and their key applications in biomedical research.
Collapse
Affiliation(s)
- Moon-Soo Kim
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, KY 42101,
USA
| | - Anu Ganesh Kini
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, KY 42101,
USA
| |
Collapse
|
25
|
Verhenne S, Vandeputte N, Pareyn I, Izsvák Z, Rottensteiner H, Deckmyn H, De Meyer SF, Vanhoorelbeke K. Long-Term Prevention of Congenital Thrombotic Thrombocytopenic Purpura in ADAMTS13 Knockout Mice by Sleeping Beauty Transposon-Mediated Gene Therapy. Arterioscler Thromb Vasc Biol 2017; 37:836-844. [PMID: 28254814 DOI: 10.1161/atvbaha.116.308680] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/17/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Severe deficiency in the von Willebrand factor-cleaving protease ADAMTS13 (a disintegrin and metalloproteinase with thrombospondin type 1 motif, member 13) because of mutations in the ADAMTS13 gene can lead to acute episodes of congenital thrombotic thrombocytopenic purpura (TTP), requiring prompt treatment. Current treatment consists of therapeutic or prophylactic infusions of fresh frozen plasma. However, lifelong treatment with plasma products is a stressful therapy for TTP patients. Here, we describe the use of the nonviral sleeping beauty (SB) transposon system as a gene therapeutic approach to realize lifelong expression of ADAMTS13 and subsequent protection against congenital TTP. APPROACH AND RESULTS We demonstrated that hydrodynamic tail vein injection of the SB100X system expressing murine ADAMTS13 in Adamts13-/- mice resulted in long-term expression of supraphysiological levels of transgene ADAMTS13 over a period of 25 weeks. Stably expressed ADAMTS13 efficiently removed the prothrombotic ultralarge von Willebrand factor multimers present in the circulation of Adamts13-/- mice. Moreover, mice stably expressing ADAMTS13 were protected against TTP. The treated mice did not develop severe thrombocytopenia or did organ damage occur when triggered with recombinant von Willebrand factor, and this up to 20 weeks after gene transfer. CONCLUSIONS These data demonstrate the feasibility of using SB100X-mediated gene therapy to achieve sustained expression of transgene ADAMTS13 and long-term prophylaxis against TTP in Adamts13-/- mice.
Collapse
Affiliation(s)
- Sebastien Verhenne
- From the Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Belgium (S.V., N.V., I.P., H.D., S.F.D.M., K.V.); Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (Z.I.); and Shire, Gene Therapy, Vienna, Austria (H.R.)
| | - Nele Vandeputte
- From the Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Belgium (S.V., N.V., I.P., H.D., S.F.D.M., K.V.); Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (Z.I.); and Shire, Gene Therapy, Vienna, Austria (H.R.)
| | - Inge Pareyn
- From the Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Belgium (S.V., N.V., I.P., H.D., S.F.D.M., K.V.); Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (Z.I.); and Shire, Gene Therapy, Vienna, Austria (H.R.)
| | - Zsuzsanna Izsvák
- From the Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Belgium (S.V., N.V., I.P., H.D., S.F.D.M., K.V.); Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (Z.I.); and Shire, Gene Therapy, Vienna, Austria (H.R.)
| | - Hanspeter Rottensteiner
- From the Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Belgium (S.V., N.V., I.P., H.D., S.F.D.M., K.V.); Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (Z.I.); and Shire, Gene Therapy, Vienna, Austria (H.R.)
| | - Hans Deckmyn
- From the Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Belgium (S.V., N.V., I.P., H.D., S.F.D.M., K.V.); Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (Z.I.); and Shire, Gene Therapy, Vienna, Austria (H.R.)
| | - Simon F De Meyer
- From the Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Belgium (S.V., N.V., I.P., H.D., S.F.D.M., K.V.); Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (Z.I.); and Shire, Gene Therapy, Vienna, Austria (H.R.)
| | - Karen Vanhoorelbeke
- From the Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Belgium (S.V., N.V., I.P., H.D., S.F.D.M., K.V.); Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (Z.I.); and Shire, Gene Therapy, Vienna, Austria (H.R.).
| |
Collapse
|
26
|
Thumann G, Harmening N, Prat-Souteyrand C, Marie C, Pastor M, Sebe A, Miskey C, Hurst LD, Diarra S, Kropp M, Walter P, Scherman D, Ivics Z, Izsvák Z, Johnen S. Engineering of PEDF-Expressing Primary Pigment Epithelial Cells by the SB Transposon System Delivered by pFAR4 Plasmids. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 6:302-314. [PMID: 28325297 PMCID: PMC5363513 DOI: 10.1016/j.omtn.2017.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/02/2017] [Accepted: 02/02/2017] [Indexed: 01/14/2023]
Abstract
Neovascular age-related macular degeneration (nvAMD) is characterized by choroidal blood vessels growing into the subretinal space, leading to retinal pigment epithelial (RPE) cell degeneration and vision loss. Vessel growth results from an imbalance of pro-angiogenic (e.g., vascular endothelial growth factor [VEGF]) and anti-angiogenic factors (e.g., pigment epithelium-derived factor [PEDF]). Current treatment using intravitreal injections of anti-VEGF antibodies improves vision in about 30% of patients but may be accompanied by side effects and non-compliance. To avoid the difficulties posed by frequent intravitreal injections, we have proposed the transplantation of pigment epithelial cells modified to overexpress human PEDF. Stable transgene integration and expression is ensured by the hyperactive Sleeping Beauty transposon system delivered by pFAR4 miniplasmids, which have a backbone free of antibiotic resistance markers. We demonstrated efficient expression of the PEDF gene and an optimized PEDF cDNA sequence in as few as 5 × 103 primary cells. At 3 weeks post-transfection, PEDF secretion was significantly elevated and long-term follow-up indicated a more stable secretion by cells transfected with the optimized PEDF transgene. Analysis of transgene insertion sites in human RPE cells showed an almost random genomic distribution. The results represent an important contribution toward a clinical trial aiming at a non-viral gene therapy of nvAMD.
Collapse
Affiliation(s)
- Gabriele Thumann
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland; Laboratory of Ophthalmology, University of Geneva, 1205 Geneva, Switzerland.
| | - Nina Harmening
- Laboratory of Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
| | | | - Corinne Marie
- CNRS, Unité de Technologies Chimiques et Biologiques pour la Santé UMR 8258, 75006 Paris, France; Université Paris Descartes, Sorbonne-Paris-Cité, UTCBS, 75006 Paris, France; INSERM, UTCBS U 1022, 75006 Paris, France; Chimie ParisTech, PSL Research University, UTCBS, 75005 Paris, France
| | - Marie Pastor
- CNRS, Unité de Technologies Chimiques et Biologiques pour la Santé UMR 8258, 75006 Paris, France; Université Paris Descartes, Sorbonne-Paris-Cité, UTCBS, 75006 Paris, France; INSERM, UTCBS U 1022, 75006 Paris, France; Chimie ParisTech, PSL Research University, UTCBS, 75005 Paris, France
| | - Attila Sebe
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Laurence D Hurst
- Department of Biology and Biochemistry, University of Bath, BA2 7AY Bath, UK
| | - Sabine Diarra
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Martina Kropp
- Laboratory of Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
| | - Peter Walter
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Daniel Scherman
- CNRS, Unité de Technologies Chimiques et Biologiques pour la Santé UMR 8258, 75006 Paris, France; Université Paris Descartes, Sorbonne-Paris-Cité, UTCBS, 75006 Paris, France; INSERM, UTCBS U 1022, 75006 Paris, France; Chimie ParisTech, PSL Research University, UTCBS, 75005 Paris, France
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13092 Berlin, Germany
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| |
Collapse
|
27
|
Vargas JE, Chicaybam L, Stein RT, Tanuri A, Delgado-Cañedo A, Bonamino MH. Retroviral vectors and transposons for stable gene therapy: advances, current challenges and perspectives. J Transl Med 2016; 14:288. [PMID: 27729044 PMCID: PMC5059932 DOI: 10.1186/s12967-016-1047-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/03/2016] [Indexed: 12/15/2022] Open
Abstract
Gene therapy protocols require robust and long-term gene expression. For two decades, retrovirus family vectors have offered several attractive properties as stable gene-delivery vehicles. These vectors represent a technology with widespread use in basic biology and translational studies that require persistent gene expression for treatment of several monogenic diseases. Immunogenicity and insertional mutagenesis represent the main obstacles to a wider clinical use of these vectors. Efficient and safe non-viral vectors are emerging as a promising alternative and facilitate clinical gene therapy studies. Here, we present an updated review for beginners and expert readers on retro and lentiviruses and the latest generation of transposon vectors (sleeping beauty and piggyBac) used in stable gene transfer and gene therapy clinical trials. We discuss the potential advantages and disadvantages of these systems such as cellular responses (immunogenicity or genome modification of the target cell) following exogenous DNA integration. Additionally, we discuss potential implications of these genome modification tools in gene therapy and other basic and applied science contexts.
Collapse
Affiliation(s)
- José Eduardo Vargas
- Centro Infantil-Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, Brazil
| | - Leonardo Chicaybam
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer (INCA), Rua Andre Cavalcanti 37/6º andar, Centro, Rio de Janeiro, 20231-050, Brazil.,Vice-presidência de Pesquisa e Laboratórios de Referência, Fundação Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Renato Tetelbom Stein
- Centro Infantil-Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, Brazil
| | - Amilcar Tanuri
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Martin H Bonamino
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer (INCA), Rua Andre Cavalcanti 37/6º andar, Centro, Rio de Janeiro, 20231-050, Brazil. .,Vice-presidência de Pesquisa e Laboratórios de Referência, Fundação Instituto Oswaldo Cruz, Rio de Janeiro, Brazil.
| |
Collapse
|
28
|
Narayanavari SA, Chilkunda SS, Ivics Z, Izsvák Z. Sleeping Beauty transposition: from biology to applications. Crit Rev Biochem Mol Biol 2016; 52:18-44. [PMID: 27696897 DOI: 10.1080/10409238.2016.1237935] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sleeping Beauty (SB) is the first synthetic DNA transposon that was shown to be active in a wide variety of species. Here, we review studies from the last two decades addressing both basic biology and applications of this transposon. We discuss how host-transposon interaction modulates transposition at different steps of the transposition reaction. We also discuss how the transposon was translated for gene delivery and gene discovery purposes. We critically review the system in clinical, pre-clinical and non-clinical settings as a non-viral gene delivery tool in comparison with viral technologies. We also discuss emerging SB-based hybrid vectors aimed at combining the attractive safety features of the transposon with effective viral delivery. The success of the SB-based technology can be fundamentally attributed to being able to insert fairly randomly into genomic regions that allow stable long-term expression of the delivered transgene cassette. SB has emerged as an efficient and economical toolkit for safe and efficient gene delivery for medical applications.
Collapse
Affiliation(s)
- Suneel A Narayanavari
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Shreevathsa S Chilkunda
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Zoltán Ivics
- b Division of Medical Biotechnology , Paul Ehrlich Institute , Langen , Germany
| | - Zsuzsanna Izsvák
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| |
Collapse
|
29
|
Enhanced CAR T-cell engineering using non-viral Sleeping Beauty transposition from minicircle vectors. Leukemia 2016; 31:186-194. [PMID: 27491640 DOI: 10.1038/leu.2016.180] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 12/28/2022]
Abstract
Immunotherapy with T cell modified with gamma-retroviral or lentiviral (LV) vectors to express a chimeric antigen receptor (CAR) has shown remarkable efficacy in clinical trials. However, the potential for insertional mutagenesis and genotoxicity of viral vectors is a safety concern, and their cost and regulatory demands a roadblock for rapid and broad clinical translation. Here, we demonstrate that CAR T cells can be engineered through non-viral Sleeping Beauty (SB) transposition of CAR genes from minimalistic DNA vectors called minicircles (MCs). We analyzed genomic distribution of SB and LV integrations and show that a significantly higher proportion of MC-derived CAR transposons compared with LV integrants had occurred outside of highly expressed and cancer-related genes into genomic safe harbor loci that are not expected to cause mutagenesis or genotoxicity. CD19-CAR T cells engineered with our enhanced SB approach conferred potent reactivity in vitro and eradicated lymphoma in a xenograft model in vivo. Intriguingly, electroporation of SB MCs is substantially more effective and less toxic compared with conventional plasmids, and enables cost-effective rapid preparation of therapeutic CAR T-cell doses. This approach sets a new standard in advanced cellular and gene therapy and will accelerate and increase the availability of CAR T-cell therapy to treat hematologic malignancies.
Collapse
|
30
|
Hoffmann OI, Kerekes A, Lipták N, Hiripi L, Bodo S, Szaloki G, Klein S, Ivics Z, Kues WA, Bosze Z. Transposon-Based Reporter Marking Provides Functional Evidence for Intercellular Bridges in the Male Germline of Rabbits. PLoS One 2016; 11:e0154489. [PMID: 27148973 PMCID: PMC4858258 DOI: 10.1371/journal.pone.0154489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/14/2016] [Indexed: 12/22/2022] Open
Abstract
The Sleeping Beauty transposon system was established as a robust and efficient method for germline transgenesis in different mammalian species. The generation of transgenic mice, rats, rabbits and swine carrying an identical Venus reporter construct delivered by transposon-mediated gene transfer enables comparative studies of gene expression in these lines of mammalian models. Whereas comparable expression patterns of the Venus reporter were found in somatic tissues, preliminary studies suggested that a striking difference in reporter expression may exist in mature spermatozoa of these species. Here we clearly show the differential expression of Venus reporter protein during spermatogenesis of the two compared species, the laboratory rabbit and mice. We provide evidence for the functionality of intercellular bridges in the male germline and genotype-independent transgenic phenotype of rabbit spermatids. Our data suggest that the reporter rabbit line may be a suitable tool to identify molecular mechanisms in testicular development, and may contribute to develop better animal models for male infertility in men.
Collapse
Affiliation(s)
| | - Andrea Kerekes
- NARIC-Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Nandor Lipták
- NARIC-Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Laszlo Hiripi
- NARIC-Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Szilard Bodo
- NARIC-Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Gabor Szaloki
- Faculty of Medicine, University of Debrecen, Department of Biophysics and Cell Biology, Debrecen, Hungary
| | - Sabine Klein
- Department of Biotechnology, Friedrich-Loeffler-Institut, Institut für Nutztiergenetik, Mariensee, Neustadt, Germany
| | | | - Wilfried A. Kues
- Department of Biotechnology, Friedrich-Loeffler-Institut, Institut für Nutztiergenetik, Mariensee, Neustadt, Germany
| | - Zsuzsanna Bosze
- NARIC-Agricultural Biotechnology Institute, Gödöllő, Hungary
- * E-mail:
| |
Collapse
|
31
|
Abstract
Sleeping Beauty (SB) is a synthetic transposon that was constructed based on sequences of transpositionally inactive elements isolated from fish genomes. SB is a Tc1/mariner superfamily transposon following a cut-and-paste transpositional reaction, during which the element-encoded transposase interacts with its binding sites in the terminal inverted repeats of the transposon, promotes the assembly of a synaptic complex, catalyzes excision of the element out of its donor site, and integrates the excised transposon into a new location in target DNA. SB transposition is dependent on cellular host factors. Transcriptional control of transposase expression is regulated by the HMG2L1 transcription factor. Synaptic complex assembly is promoted by the HMGB1 protein and regulated by chromatin structure. SB transposition is highly dependent on the nonhomologous end joining (NHEJ) pathway of double-strand DNA break repair that generates a transposon footprint at the excision site. Through its association with the Miz-1 transcription factor, the SB transposase downregulates cyclin D1 expression that results in a slowdown of the cell-cycle in the G1 phase, where NHEJ is preferentially active. Transposon integration occurs at TA dinucleotides in the target DNA, which are duplicated at the flanks of the integrated transposon. SB shows a random genome-wide insertion profile in mammalian cells when launched from episomal vectors and "local hopping" when launched from chromosomal donor sites. Some of the excised transposons undergo a self-destructive autointegration reaction, which can partially explain why longer elements transpose less efficiently. SB became an important molecular tool for transgenesis, insertional mutagenesis, and gene therapy.
Collapse
|
32
|
Wang J, Singh M, Sun C, Besser D, Prigione A, Ivics Z, Hurst LD, Izsvák Z. Isolation and cultivation of naive-like human pluripotent stem cells based on HERVH expression. Nat Protoc 2016; 11:327-46. [PMID: 26797457 DOI: 10.1038/nprot.2016.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ability to derive and stably maintain ground-state human pluripotent stem cells (hPSCs) that resemble the cells seen in vivo in the inner cell mass has the potential to be an invaluable tool for researchers developing stem cell-based therapies. To date, derivation of human naive-like pluripotent stem cell lines has been limited to a small number of lineages, and their long-term culturing remains problematic. We describe a protocol for genetic and phenotypic tagging, selecting and maintaining naive-like hPSCs. We tag hPSCs by GFP, expressed by the long terminal repeat (LTR7) of HERVH endogenous retrovirus. This simple and efficient protocol has been reproduced with multiple hPSC lines, including embryonic and induced pluripotent stem cells, and it takes ∼6 weeks. By using the reporter, homogeneous hPSC cultures can be derived, characterized and maintained for the long term by repeated re-sorting and re-plating steps. The HERVH-expressing cells have a similar, but nonidentical, expression pattern to other naive-like cells, suggesting that alternative pluripotent states might exist.
Collapse
Affiliation(s)
- Jichang Wang
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Manvendra Singh
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Chuanbo Sun
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Daniel Besser
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Alessandro Prigione
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Zoltán Ivics
- Paul Ehrlich Institute, Division of Medical Biotechnology, Langen, Germany
| | - Laurence D Hurst
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| |
Collapse
|
33
|
Genome-wide Profiling Reveals Remarkable Parallels Between Insertion Site Selection Properties of the MLV Retrovirus and the piggyBac Transposon in Primary Human CD4(+) T Cells. Mol Ther 2016; 24:592-606. [PMID: 26755332 PMCID: PMC4786924 DOI: 10.1038/mt.2016.11] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 01/06/2016] [Indexed: 12/17/2022] Open
Abstract
The inherent risks associated with vector insertion in gene therapy need to be carefully assessed. We analyzed the genome-wide distributions of Sleeping Beauty (SB) and piggyBac (PB) transposon insertions as well as MLV retrovirus and HIV lentivirus insertions in human CD4+ T cells with respect to a panel of 40 chromatin states. The distribution of SB transposon insertions displayed the least deviation from random, while the PB transposon and the MLV retrovirus showed unexpected parallels across all chromatin states. Both MLV and PB insertions are enriched at transcriptional start sites (TSSs) and co-localize with BRD4-associated sites. We demonstrate physical interaction between the PB transposase and bromodomain and extraterminal domain proteins (including BRD4), suggesting convergent evolution of a tethering mechanism that directs integrating genetic elements into TSSs. We detect unequal biases across the four systems with respect to targeting genes whose deregulation has been previously linked to serious adverse events in gene therapy clinical trials. The SB transposon has the highest theoretical chance of targeting a safe harbor locus in the human genome. The data underscore the significance of vector choice to reduce the mutagenic load on cells in clinical applications.
Collapse
|
34
|
Abstract
Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.
Collapse
Affiliation(s)
- Isaac B Hilton
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
| |
Collapse
|
35
|
Pindyurin AV, de Jong J, Akhtar W. TRIP through the chromatin: a high throughput exploration of enhancer regulatory landscapes. Genomics 2015; 106:171-177. [PMID: 26080039 DOI: 10.1016/j.ygeno.2015.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/01/2015] [Accepted: 06/09/2015] [Indexed: 11/25/2022]
Abstract
Enhancers are regulatory elements that promote gene expression in a spatio-temporal way and are involved in a wide range of developmental and disease processes. Both the identification and subsequent functional dissection of enhancers are key steps in understanding these processes. Several high-throughput approaches were recently developed for these purposes; however, in almost all cases enhancers are being tested outside their native chromatin context. Until recently, the analysis of enhancer activities at their native genomic locations was low throughput, laborious and time-consuming. Here, we discuss the potential of a powerful approach, TRIP, to study the functioning of enhancers in their native chromatin environments by introducing sensor constructs directly in the genome. TRIP allows for simultaneously analyzing the quantitative readout of numerous sensor constructs integrated at random locations in the genome. The high-throughput and flexible nature of TRIP opens up potential to study different aspects of enhancer biology at an unprecedented level.
Collapse
Affiliation(s)
- Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Johann de Jong
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
| |
Collapse
|
36
|
de Jong J, Wessels LFA, van Lohuizen M, de Ridder J, Akhtar W. Applications of DNA integrating elements: Facing the bias bully. Mob Genet Elements 2015; 4:1-6. [PMID: 26442173 PMCID: PMC4588226 DOI: 10.4161/2159256x.2014.992694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/19/2014] [Accepted: 11/25/2014] [Indexed: 12/17/2022] Open
Abstract
Retroviruses and DNA transposons are an important part of molecular biologists' toolbox. The applications of these elements range from functional genomics to oncogene discovery and gene therapy. However, these elements do not integrate uniformly across the genome, which is an important limitation to their use. A number of genetic and epigenetic factors have been shown to shape the integration preference of these elements. Insight into integration bias can significantly enhance the analysis and interpretation of results obtained using these elements. For three different applications, we outline how bias can affect results, and can potentially be addressed.
Collapse
Affiliation(s)
- Johann de Jong
- Computational Cancer Biology Group; Division of Molecular Carcinogenesis; The Netherlands Cancer Institute ; Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Computational Cancer Biology Group; Division of Molecular Carcinogenesis; The Netherlands Cancer Institute ; Amsterdam, The Netherlands ; Delft Bioinformatics Lab; TU Delft ; Delft, The Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics; The Netherlands Cancer Institute ; Amsterdam, The Netherlands
| | | | - Waseem Akhtar
- Division of Molecular Genetics; The Netherlands Cancer Institute ; Amsterdam, The Netherlands
| |
Collapse
|
37
|
Turchiano G, Latella MC, Gogol-Döring A, Cattoglio C, Mavilio F, Izsvák Z, Ivics Z, Recchia A. Genomic analysis of Sleeping Beauty transposon integration in human somatic cells. PLoS One 2014; 9:e112712. [PMID: 25390293 PMCID: PMC4229213 DOI: 10.1371/journal.pone.0112712] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/14/2014] [Indexed: 12/21/2022] Open
Abstract
The Sleeping Beauty (SB) transposon is a non-viral integrating vector system with proven efficacy for gene transfer and functional genomics. However, integration efficiency is negatively affected by the length of the transposon. To optimize the SB transposon machinery, the inverted repeats and the transposase gene underwent several modifications, resulting in the generation of the hyperactive SB100X transposase and of the high-capacity “sandwich” (SA) transposon. In this study, we report a side-by-side comparison of the SA and the widely used T2 arrangement of transposon vectors carrying increasing DNA cargoes, up to 18 kb. Clonal analysis of SA integrants in human epithelial cells and in immortalized keratinocytes demonstrates stability and integrity of the transposon independently from the cargo size and copy number-dependent expression of the cargo cassette. A genome-wide analysis of unambiguously mapped SA integrations in keratinocytes showed an almost random distribution, with an overrepresentation in repetitive elements (satellite, LINE and small RNAs) compared to a library representing insertions of the first-generation transposon vector and to gammaretroviral and lentiviral libraries. The SA transposon/SB100X integrating system therefore shows important features as a system for delivering large gene constructs for gene therapy applications.
Collapse
Affiliation(s)
- Giandomenico Turchiano
- Center for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Maria Carmela Latella
- Center for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Andreas Gogol-Döring
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Claudia Cattoglio
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Fulvio Mavilio
- Center for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Genethon, Evry, France
| | | | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Alessandra Recchia
- Center for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- * E-mail:
| |
Collapse
|
38
|
Leighton GO, Konnova TA, Idiyatullin B, Hurr SH, Zuev YF, Nesmelova IV. The folding of the specific DNA recognition subdomain of the sleeping beauty transposase is temperature-dependent and is required for its binding to the transposon DNA. PLoS One 2014; 9:e112114. [PMID: 25375127 PMCID: PMC4222973 DOI: 10.1371/journal.pone.0112114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/13/2014] [Indexed: 12/26/2022] Open
Abstract
The reaction of DNA transposition begins when the transposase enzyme binds to the transposon DNA. Sleeping Beauty is a member of the mariner family of DNA transposons. Although it is an important tool in genetic applications and has been adapted for human gene therapy, its molecular mechanism remains obscure. Here, we show that only the folded conformation of the specific DNA recognition subdomain of the Sleeping Beauty transposase, the PAI subdomain, binds to the transposon DNA. Furthermore, we show that the PAI subdomain is well folded at low temperatures, but the presence of unfolded conformation gradually increases at temperatures above 15°C, suggesting that the choice of temperature may be important for the optimal transposase activity. Overall, the results provide a molecular-level insight into the DNA recognition by the Sleeping Beauty transposase.
Collapse
Affiliation(s)
- Gage O. Leighton
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Tatiana A. Konnova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, United States of America
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russian Federation
| | - Bulat Idiyatullin
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russian Federation
| | - Sophia H. Hurr
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Yuriy F. Zuev
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russian Federation
| | - Irina V. Nesmelova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, United States of America
- Center for Biomedical Engineering and Science, University of North Carolina, Charlotte, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
39
|
Nakanishi H, Higuchi Y, Yamashita F, Hashida M. Targeted gene integration using the combination of a sequence-specific DNA-binding protein and phiC31 integrase. J Biotechnol 2014; 186:139-47. [PMID: 25038544 DOI: 10.1016/j.jbiotec.2014.07.012] [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: 02/13/2014] [Revised: 06/06/2014] [Accepted: 07/09/2014] [Indexed: 01/04/2023]
Abstract
PhiC31 integrase-based vectors can integrate therapeutic genes selectively into attP or pseudo-attP sites in genomes, but considerable numbers of pseudo-attP sites in human genomes exist inside endogenous gene-coding regions. To avoid endogenous gene disruptions, we aimed to enhance the integration site-specificity of the phiC31 integrase-based vector using a sequence-specific DNA-binding protein containing Gal4 and LexA DNA-binding motifs. The dual DNA-binding protein was designed to tether the UAS-containing donor vector to the target sequence, the LexA operator, and restrict integration to sites close to the LexA operator. To analyze the site-specificity in chromosomal integration, a human cell line having LexA operators on the genome was established, and the cell line was transfected with donor vectors expressing the DNA-binding protein and the phiC31 integrase expression vector (helper vector). Quantitative PCR indicated that integration around the LexA operator was 26-fold higher with the UAS-containing donor vector than with the control. Sequence analysis confirmed that the integration occurred around the LexA operator. The dual DNA-binding protein-based targeted integration strategy developed herein would allow safer and more reliable genetic manipulations for various applications, including gene and cell therapies.
Collapse
Affiliation(s)
- Hideyuki Nakanishi
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan; Japan Society for the Promotion of Science (JSPS), Sumitomo-Ichibancho FS Bldg., 8 Ichibancho, Chiyoda-ku, Tokyo 102-8472, Japan
| | - Yuriko Higuchi
- Institute for Innovative NanoBio Drug Discovery and Development, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan; PRESTO, Japan Science and Technology Agency (JST), Kawaguchi Center Building 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Fumiyoshi Yamashita
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitsuru Hashida
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, 69 Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| |
Collapse
|
40
|
Gersbach CA, Gaj T, Barbas CF. Synthetic zinc finger proteins: the advent of targeted gene regulation and genome modification technologies. Acc Chem Res 2014; 47:2309-18. [PMID: 24877793 PMCID: PMC4139171 DOI: 10.1021/ar500039w] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
The understanding
of gene regulation and the structure and function
of the human genome increased dramatically at the end of the 20th
century. Yet the technologies for manipulating the genome have been
slower to develop. For instance, the field of gene therapy has been
focused on correcting genetic diseases and augmenting tissue repair
for more than 40 years. However, with the exception of a few very
low efficiency approaches, conventional genetic engineering methods
have only been able to add auxiliary genes to cells. This has been
a substantial obstacle to the clinical success of gene therapies and
has also led to severe unintended consequences in several cases. Therefore,
technologies that facilitate the precise modification of cellular
genomes have diverse and significant implications in many facets of
research and are essential for translating the products of the Genomic
Revolution into tangible benefits for medicine and biotechnology.
To address this need, in the 1990s, we embarked on a mission to develop
technologies for engineering protein–DNA interactions with
the aim of creating custom tools capable of targeting any DNA sequence.
Our goal has been to allow researchers to reach into genomes to specifically
regulate, knock out, or replace any gene. To realize these goals,
we initially focused on understanding and manipulating zinc finger
proteins. In particular, we sought to create a simple and straightforward
method that enables unspecialized laboratories to engineer custom
DNA-modifying proteins using only defined modular components, a web-based
utility, and standard recombinant DNA technology. Two significant
challenges we faced were (i) the development of zinc finger domains
that target sequences not recognized by naturally occurring zinc finger
proteins and (ii) determining how individual zinc finger domains could
be tethered together as polydactyl proteins to recognize unique locations
within complex genomes. We and others have since used this modular
assembly method to engineer artificial proteins and enzymes that activate,
repress, or create defined changes to user-specified genes in human
cells, plants, and other organisms. We have also engineered novel
methods for externally controlling protein activity and delivery,
as well as developed new strategies for the directed evolution of
protein and enzyme function. This Account summarizes our work in these
areas and highlights independent studies that have successfully used
the modular assembly approach to create proteins with novel function.
We also discuss emerging alternative methods for genomic targeting,
including transcription activator-like effectors (TALEs) and CRISPR/Cas
systems, and how they complement the synthetic zinc finger protein
technology.
Collapse
Affiliation(s)
- Charles A. Gersbach
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Thomas Gaj
- The
Skaggs Institute for Chemical Biology and the Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The
Skaggs Institute for Chemical Biology and the Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
41
|
Di Matteo M, Samara-Kuko E, Ward NJ, Waddington SN, Waddingon SN, McVey JH, Chuah MKL, VandenDriessche T. Hyperactive piggyBac transposons for sustained and robust liver-targeted gene therapy. Mol Ther 2014; 22:1614-24. [PMID: 25034357 PMCID: PMC4435487 DOI: 10.1038/mt.2014.131] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/27/2014] [Indexed: 01/14/2023] Open
Abstract
The development of robust nonviral vectors could facilitate clinical gene therapy applications and may overcome some of the immune complications of viral vectors. Nevertheless, most nonviral gene deliver approaches typically yield only transient and/or low gene expression. To address these caveats, we have explored piggyBac transposons to correct hemophilia B by liver-directed factor IX (FIX) gene therapy in hemophilic mice. To achieve this, we combined the use of: (i) a hyperactive codon-optimized piggyBac transposase, (ii) a computationally enhanced liver-specific promoter, (iii) a hyperfunctional codon-optimized FIX transgene (FIX R338L Padua), and (iv) a modification of the transposon terminal repeats. This combination strategy resulted in a robust 400-fold improvement in vector performance in hepatocytes, yielding stable supraphysiologic human FIX activity (>1 year). Liver-specific expression resulted in the induction of FIX-specific immune tolerance. Remarkably, only very low transposon/transposase doses were required to cure the bleeding diathesis. Similarly, PB transposons could be used to express supraphysiologic factor VIII levels using low transposon/transposase doses. PB transposition did not induce tumors in a sensitive hepatocellular carcinoma-prone mouse model. These results underscore the potency and relative safety of the latest generation PB transposons, which constitutes a versatile platform for stable and robust secretion of therapeutic proteins.
Collapse
Affiliation(s)
- Mario Di Matteo
- 1] Department of Gene Therapy and Regenerative Medicine, Free University of Brussels, Brussels, Belgium [2] Center for Molecular and Vascular Biology, Department of Cardiovascular Medicine, University of Leuven, Leuven, Belgium
| | - Emira Samara-Kuko
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels, Brussels, Belgium
| | - Natalie J Ward
- Molecular Immunology Unit, Institute of Child Health, University College London, London, UK
| | - Simon N Waddington
- 1] Institute for Women's Health Gene Transfer Technology Group, University College London, London, UK [2] School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, South Africa
| | | | - John H McVey
- University of Surrey, Molecular Medicine Group, Surrey, UK
| | - Marinee K L Chuah
- 1] Department of Gene Therapy and Regenerative Medicine, Free University of Brussels, Brussels, Belgium [2] Center for Molecular and Vascular Biology, Department of Cardiovascular Medicine, University of Leuven, Leuven, Belgium
| | - Thierry VandenDriessche
- 1] Department of Gene Therapy and Regenerative Medicine, Free University of Brussels, Brussels, Belgium [2] Center for Molecular and Vascular Biology, Department of Cardiovascular Medicine, University of Leuven, Leuven, Belgium
| |
Collapse
|
42
|
Gabriel R, Kutschera I, Bartholomae CC, von Kalle C, Schmidt M. Linear amplification mediated PCR--localization of genetic elements and characterization of unknown flanking DNA. J Vis Exp 2014:e51543. [PMID: 24998871 DOI: 10.3791/51543] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Linear-amplification mediated PCR (LAM-PCR) has been developed to study hematopoiesis in gene corrected cells of patients treated by gene therapy with integrating vector systems. Due to the stable integration of retroviral vectors, integration sites can be used to study the clonal fate of individual cells and their progeny. LAM- PCR for the first time provided evidence that leukemia in gene therapy treated patients originated from provirus induced overexpression of a neighboring proto-oncogene. The high sensitivity and specificity of LAM-PCR compared to existing methods like inverse PCR and ligation mediated (LM)-PCR is achieved by an initial preamplification step (linear PCR of 100 cycles) using biotinylated vector specific primers which allow subsequent reaction steps to be carried out on solid phase (magnetic beads). LAM-PCR is currently the most sensitive method available to identify unknown DNA which is located in the proximity of known DNA. Recently, a variant of LAM-PCR has been developed that circumvents restriction digest thus abrogating retrieval bias of integration sites and enables a comprehensive analysis of provirus locations in host genomes. The following protocol explains step-by-step the amplification of both 3'- and 5'- sequences adjacent to the integrated lentiviral vector.
Collapse
Affiliation(s)
- Richard Gabriel
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ)
| | - Ina Kutschera
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ)
| | - Cynthia C Bartholomae
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ)
| | - Christof von Kalle
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ)
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ);
| |
Collapse
|
43
|
Abstract
The influence of local chromatin context on gene expression can be explored by integrating a transcription reporter at different locations in the genome as a sensor. Here we provide a detailed protocol for analyzing thousands of reporters integrated in parallel (TRIP) at a genome-wide level. TRIP is based on tagging each reporter with a unique barcode, which is used for independent reporter expression analysis and integration site mapping. Compared with previous methods for studying position effects, TRIP offers a 100-1,000-fold higher throughput in a faster and less-labor-intensive manner. The entire experimental protocol takes ∼42 d to complete, with high-throughput sequencing and data analysis requiring an additional ∼11 d. TRIP was developed by using transcription reporters in mouse embryonic stem (mES) cells, but because of its flexibility the method can be used to probe the influence of chromatin context on a variety of molecular processes in any transfectable cell line.
Collapse
|
44
|
Germline transgenesis in rabbits by pronuclear microinjection of Sleeping Beauty transposons. Nat Protoc 2014; 9:794-809. [PMID: 24625779 DOI: 10.1038/nprot.2014.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The laboratory rabbit (Oryctolagus cuniculus) is widely used as a model for a variety of inherited and acquired human diseases. In addition, the rabbit is the smallest livestock animal that is used to transgenically produce pharmaceutical proteins in its milk. Here we describe a protocol for high-efficiency germline transgenesis and sustained transgene expression in rabbits by using the Sleeping Beauty (SB) transposon system. The protocol is based on co-injection into the pronuclei of fertilized oocytes of synthetic mRNA encoding the SB100X hyperactive transposase together with plasmid DNA carrying a transgene construct flanked by binding sites for the transposase. The translation of the transposase mRNA is followed by enzyme-mediated excision of the transgene cassette from the plasmids and its permanent genomic insertion to produce stable transgenic animals. Generation of a germline-transgenic founder animal by using this protocol takes ∼2 months. Transposon-mediated transgenesis compares favorably in terms of both efficiency and reliable transgene expression with classic pronuclear microinjection, and it offers comparable efficacies (numbers of transgenic founders obtained per injected embryo) to lentiviral approaches, without limitations on vector design, issues of transgene silencing, and the toxicity and biosafety concerns of working with viral vectors.
Collapse
|
45
|
Germline transgenesis in pigs by cytoplasmic microinjection of Sleeping Beauty transposons. Nat Protoc 2014; 9:810-27. [DOI: 10.1038/nprot.2014.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
46
|
Ivics Z, Mátés L, Yau TY, Landa V, Zidek V, Bashir S, Hoffmann OI, Hiripi L, Garrels W, Kues WA, Bösze Z, Geurts A, Pravenec M, Rülicke T, Izsvák Z. Germline transgenesis in rodents by pronuclear microinjection of Sleeping Beauty transposons. Nat Protoc 2014; 9:773-93. [PMID: 24625778 DOI: 10.1038/nprot.2014.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We describe a protocol for high-efficiency germline transgenesis and sustained transgene expression in two important biomedical models, the mouse and the rat, by using the Sleeping Beauty transposon system. The procedure is based on co-injection of synthetic mRNA encoding the SB100X hyperactive transposase, together with circular plasmid DNA carrying a transgene construct flanked by binding sites for the transposase, into the pronuclei of fertilized oocytes. Upon translation of the transposase mRNA, enzyme-mediated excision of the transgene cassettes from the injected plasmids followed by permanent genomic insertion produces stable transgenic animals. Generation of a germline-transgenic founder animal by using this protocol takes ∼3 months. Transposon-mediated transgenesis compares favorably in terms of both efficiency and reliable transgene expression with classic pronuclear microinjection, and it offers comparable efficacies to lentiviral approaches without limitations on vector design, issues of transgene silencing, and the toxicity and biosafety concerns of working with viral vectors.
Collapse
Affiliation(s)
- Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Lajos Mátés
- Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Tien Yin Yau
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Vladimír Landa
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vaclav Zidek
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Sanum Bashir
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | | | - Wiebke Garrels
- Friedrich Loeffler Institut, Institut für Nutztiergenetik, Neustadt, Germany
| | - Wilfried A Kues
- Friedrich Loeffler Institut, Institut für Nutztiergenetik, Neustadt, Germany
| | | | - Aron Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michal Pravenec
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Thomas Rülicke
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, Vienna, Austria
| | | |
Collapse
|
47
|
Mossine VV, Waters JK, Hannink M, Mawhinney TP. piggyBac transposon plus insulators overcome epigenetic silencing to provide for stable signaling pathway reporter cell lines. PLoS One 2013; 8:e85494. [PMID: 24376882 PMCID: PMC3869926 DOI: 10.1371/journal.pone.0085494] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 12/04/2013] [Indexed: 12/28/2022] Open
Abstract
Genetically modified hematopoietic progenitors represent an important testing platform for a variety of cell-based therapies, pharmaceuticals, diagnostics and other applications. Stable expression of a transfected gene of interest in the cells is often obstructed by its silencing. DNA transposons offer an attractive non-viral alternative of transgene integration into the host genome, but their broad applicability to leukocytes and other "transgene unfriendly" cells has not been fully demonstrated. Here we assess stability of piggyBac transposon-based reporter expression in murine prostate adenocarcinoma TRAMP-C2, human monocyte THP-1 and erythroleukemia K562 cell lines, along with macrophages and dendritic cells (DCs) that have differentiated from the THP-1 transfects. The most efficient and stable reporter activity was observed for combinations of the transposon inverted terminal repeats and one 5'- or two cHS4 core insulators flanking a green fluorescent protein reporter construct, with no detectable silencing over 10 months of continuous cell culture in absence of any selective pressure. In monocytic THP-1 cells, the functional activity of luciferase reporters for NF-κB, Nrf2, or HIF-1α has not decreased over time and was retained following differentiation into macrophages and DCs, as well. These results imply pB as a versatile tool for gene integration in monocytic cells in general, and as a convenient access route to DC-based signaling pathway reporters suitable for high-throughput assays, in particular.
Collapse
Affiliation(s)
- Valeri V. Mossine
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
- Experiment Station Chemical Labs, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
| | - James K. Waters
- Experiment Station Chemical Labs, University of Missouri, Columbia, Missouri, United States of America
| | - Mark Hannink
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Thomas P. Mawhinney
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
- Experiment Station Chemical Labs, University of Missouri, Columbia, Missouri, United States of America
- Department of Child Health, University of Missouri, Columbia, Missouri, United States of America
| |
Collapse
|
48
|
Abstract
The transposon piggyBac is being used increasingly for genetic studies. Here, we describe modified versions of piggyBac transposase that have potentially wide-ranging applications, such as reversible transgenesis and modified targeting of insertions. piggyBac is distinguished by its ability to excise precisely, restoring the donor site to its pretransposon state. This characteristic makes piggyBac useful for reversible transgenesis, a potentially valuable feature when generating induced pluripotent stem cells without permanent alterations to genomic sequence. To avoid further genome modification following piggyBac excision by reintegration, we generated an excision competent/integration defective (Exc(+)Int(-)) transposase. Our findings also suggest the position of a target DNA-transposase interaction. Another goal of genome engineering is to develop reagents that can guide transgenes to preferred genomic regions. Others have shown that piggyBac transposase can be active when fused to a heterologous DNA-binding domain. An Exc(+)Int(-) transposase, the intrinsic targeting of which is defective, might also be a useful intermediate in generating a transposase whose integration activity could be rescued and redirected by fusion to a site-specific DNA-binding domain. We show that fusion to two designed zinc finger proteins rescued the Int(-) phenotype. Successful guided transgene integration into genomic DNA would have broad applications to gene therapy and molecular genetics. Thus, an Exc(+)Int(-) transposase is a potentially useful reagent for genome engineering and provides insight into the mechanism of transposase-target DNA interaction.
Collapse
|
49
|
Hackett PB, Largaespada DA, Switzer KC, Cooper LJN. Evaluating risks of insertional mutagenesis by DNA transposons in gene therapy. Transl Res 2013; 161:265-83. [PMID: 23313630 PMCID: PMC3602164 DOI: 10.1016/j.trsl.2012.12.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 12/30/2022]
Abstract
Investigational therapy can be successfully undertaken using viral- and nonviral-mediated ex vivo gene transfer. Indeed, recent clinical trials have established the potential for genetically modified T cells to improve and restore health. Recently, the Sleeping Beauty (SB) transposon/transposase system has been applied in clinical trials to stably insert a chimeric antigen receptor (CAR) to redirect T-cell specificity. We discuss the context in which the SB system can be harnessed for gene therapy and describe the human application of SB-modified CAR(+) T cells. We have focused on theoretical issues relating to insertional mutagenesis in the context of human genomes that are naturally subjected to remobilization of transposons and the experimental evidence over the last decade of employing SB transposons for defining genes that induce cancer. These findings are put into the context of the use of SB transposons in the treatment of human disease.
Collapse
Affiliation(s)
- Perry B Hackett
- Department of Genetics Cell Biology and Development, Center for Genome Engineering and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | | | | | | |
Collapse
|