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Transposase-CRISPR mediated targeted integration (TransCRISTI) in the human genome. Sci Rep 2022; 12:3390. [PMID: 35232993 PMCID: PMC8888626 DOI: 10.1038/s41598-022-07158-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/08/2022] [Indexed: 11/08/2022] Open
Abstract
Various methods have been used in targeted gene knock-in applications. CRISPR-based knock-in strategies based on homology-independent repair pathways such as CRISPR HITI have been shown to possess the best efficiency for gene knock-in in mammalian cells. However, these methods suffer from the probability of plasmid backbone insertion at the target site. On the other hand, studies trying to combine the targeting ability of the Cas9 molecule and the excision/integration capacity of the PB transposase have shown random integrations. In this study, we introduce a new homology-independent knock-in strategy, Transposase-CRISPR mediated Targeted Integration (TransCRISTI), that exploits a fusion of Cas9 nuclease and a double mutant piggyBac transposase. In isogenic mammalian cell lines, we show that the TransCRISTI method demonstrates higher efficiency (72%) for site-specific insertions than the CRISPR HITI (44%) strategy. Application of the TransCRISTI method resulted in site-directed integration in 4.13% and 3.69% of the initially transfected population in the human AAVS1and PML loci, respectively, while the CRISPR HITI strategy resulted in site-directed integration in the PML locus in only 0.6% of cells. We also observed lower off-target and random insertions in the TransCRISTI group than the CRISPR HITI group. The TransCRISTI technology represents a great potential for the accurate and high-efficiency knock-in of the desired transposable elements into the predetermined genomic locations.
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2
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Urena F, Ma C, Hoffmann FW, Nunes LGA, Urschitz J, Moisyadi S, Khadka VS, Deng Y, Hoffmann PR. T-cell activation decreases miRNA-15a/16 levels to promote MEK1-ERK1/2-Elk1 signaling and proliferative capacity. J Biol Chem 2022; 298:101634. [PMID: 35085550 PMCID: PMC8861121 DOI: 10.1016/j.jbc.2022.101634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 02/08/2023] Open
Abstract
While miRs have been extensively studied in the context of malignancy and tumor progression, their functions in regulating T-cell activation are less clear. In initial studies, we found reduced levels of miR-15a/16 at 3 to 18 h post-T-cell receptor (TCR) stimulation, suggesting a role for decreased levels of this miR pair in shaping T-cell activation. To further explore this, we developed an inducible miR15a/16 transgenic mouse model to determine how elevating miR-15a/16 levels during early stages of activation would affect T-cell proliferation and to identify TCR signaling pathways regulated by this miR pair. Doxycycline (DOX)-induced expression of miR-15a/16 from 0 to 18 h post-TCR stimulation decreased ex vivo T-cell proliferation as well as in vivo antigen-specific T-cell proliferation. We also combined bioinformatics and proteomics approaches to identify the mitogen-activated protein kinase kinase 1 (MEK1) (Map2k1) as a target of miR-15a/16. MEK1 targeting by miR-15a/16 was confirmed using miR mimics that decreased Map2k1 mRNA containing the 3'-UTR target nucleotide sequence (UGCUGCUA) but did not decrease Map2k1 containing a mutated control sequence (AAAAAAAA). Phosphorylation of downstream signaling molecules, extracellular signal-regulated protein kinase 1/2 (ERK1/2) and Elk1, was also decreased by DOX-induced miR-15a/16 expression. In addition to MEK1, ERK1 was subsequently found to be targeted by miR-15a/16, with DOX-induced miR-15a/16 reducing total ERK1 levels in T cells. These findings show that TCR stimulation reduces miR-15a/16 levels at early stages of T-cell activation to facilitate increased MEK1 and ERK1, which promotes the sustained MEK1-ERK1/2-Elk1 signaling required for optimal proliferation.
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Affiliation(s)
- Frank Urena
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA; Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Chi Ma
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - FuKun W Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Lance G A Nunes
- Department of Anatomy, Physiology and Biochemistry, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Johann Urschitz
- Department of Anatomy, Physiology and Biochemistry, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Stefan Moisyadi
- Department of Anatomy, Physiology and Biochemistry, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Vedbar S Khadka
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Peter R Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA.
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3
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Li G, Li X, Zhuang S, Wang L, Zhu Y, Chen Y, Sun W, Wu Z, Zhou Z, Chen J, Huang X, Wang J, Li D, Li W, Wang H, Wei W. Gene editing and its applications in biomedicine. SCIENCE CHINA. LIFE SCIENCES 2022; 65:660-700. [PMID: 35235150 PMCID: PMC8889061 DOI: 10.1007/s11427-021-2057-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
The steady progress in genome editing, especially genome editing based on the use of clustered regularly interspaced short palindromic repeats (CRISPR) and programmable nucleases to make precise modifications to genetic material, has provided enormous opportunities to advance biomedical research and promote human health. The application of these technologies in basic biomedical research has yielded significant advances in identifying and studying key molecular targets relevant to human diseases and their treatment. The clinical translation of genome editing techniques offers unprecedented biomedical engineering capabilities in the diagnosis, prevention, and treatment of disease or disability. Here, we provide a general summary of emerging biomedical applications of genome editing, including open challenges. We also summarize the tools of genome editing and the insights derived from their applications, hoping to accelerate new discoveries and therapies in biomedicine.
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Affiliation(s)
- Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Songkuan Zhuang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China
| | - Liren Wang
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yifan Zhu
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeguang Wu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China.
| | - Dali Li
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, 150001, China.
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
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4
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Bire S, Dusserre Y, Bigot Y, Mermod N. PiggyBac transposase and transposon derivatives for gene transfer targeting the ribosomal DNA loci of CHO cells. J Biotechnol 2021; 341:103-112. [PMID: 34560160 DOI: 10.1016/j.jbiotec.2021.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022]
Abstract
Integrative non-viral vectors such as transposons engineered to mediate targeted gene transfer into safe harbor sites in the genome may be a promising approach for the production of therapeutic proteins or for gene therapy in an efficient and secure way. In this context, we designed and evaluated two strategies for targeting the nuclear ribosomal DNA (rDNA) loci. One approach relied on the co-location of the transposase and transposon near transcriptionally active rDNA copies using a nucleolar localization signal (NoLS). Another one consisted of targeting the 18S-coding region in the rDNA loci using a NoLS-FokI-dCas9 endonuclease to perform targeted transgene knock-in. We show that integration into the rDNA of Chinese hamster ovary (CHO) cells can be achieved at a high frequency using the piggyBac transposon system, indicating that the rDNA is highly accessible for transposition. Consistently, rDNA-targeted transposition events were most frequently obtained when both the piggyBac transposon DNA and the transposase were nucleoli-targeted, yielding cells displaying stable and homogeneous expression of the transgene. This approach thus provides an alternative strategy to improve targeted transgene delivery and protein expression using CHO cells.
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Affiliation(s)
- Solenne Bire
- Institute of Biotechnology and Department of Fundamental Microbiology, Center for Biotechnology UNIL-EPFL, University of Lausanne, Lausanne, Switzerland
| | - Yves Dusserre
- Institute of Biotechnology and Department of Fundamental Microbiology, Center for Biotechnology UNIL-EPFL, University of Lausanne, Lausanne, Switzerland
| | - Yves Bigot
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Nicolas Mermod
- Institute of Biotechnology and Department of Fundamental Microbiology, Center for Biotechnology UNIL-EPFL, University of Lausanne, Lausanne, Switzerland.
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The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5'-transposon end. Mol Cell 2021; 81:4271-4286.e4. [PMID: 34403695 DOI: 10.1016/j.molcel.2021.07.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022]
Abstract
Helitrons are widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, in part because of their distinctive, replicative rolling-circle mechanism, which often mobilizes adjacent genes. Although most eukaryotic transposases form oligomers and use RNase H-like domains to break and rejoin double-stranded DNA (dsDNA), Helitron transposases contain a single-stranded DNA (ssDNA)-specific HUH endonuclease domain. Here, we report the cryo-electron microscopy structure of a Helitron transposase bound to the 5'-transposon end, providing insight into its multidomain architecture and function. The monomeric transposase forms a tightly packed assembly that buries the covalently attached cleaved end, protecting it until the second end becomes available. The structure reveals unexpected architectural similarity to TraI, a bacterial relaxase that also catalyzes ssDNA movement. The HUH active site suggests how two juxtaposed tyrosines, a feature of many replication initiators that use HUH nucleases, couple the conformational shift of an α-helix to control strand cleavage and ligation reactions.
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6
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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.
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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
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7
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Hu H, Zhang Z, Wang R, Wang Y, Jin J, Cai L, Yang J, Duan H, Wu Z, Fang Z, Liu B. BGC823 Cell Line with the Stable Expression of iRFP720 Retains Its Primary Properties with Promising Fluorescence Imaging Ability. DNA Cell Biol 2020; 39:900-908. [PMID: 32096664 DOI: 10.1089/dna.2019.5057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reliable animal models are required for understanding the molecular events of gastric tumor growth and metastasis. Tracing techniques based on iRFP720 may optimize the noninvasive monitoring of tumors in vivo. The present study established a human gastric adenocarcinoma cell line BGC823-iRFP720-GFP (abbreviated as BGC823-iRFP) that stably expressed iRFP720 and green fluorescent protein (GFP) by piggyBac transposon system. The monoclonal cell line BGC823-iRFP was isolated under puromycin selection. The cell morphology and proliferation ability of BGC823-iRFP cells in vitro were similar to that of the BGC823 cells. The iRFP720 and GFP expressions were confirmed by laser confocal microscopy and Cytation™ 5. Hematoxylin and eosin staining, immunohistochemical analysis, and animal experiments also revealed that BGC823-iRFP exhibited no significant changes in morphology, growth kinetics, and tumorigenicity in vivo. IVIS Lumina III imaging indicated that the iRFP720 signals of the BGC823-iRFP cells could be used to evaluate the antitumor efficacy of oncolytic viruses and chemotherapy drugs. Therefore, the BGC823-iRFP cells would be a useful tool for gastric cancer research and antitumor drug evaluation.
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Affiliation(s)
- Han Hu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Ziyi Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Runyang Wang
- Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
| | - Yang Wang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Jing Jin
- Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
| | - Linkang Cai
- Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
| | - Junhan Yang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Haixiao Duan
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Zhen Wu
- Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
| | | | - Binlei Liu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, China.,Wuhan Binhui Biotechnology Co. Ltd., Wuhan, China
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8
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Bhatt S, Chalmers R. Targeted DNA transposition in vitro using a dCas9-transposase fusion protein. Nucleic Acids Res 2019; 47:8126-8135. [PMID: 31429873 PMCID: PMC6735945 DOI: 10.1093/nar/gkz552] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/21/2022] Open
Abstract
Homology-directed genome engineering is limited by transgene size. Although DNA transposons are more efficient with large transgenes, random integrations are potentially mutagenic. Here we present an in vitro mechanistic study that demonstrates efficient Cas9 targeting of the mariner transposon Hsmar1. Integrations were unidirectional and tightly constrained to one side of the sgRNA binding site. Further analysis of the nucleoprotein intermediates demonstrated that the transposase and Cas9 moieties can bind their respective substrates independently or in concert. Kinetic analysis of the reaction in the presence of the Cas9 target-DNA revealed a delay between first and second strand cleavage at the transposon end. This step involves a significant conformational change that may be hindered by the properties of the interdomainal linker. Otherwise, the transposase moiety behaved normally and was proficient for integration in vitro and in Escherichia coli. Specific integration into the lacZ gene in E. coli was obscured by a high background of random integrations. Nevertheless, Cas9 is an attractive candidate for transposon-targeting because it has a high affinity and long dwell-time at its target site. This will facilitate a future optogenetic strategy for the temporal control of integration, which will increase the ratio of targeted to untargeted events.
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Affiliation(s)
- Shivam Bhatt
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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9
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Chen SP, Wang HH. An Engineered Cas-Transposon System for Programmable and Site-Directed DNA Transpositions. CRISPR J 2019; 2:376-394. [PMID: 31742433 DOI: 10.1089/crispr.2019.0030] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Efficient site-directed insertion of heterologous DNA into a genome remains an outstanding challenge. Recombinases that can integrate kilobase-sized DNA constructs are difficult to reprogram to user-defined loci, while genomic insertion using CRISPR-Cas methods relies on inefficient host DNA repair machinery. Here, we describe a Cas-Transposon (CasTn) system for genomic insertions that uses a Himar1 transposase fused to a catalytically dead dCas9 nuclease to mediate programmable, site-directed transposition. Using cell-free in vitro assays, we demonstrated that the Himar-dCas9 fusion protein increased the frequency of transposon insertion at a single targeted TA dinucleotide by >300-fold compared to a random transposase, and that site-directed transposition is dependent on target choice while robust to log-fold variations in protein and DNA concentrations. We also showed that Himar-dCas9 mediates directed transposition into plasmids in Escherichia coli. This work highlights CasTn as a new modality for host-independent, programmable, site-directed DNA insertions.
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Affiliation(s)
- Sway P Chen
- Department of Systems Biology, Columbia University Medical Center, New York, New York.,Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, New York
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, New York.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
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10
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Hew BE, Sato R, Mauro D, Stoytchev I, Owens JB. RNA-guided piggyBac transposition in human cells. Synth Biol (Oxf) 2019; 4:ysz018. [PMID: 31355344 PMCID: PMC6642342 DOI: 10.1093/synbio/ysz018] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/11/2019] [Accepted: 06/26/2019] [Indexed: 01/12/2023] Open
Abstract
Safer and more efficient methods for directing therapeutic genes to specific sequences could increase the repertoire of treatable conditions. Many current approaches act passively, first initiating a double-stranded break, then relying on host repair to uptake donor DNA. Alternatively, we delivered an actively integrating transposase to the target sequence to initiate gene insertion. We fused the hyperactive piggyBac transposase to the highly specific, catalytically dead SpCas9-HF1 (dCas9) and designed guide RNAs (gRNAs) to the CCR5 safe harbor sequence. We introduced mutations to the native DNA-binding domain of piggyBac to reduce non-specific binding of the transposase and cause the fusion protein to favor binding by dCas9. This strategy enabled us, for the first time, to direct transposition to the genome using RNA. We showed that increasing the number of gRNAs improved targeting efficiency. Interestingly, over half of the recovered insertions were found at a single TTAA hotspot. We also found that the fusion increased the error rate at the genome-transposon junction. We isolated clonal cell lines containing a single insertion at CCR5 and demonstrated long-term expression from this locus. These vectors expand the utility of the piggyBac system for applications in targeted gene addition for biomedical research and gene therapy.
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Affiliation(s)
- Brian E Hew
- Department of Anatomy, Biochemistry, and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Ryuei Sato
- Department of Anatomy, Biochemistry, and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Damiano Mauro
- Department of Anatomy, Biochemistry, and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Ilko Stoytchev
- Department of Anatomy, Biochemistry, and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jesse B Owens
- Department of Anatomy, Biochemistry, and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
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11
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Sumikawa T, Ohno S, Watanabe T, Yamamoto R, Yamano M, Mori T, Mori K, Tobimatsu T, Sera T. Site-Specific Integration by Recruitment of a Complex of ΦC31 Integrase and Donor DNA to a Target Site by Using a Tandem, Artificial Zinc-Finger Protein. Biochemistry 2018; 57:6868-6877. [PMID: 30462489 DOI: 10.1021/acs.biochem.8b00979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To solve the problem of uncontrolled therapeutic gene integration, which is a critical drawback of retroviral vectors for gene therapy, the integration sites of exogenous genes should be precisely controlled not to perturb endogenous gene expression. To accomplish this, we explored the possibility of site-specific integration using two six-finger artificial zinc-finger proteins (AZPs) tandemly conjugated via a flexible peptide linker (designated "Tandem AZP"). A Tandem AZP in which two AZPs recognize specific 19 bp targets in a donor and acceptor DNA was expected to site-specifically recruit the donor DNA to the acceptor DNA. Thereafter, an exogenously added integrase was expected to integrate the donor DNA into a specific site in the acceptor DNA (as it might be in the human genome). We demonstrated in vitro that in the presence of Tandem AZP, ΦC31 integrase selectively integrated a donor plasmid into a target acceptor plasmid not only at 30 °C (the optimum temperature of the integrase) but also at 37 °C (for future application in humans). We expect that with further improvement of our current system, a combination of Tandem AZP with integrase/recombinase will enable site-specific integration in mammalian cells and provide safer gene therapy technology.
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Affiliation(s)
- Tatsuhiko Sumikawa
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology , Okayama University , Tsushima-Naka, Kita-ku , Okayama 700-8530 , Japan
| | - Serika Ohno
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology , Okayama University , Tsushima-Naka, Kita-ku , Okayama 700-8530 , Japan
| | - Takeharu Watanabe
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology , Okayama University , Tsushima-Naka, Kita-ku , Okayama 700-8530 , Japan
| | - Ryo Yamamoto
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology , Okayama University , Tsushima-Naka, Kita-ku , Okayama 700-8530 , Japan
| | - Miyu Yamano
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology , Okayama University , Tsushima-Naka, Kita-ku , Okayama 700-8530 , Japan
| | - Tomoaki Mori
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology , Okayama University , Tsushima-Naka, Kita-ku , Okayama 700-8530 , Japan
| | - Koichi Mori
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology , Okayama University , Tsushima-Naka, Kita-ku , Okayama 700-8530 , Japan
| | - Takamasa Tobimatsu
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology , Okayama University , Tsushima-Naka, Kita-ku , Okayama 700-8530 , Japan
| | - Takashi Sera
- Department of Applied Chemistry and Biotechnology, Graduate School of Natural Science and Technology , Okayama University , Tsushima-Naka, Kita-ku , Okayama 700-8530 , Japan
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12
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Eckermann KN, Ahmed HMM, KaramiNejadRanjbar M, Dippel S, Ogaugwu CE, Kitzmann P, Isah MD, Wimmer EA. Hyperactive piggyBac transposase improves transformation efficiency in diverse insect species. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 98:16-24. [PMID: 29653176 DOI: 10.1016/j.ibmb.2018.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 04/06/2018] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Even in times of advanced site-specific genome editing tools, the improvement of DNA transposases is still on high demand in the field of transgenesis: especially in emerging model systems where evaluated integrase landing sites have not yet been created and more importantly in non-model organisms such as agricultural pests and disease vectors, in which reliable sequence information and genome annotations are still pending. In fact, random insertional mutagenesis is essential to identify new genomic locations that are not influenced by position effects and thus can serve as future stable transgene integration sites. In this respect, a hyperactive version of the most widely used piggyBac transposase (PBase) has been engineered. The hyperactive version (hyPBase) is currently available with the original insect codon-based coding sequence (ihyPBase) as well as in a mammalian codon-optimized (mhyPBase) version. Both facilitate significantly higher rates of transposition when expressed in mammalian in vitro and in vivo systems compared to the classical PBase at similar protein levels. Here we demonstrate that the usage of helper plasmids encoding the hyPBase - irrespective of the codon-usage - also strikingly increases the rate of successful germline transformation in the Mediterranean fruit fly (Medfly) Ceratitis capitata, the red flour beetle Tribolium castaneum, and the vinegar fly Drosophila melanogaster. hyPBase-encoding helpers are therefore highly suitable for the generation of transgenic strains of diverse insect orders. Depending on the species, we achieved up to 15-fold higher germline transformation rates compared to PBase and generated hard to obtain transgenic T. castaneum strains that express constructs affecting fitness and viability. Moreover, previously reported high sterility rates supposedly caused by hyPBase (iPB7), encoded by ihyPBase, could not be confirmed by our study. Therefore, we value hyPBase as an effective genetic engineering tool that we highly recommend for insect transgenesis.
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Affiliation(s)
- Kolja N Eckermann
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany; Göttingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, University of Göttingen, 37077 Goettingen, Germany; Molecular Cell Dynamics, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Hassan M M Ahmed
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Mohammad KaramiNejadRanjbar
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Stefan Dippel
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Christian E Ogaugwu
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Peter Kitzmann
- Göttingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, University of Göttingen, 37077 Goettingen, Germany; Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Musa D Isah
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Ernst A Wimmer
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany; Göttingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, University of Göttingen, 37077 Goettingen, Germany.
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13
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Preclinical and clinical advances in transposon-based gene therapy. Biosci Rep 2017; 37:BSR20160614. [PMID: 29089466 PMCID: PMC5715130 DOI: 10.1042/bsr20160614] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 02/08/2023] Open
Abstract
Transposons derived from Sleeping Beauty (SB), piggyBac (PB), or Tol2 typically require cotransfection of transposon DNA with a transposase either as an expression plasmid or mRNA. Consequently, this results in genomic integration of the potentially therapeutic gene into chromosomes of the desired target cells, and thus conferring stable expression. Non-viral transfection methods are typically preferred to deliver the transposon components into the target cells. However, these methods do not match the efficacy typically attained with viral vectors and are sometimes associated with cellular toxicity evoked by the DNA itself. In recent years, the overall transposition efficacy has gradually increased by codon optimization of the transposase, generation of hyperactive transposases, and/or introduction of specific mutations in the transposon terminal repeats. Their versatility enabled the stable genetic engineering in many different primary cell types, including stem/progenitor cells and differentiated cell types. This prompted numerous preclinical proof-of-concept studies in disease models that demonstrated the potential of DNA transposons for ex vivo and in vivo gene therapy. One of the merits of transposon systems relates to their ability to deliver relatively large therapeutic transgenes that cannot readily be accommodated in viral vectors such as full-length dystrophin cDNA. These emerging insights paved the way toward the first transposon-based phase I/II clinical trials to treat hematologic cancer and other diseases. Though encouraging results were obtained, controlled pivotal clinical trials are needed to corroborate the efficacy and safety of transposon-based therapies.
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14
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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.
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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.
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15
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Tipanee J, VandenDriessche T, Chuah MK. Transposons: Moving Forward from Preclinical Studies to Clinical Trials. Hum Gene Ther 2017; 28:1087-1104. [DOI: 10.1089/hum.2017.128] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Jaitip Tipanee
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
| | - Thierry VandenDriessche
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Marinee K. Chuah
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
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16
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Sharma N, Huynh DL, Kim SW, Ghosh M, Sodhi SS, Singh AK, Kim NE, Lee SJ, Hussain K, Oh SJ, Jeong DK. A PiggyBac mediated approach for lactoferricin gene transfer in bovine mammary epithelial stem cells for management of bovine mastitis. Oncotarget 2017; 8:104272-104285. [PMID: 29262639 PMCID: PMC5732805 DOI: 10.18632/oncotarget.22210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/21/2017] [Indexed: 12/31/2022] Open
Abstract
The antibacterial and anti-inflammatory properties of lactoferricin have been ascribed to its ability to sequester essential iron. The objective of the study was to clone bovine lactoferricin (LFcinB) gene into PiggyBac Transposon vector, expression study in the bovine mammary epithelial stem cells (bMESCs) and also to determine the antimicrobial property of recombinant LFcinB against bovine mastitis-causing organisms. The PiggyBac-LFcinB was transfected into bMESCs by electroporation and a three fold of LFcinB secretion was observed in the transfected bMESCs medium by ELISA assay. Furthermore, the assessment of antimicrobial activity against mastitis causing pathogens Staphylococcus aureus and Escherichia coli demonstrated convincing evidence to prove strong antibacterial activity of LFcinB with 14.0±1.0 mm and 18.0±1.5 mm zone of inhibition against both organisms, respectively. The present study provides the convincing evidence to suggest the potential of PiggyBac transposon system to transfer antibacterial peptide into bMESCs or cow mammary gland and also pave the way to use bovine mammary gland as the bioreactors. Simultaneously, it also suggest toward commercial utilization of LFcinB bioreactor system in pharmaceutical industry.
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Affiliation(s)
- Neelesh Sharma
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, Republic of Korea.,Division of Veterinary Medicine, Faculty of Veterinary Science & Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Jammu, India
| | - Do Luong Huynh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, Republic of Korea
| | - Sung Woo Kim
- Animal Genetic Resources Station, National Institute of Animal Science, Rural Development Administration, Namwon, Republic of Korea
| | - Mrinmoy Ghosh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, Republic of Korea
| | - Simrinder Singh Sodhi
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, Republic of Korea
| | - Amit Kumar Singh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, Republic of Korea
| | - Nam Eun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, Republic of Korea
| | - Sung Jin Lee
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Kangwon National University, Chuncheon, Republic of Korea
| | - Kafil Hussain
- Division of Veterinary Medicine, Faculty of Veterinary Science & Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Jammu, India
| | - Sung Jong Oh
- National Institute of Animal Science, Wanju-gun, Republic of Korea
| | - Dong Kee Jeong
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, Republic of Korea
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17
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Luo W, Galvan DL, Woodard LE, Dorset D, Levy S, Wilson MH. Comparative analysis of chimeric ZFP-, TALE- and Cas9-piggyBac transposases for integration into a single locus in human cells. Nucleic Acids Res 2017; 45:8411-8422. [PMID: 28666380 PMCID: PMC5737283 DOI: 10.1093/nar/gkx572] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/22/2017] [Indexed: 01/02/2023] Open
Abstract
Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes without requiring homologous recombination. We systematically compared four different engineered zinc finger proteins (ZFP), four transcription activator-like effector proteins (TALE), CRISPR associated protein 9 (SpCas9) and the catalytically inactive dSpCas9 protein fused to the amino-terminus of the transposase enzyme designed to target the hypoxanthine phosphoribosyltransferase (HPRT) gene located on human chromosome X. Chimeric transposases were evaluated for expression, transposition activity, chromatin immunoprecipitation at the target loci, and targeted knockout of the HPRT gene in human cells. One ZFP-PB and one TALE-PB chimera demonstrated notable HPRT gene targeting. In contrast, Cas9/dCas9-PB chimeras did not result in gene targeting. Instead, the HPRT locus appeared to be protected from transposon integration. Supplied separately, PB permitted highly efficient isolation of Cas9-mediated knockout of HPRT, with zero transposon integrations in HPRT by deep sequencing. In summary, these tools may allow isolation of 'targeted-only' cells, be utilized to protect a genomic locus from transposon integration, and enrich for Cas9-mutated cells.
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Affiliation(s)
- Wentian Luo
- Department of Veterans Affairs, Nashville, TN 37212 USA and Department of Medicine, Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daniel L Galvan
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lauren E Woodard
- Department of Veterans Affairs, Nashville, TN 37212 USA and Department of Medicine, Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Dan Dorset
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Matthew H Wilson
- Department of Veterans Affairs, Nashville, TN 37212 USA and Department of Medicine, Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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18
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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.
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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
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19
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Johnson ET, Owens JB, Moisyadi S. Vast potential for using the piggyBac transposon to engineer transgenic plants at specific genomic locations. Bioengineered 2016; 7:3-6. [PMID: 26930269 DOI: 10.1080/21655979.2015.1131367] [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] [Indexed: 12/21/2022] Open
Abstract
The acceptance of bioengineered plants by some nations is hampered by a number of factors, including the random insertion of a transgene into the host genome. Emerging technologies, such as site-specific nucleases, are enabling plant scientists to promote recombination or mutations at specific plant loci. Off target activity of these nucleases may limit widespread use. Insertion of transgenes by transposases engineered with a specific DNA binding domain has been accomplished in a number of organisms, but not in plants. The piggyBac transposon system, originally isolated from an insect, has been utilized to transform a variety of organisms. The piggyBac transposase is amendable to structural modifications, and was able to insert a transgene at a specific human locus through fusion of a DNA binding domain to its N-terminus. Recent developments demonstrating the activity of piggyBac transposase in plants is an important first step toward the potential use of engineered versions of piggyBac transposase for site-specific transgene insertion in plants.
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Affiliation(s)
- Eric T Johnson
- a Crop Bioprotection Research, USDA ARS , Peoria , Illinois
| | - Jesse B Owens
- b Institute for Biogenesis Research, University of Hawaii at Manoa , Honolulu , Hawaii
| | - Stefan Moisyadi
- b Institute for Biogenesis Research, University of Hawaii at Manoa , Honolulu , Hawaii
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20
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Abstract
DNA transposons are defined segments of DNA that are able to move from one genomic location to another. Movement is facilitated by one or more proteins, called the transposase, typically encoded by the mobile element itself. Here, we first provide an overview of the classification of such mobile elements in a variety of organisms. From a mechanistic perspective, we have focused on one particular group of DNA transposons that encode a transposase with a DD(E/D) catalytic domain that is topologically similar to RNase H. For these, a number of three-dimensional structures of transpososomes (transposase-nucleic acid complexes) are available, and we use these to describe the basics of their mechanisms. The DD(E/D) group, in addition to being the largest and most common among all DNA transposases, is the one whose members have been used for a wide variety of genomic applications. Therefore, a second focus of the article is to provide a nonexhaustive overview of transposon applications. Although several non-transposon-based approaches to site-directed genome modifications have emerged in the past decade, transposon-based applications are highly relevant when integration specificity is not sought. In fact, for many applications, the almost-perfect randomness and high frequency of integration make transposon-based approaches indispensable.
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Affiliation(s)
- Alison B. Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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21
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Alessio AP, Fili AE, Garrels W, Forcato DO, Olmos Nicotra MF, Liaudat AC, Bevacqua RJ, Savy V, Hiriart MI, Talluri TR, Owens JB, Ivics Z, Salamone DF, Moisyadi S, Kues WA, Bosch P. Establishment of cell-based transposon-mediated transgenesis in cattle. Theriogenology 2015; 85:1297-311.e2. [PMID: 26838464 DOI: 10.1016/j.theriogenology.2015.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/10/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022]
Abstract
Transposon-mediated transgenesis is a well-established tool for genome modification in small animal models. However, translation of this active transgenic method to large animals warrants further investigations. Here, the piggyBac (PB) and sleeping beauty (SB) transposon systems were assessed for stable gene transfer into the cattle genome. Bovine fibroblasts were transfected either with a helper-independent PB system or a binary SB system. Both transposons were highly active in bovine cells increasing the efficiency of DNA integration up to 88 times over basal nonfacilitated integrations in a colony formation assay. SB transposase catalyzed multiplex transgene integrations in fibroblast cells transfected with the helper vector and two donor vectors carrying different transgenes (fluorophore and neomycin resistance). Stably transfected fibroblasts were used for SCNT and on in vitro embryo culture, morphologically normal blastocysts that expressed the fluorophore were obtained with both transposon systems. The data indicate that transposition is a feasible approach for genetic engineering in the cattle genome.
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Affiliation(s)
- Ana P Alessio
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - Alejandro E Fili
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - Wiebke Garrels
- Department of Biotechnology, Friedrich-Loeffler-Institut, Institut für Nutztiergenetik, Neustadt, Germany
| | - Diego O Forcato
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - María F Olmos Nicotra
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - Ana C Liaudat
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - Romina J Bevacqua
- Laboratorio de Biotecnología Animal, Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, República Argentina
| | - Virginia Savy
- Laboratorio de Biotecnología Animal, Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, República Argentina
| | - María I Hiriart
- Laboratorio de Biotecnología Animal, Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, República Argentina
| | - Thirumala R Talluri
- Department of Biotechnology, Friedrich-Loeffler-Institut, Institut für Nutztiergenetik, Neustadt, Germany
| | - Jesse B Owens
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Daniel F Salamone
- Laboratorio de Biotecnología Animal, Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, República Argentina
| | - Stefan Moisyadi
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Wilfried A Kues
- Department of Biotechnology, Friedrich-Loeffler-Institut, Institut für Nutztiergenetik, Neustadt, Germany
| | - Pablo Bosch
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina.
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22
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Davy PM, Lye KD, Mathews J, Owens JB, Chow AY, Wong L, Moisyadi S, Allsopp RC. Human adipose stem cell and ASC-derived cardiac progenitor cellular therapy improves outcomes in a murine model of myocardial infarction. STEM CELLS AND CLONING-ADVANCES AND APPLICATIONS 2015; 8:135-48. [PMID: 26604802 PMCID: PMC4631407 DOI: 10.2147/sccaa.s86925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND Adipose tissue is an abundant and potent source of adult stem cells for transplant therapy. In this study, we present our findings on the potential application of adipose-derived stem cells (ASCs) as well as induced cardiac-like progenitors (iCPs) derived from ASCs for the treatment of myocardial infarction. METHODS AND RESULTS Human bone marrow (BM)-derived stem cells, ASCs, and iCPs generated from ASCs using three defined cardiac lineage transcription factors were assessed in an immune-compromised mouse myocardial infarction model. Analysis of iCP prior to transplant confirmed changes in gene and protein expression consistent with a cardiac phenotype. Endpoint analysis was performed 1 month posttransplant. Significantly increased endpoint fractional shortening, as well as reduction in the infarct area at risk, was observed in recipients of iCPs as compared to the other recipient cohorts. Both recipients of iCPs and ASCs presented higher myocardial capillary densities than either recipients of BM-derived stem cells or the control cohort. Furthermore, mice receiving iCPs had a significantly higher cardiac retention of transplanted cells than all other groups. CONCLUSION Overall, iCPs generated from ASCs outperform BM-derived stem cells and ASCs in facilitating recovery from induced myocardial infarction in mice.
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Affiliation(s)
- Philip Mc Davy
- Institute for Biogenesis Research, University of Hawaii at Mānoa, Honolulu, HI, USA
| | - Kevin D Lye
- John A. Burns School of Medicine, University of Hawaii at Mānoa, Honolulu, HI, USA ; Tissue Genesis, Inc., Honolulu, HI, USA
| | - Juanita Mathews
- Institute for Biogenesis Research, University of Hawaii at Mānoa, Honolulu, HI, USA
| | - Jesse B Owens
- Institute for Biogenesis Research, University of Hawaii at Mānoa, Honolulu, HI, USA
| | - Alice Y Chow
- Institute for Biogenesis Research, University of Hawaii at Mānoa, Honolulu, HI, USA
| | - Livingston Wong
- John A. Burns School of Medicine, University of Hawaii at Mānoa, Honolulu, HI, USA
| | - Stefan Moisyadi
- Institute for Biogenesis Research, University of Hawaii at Mānoa, Honolulu, HI, USA
| | - Richard C Allsopp
- Institute for Biogenesis Research, University of Hawaii at Mānoa, Honolulu, HI, USA
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23
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Abstract
DNA transposons offer an efficient nonviral method of permanently modifying the genomes of mammalian cells. The piggyBac transposon system has proven effective in genomic engineering of mammalian cells for preclinical applications, including gene discovery, simultaneous multiplexed genome modification, animal transgenesis, gene transfer in vivo achieving long-term gene expression in animals, and the genetic modification of clinically relevant cell types, such as induced pluripotent stem cells and human T lymphocytes. piggyBac has many desirable features, including seamless excision of transposons from the genomic DNA and the potential to target integration events to desired DNA sequences. In this review, we explore these recent applications and also highlight the unique advantages of using piggyBac for developing new molecular therapeutic strategies.
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Affiliation(s)
- Lauren E Woodard
- Department of Veterans Affairs, Tennessee Valley Health System, Nashville, TN, USA; Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew H Wilson
- Department of Veterans Affairs, Tennessee Valley Health System, Nashville, TN, USA; Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.
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24
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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.
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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.
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25
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Saha S, Woodard LE, Charron EM, Welch RC, Rooney CM, Wilson MH. Evaluating the potential for undesired genomic effects of the piggyBac transposon system in human cells. Nucleic Acids Res 2015; 43:1770-82. [PMID: 25605795 PMCID: PMC4330379 DOI: 10.1093/nar/gkv017] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Non-viral transposons have been used successfully for genetic modification of clinically relevant cells including embryonic stem, induced pluripotent stem, hematopoietic stem and primary human T cell types. However, there has been limited evaluation of undesired genomic effects when using transposons for human genome modification. The prevalence of piggyBac(PB)-like terminal repeat (TR) elements in the human genome raises concerns. We evaluated if there were undesired genomic effects of the PB transposon system to modify human cells. Expression of the transposase alone revealed no mobilization of endogenous PB-like sequences in the human genome and no increase in DNA double-strand breaks. The use of PB in a plasmid containing both transposase and transposon greatly increased the probability of transposase integration; however, using transposon and transposase from separate vectors circumvented this. Placing a eGFP transgene within transposon vector backbone allowed isolation of cells free from vector backbone DNA. We confirmed observable directional promoter activity within the 5'TR element of PB but found no significant enhancer effects from the transposon DNA sequence. Long-term culture of primary human cells modified with eGFP-transposons revealed no selective growth advantage of transposon-harboring cells. PB represents a promising vector system for genetic modification of human cells with limited undesired genomic effects.
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Affiliation(s)
- Sunandan Saha
- Department of Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lauren E Woodard
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elizabeth M Charron
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard C Welch
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cliona M Rooney
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA Department of Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew H Wilson
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA Department of Immunology, Baylor College of Medicine, Houston, TX 77030, USA
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26
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Ul Ain Q, Chung JY, Kim YH. Current and future delivery systems for engineered nucleases: ZFN, TALEN and RGEN. J Control Release 2014; 205:120-7. [PMID: 25553825 DOI: 10.1016/j.jconrel.2014.12.036] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/19/2014] [Accepted: 12/24/2014] [Indexed: 12/14/2022]
Abstract
Gene therapy by engineered nucleases is a genetic intervention being investigated for curing the hereditary disorders by targeting selected genes with specific nucleotides for establishment, suppression, abolishment of a function or correction of mutation. Here, we review the fast developing technology of targeted genome engineering using site specific programmable nucleases zinc finger nucleases (ZFNs), transcription activator like nucleases (TALENs) and cluster regulatory interspaced short palindromic repeat/CRISPR associated proteins (CRISPR/Cas) based RNA-guided DNA endonucleases (RGENs) and their different characteristics including pros and cons of genome modifications by these nucleases. We have further discussed different types of delivery methods to induce gene editing, novel development in genetic engineering other than nucleases and future prospects.
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Affiliation(s)
- Qurrat Ul Ain
- Department of Bioengineering, Institute for Bioengineering and Biopharmaceutical Research, BK 21 Plus Future Biopharmaceutical Human Resources Training and Research Team, Hanyang University, 133-791 Seoul, Republic of Korea
| | - Jee Young Chung
- Department of Bioengineering, Institute for Bioengineering and Biopharmaceutical Research, BK 21 Plus Future Biopharmaceutical Human Resources Training and Research Team, Hanyang University, 133-791 Seoul, Republic of Korea
| | - Yong-Hee Kim
- Department of Bioengineering, Institute for Bioengineering and Biopharmaceutical Research, BK 21 Plus Future Biopharmaceutical Human Resources Training and Research Team, Hanyang University, 133-791 Seoul, Republic of Korea.
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27
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Johnson ET, Dowd PF. A non-autonomous insect piggyBac transposable element is mobile in tobacco. Mol Genet Genomics 2014; 289:895-902. [PMID: 24858840 DOI: 10.1007/s00438-014-0860-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
The piggyBac transposable element, originally isolated from a virus in an insect cell line, is a valuable molecular tool for transgenesis and mutagenesis of invertebrates. For heterologous transgenesis in a variety of mammals, transfer of the piggyBac transposable element from an ectopic plasmid only requires expression of piggyBac transposase. To determine if piggyBac could function in dicotyledonous plants, a two-element system was developed in tobacco (Nicotiana tabacum) to test for transposable element excision and insertion. The first transgenic line constitutively expressed piggyBac transposase, while the second transgenic line contained at least two non-autonomous piggyBac transposable elements. Progeny from crosses of the two transgenic lines was analyzed for piggyBac excision and transposition. Several progeny displayed excision events, and all the sequenced excision sites exhibited evidence of the precise excision mechanism characteristic of piggyBac transposase. Two unique transposition insertion events were identified that each included diagnostic duplication of the target site. These data indicate that piggyBac transposase is active in a dicotyledonous plant, although at a low frequency.
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Affiliation(s)
- Eric T Johnson
- Crop Bioprotection Research, USDA ARS, 1815 N. University St, Peoria, IL, 61604, USA,
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28
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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.
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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.
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29
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Nemudryi AA, Valetdinova KR, Medvedev SP, Zakian SM. TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery. Acta Naturae 2014; 6:19-40. [PMID: 25349712 PMCID: PMC4207558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Precise studies of plant, animal and human genomes enable remarkable opportunities of obtained data application in biotechnology and medicine. However, knowing nucleotide sequences isn't enough for understanding of particular genomic elements functional relationship and their role in phenotype formation and disease pathogenesis. In post-genomic era methods allowing genomic DNA sequences manipulation, visualization and regulation of gene expression are rapidly evolving. Though, there are few methods, that meet high standards of efficiency, safety and accessibility for a wide range of researchers. In 2011 and 2013 novel methods of genome editing appeared - this are TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems. Although TALEN and CRISPR/Cas9 appeared recently, these systems have proved to be effective and reliable tools for genome engineering. Here we generally review application of these systems for genome editing in conventional model objects of current biology, functional genome screening, cell-based human hereditary disease modeling, epigenome studies and visualization of cellular processes. Additionally, we review general strategies for designing TALEN and CRISPR/Cas9 and analyzing their activity. We also discuss some obstacles researcher can face using these genome editing tools.
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Affiliation(s)
- A. A. Nemudryi
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
| | - K. R. Valetdinova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S. P. Medvedev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S. M. Zakian
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
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30
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Nemudryi AA, Valetdinova KR, Medvedev SP, Zakian SM. TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery. Acta Naturae 2014; 85:209-18. [PMID: 25349712 DOI: 10.1007/s11103-014-0188-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/05/2014] [Indexed: 05/07/2023] Open
Abstract
Precise studies of plant, animal and human genomes enable remarkable opportunities of obtained data application in biotechnology and medicine. However, knowing nucleotide sequences isn't enough for understanding of particular genomic elements functional relationship and their role in phenotype formation and disease pathogenesis. In post-genomic era methods allowing genomic DNA sequences manipulation, visualization and regulation of gene expression are rapidly evolving. Though, there are few methods, that meet high standards of efficiency, safety and accessibility for a wide range of researchers. In 2011 and 2013 novel methods of genome editing appeared - this are TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems. Although TALEN and CRISPR/Cas9 appeared recently, these systems have proved to be effective and reliable tools for genome engineering. Here we generally review application of these systems for genome editing in conventional model objects of current biology, functional genome screening, cell-based human hereditary disease modeling, epigenome studies and visualization of cellular processes. Additionally, we review general strategies for designing TALEN and CRISPR/Cas9 and analyzing their activity. We also discuss some obstacles researcher can face using these genome editing tools.
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Affiliation(s)
- A A Nemudryi
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
| | - K R Valetdinova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 ; Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S P Medvedev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 ; Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S M Zakian
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 ; Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
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31
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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.
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32
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Hong JB, Chou FJ, Ku AT, Fan HH, Lee TL, Huang YH, Yang TL, Su IC, Yu IS, Lin SW, Chien CL, Ho HN, Chen YT. A nucleolus-predominant piggyBac transposase, NP-mPB, mediates elevated transposition efficiency in mammalian cells. PLoS One 2014; 9:e89396. [PMID: 24586748 PMCID: PMC3933532 DOI: 10.1371/journal.pone.0089396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 01/20/2014] [Indexed: 11/25/2022] Open
Abstract
PiggyBac is a prevalent transposon system used to deliver transgenes and functionally explore the mammalian untouched genomic territory. The important features of piggyBac transposon are the relatively low insertion site preference and the ability of seamless removal from genome, which allow its potential uses in functional genomics and regenerative medicine. Efforts to increase its transposition efficiency in mammals were made through engineering the corresponding transposase (PBase) codon usage to enhance its expression level and through screening for mutant PBase variants with increased enzyme activity. To improve the safety for its potential use in regenerative medicine applications, site-specific transposition was achieved by using engineered zinc finger- and Gal4-fused PBases. An excision-prone PBase variant has also been successfully developed. Here we describe the construction of a nucleolus-predominant PBase, NP-mPB, by adding a nucleolus-predominant (NP) signal peptide from HIV-1 TAT protein to a mammalian codon-optimized PBase (mPB). Although there is a predominant fraction of the NP-mPB-tGFP fusion proteins concentrated in the nucleoli, an insertion site preference toward nucleolar organizer regions is not detected. Instead a 3–4 fold increase in piggyBac transposition efficiency is reproducibly observed in mouse and human cells.
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Affiliation(s)
- Jin-Bon Hong
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Fu-Ju Chou
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Amy T. Ku
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsiang-Hsuan Fan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tung-Lung Lee
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Yung-Hsin Huang
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Tsung-Lin Yang
- Department of Otolaryngology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Chang Su
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - I-Shing Yu
- Transgenic Mouse Model Core Facility of the National Research Program for Genomic Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Laboratory Animal Center, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Wha Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chung-Liang Chien
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Stem Cell Core Laboratory, National Taiwan University Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hong-Nerng Ho
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Stem Cell Core Laboratory, National Taiwan University Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - You-Tzung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Stem Cell Core Laboratory, National Taiwan University Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Program, National Taiwan University, Taipei, Taiwan
- * E-mail:
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33
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Bertino P, Urschitz J, Hoffmann FW, You BR, Rose AH, Park WH, Moisyadi S, Hoffmann PR. Vaccination with a piggyBac plasmid with transgene integration potential leads to sustained antigen expression and CD8(+) T cell responses. Vaccine 2014; 32:1670-7. [PMID: 24513010 DOI: 10.1016/j.vaccine.2014.01.063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 12/28/2022]
Abstract
DNA vaccination with plasmid has conventionally involved vectors designed for transient expression of antigens in injected tissues. Next generation plasmids are being developed for site-directed integration of transgenes into safe sites in host genomes and may provide an innovative approach for stable and sustained expression of antigens for vaccination. The goal of this study was to evaluate in vivo antigen expression and the generation of cell mediated immunity in mice injected with a non-integrating plasmid compared to a plasmid with integrating potential. Hyperactive piggyBac transposase-based integrating vectors (pmhyGENIE-3) contained a transgene encoding either eGFP (pmhyGENIE-3-eGFP) or luciferase (pmhyGENIE-3-GL3), and were compared to transposase-deficient plasmids with the same transgene and DNA backbone. Both non-integrating and integrating plasmids were equivalent at day 1 for protein expression at the site of injection. While protein expression from the non-integrating plasmid was lost by day 14, the pmhyGENIE-3 was found to exhibit sustained protein expression up to 28 days post-injection. Vaccination with pmhyGENIE-3-eGFP resulted in a robust CD8(+) T cell response that was three-fold higher than that of non-integrating plasmid vaccinations. Additionally we observed in splenocyte restimulation experiments that only the vaccination with pmhyGENIE-3-eGFP was characterized by IFNγ producing CD8(+) T cells. Overall, these findings suggest that plasmids designed to direct integration of transgenes into the host genome are a promising approach for designing DNA vaccines. Robust cell mediated CD8(+) T cell responses generated using integrating plasmids may provide effective, sustained protection against intracellular pathogens or tumor antigens.
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Affiliation(s)
- Pietro Bertino
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA.
| | - Johann Urschitz
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Fukun W Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Bo Ra You
- Department of Physiology, Medical School, Chonbuk National University, Jeonju, South Korea
| | - Aaron H Rose
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Woo Hyun Park
- Department of Physiology, Medical School, Chonbuk National University, Jeonju, South Korea
| | - Stefan Moisyadi
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA; Manoa BioSciences, Honolulu, HI 96822, USA
| | - Peter R Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
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Galvan DL, Kettlun CS, Wilson MH. Targeting piggyBac transposon integrations in the human genome. Methods Mol Biol 2014; 1114:143-61. [PMID: 24557901 DOI: 10.1007/978-1-62703-761-7_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA based transposon systems offer a technology for active and efficient delivery of genes into human cells. An emerging field is directed at manipulating such systems to achieve site-directed integration as compared to un-targeted integration which occurs with native or unmodified transposon systems. The naturally active piggyBac transposon system is derived from insects but has been shown to be very efficient in gene-modifying human cells. Recent efforts have utilized the fusion of DNA binding domains to the piggyBac transposase enzyme with the goal of targeting integration to specific locations in the human genome. In this chapter, we describe methodology for engineering and characterizing chimeric piggyBac transposase enzymes, including experimental approaches for evaluating activity and targeting specificity in the human genome.
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Affiliation(s)
- Daniel L Galvan
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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Owens JB, Mathews J, Davy P, Stoytchev I, Moisyadi S, Allsopp R. Effective Targeted Gene Knockdown in Mammalian Cells Using the piggyBac Transposase-based Delivery System. MOLECULAR THERAPY. NUCLEIC ACIDS 2013; 2:e137. [PMID: 24326734 PMCID: PMC3894583 DOI: 10.1038/mtna.2013.61] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/08/2013] [Indexed: 11/09/2022]
Abstract
Nonviral gene delivery systems are rapidly becoming a desirable and applicable method to overexpress genes in various types of cells. We have recently developed a piggyBac transposase-based, helper-independent and self-inactivating delivery system (pmGENIE-3) capable of high-efficiency transfection of mammalian cells including human cells. In the following study, we have assessed the potential of this delivery system to drive the expression of short hairpin RNAs to knock down genes in human cells. Two independent pmGENIE-3 vectors were developed to specifically target knockdown of an endogenous gene, telomerase reverse transcriptase (TERT), in telomerase-positive human immortalized cell lines. As compared with a transposase-deficient vector, pmGENIE-3 showed significantly improved short-term transfection efficiency (~4-fold enhancement, 48 hours posttransfection) and long-term integration efficiency (~5-fold enhancement) following antibiotic selection. We detected a significant reduction of both TERT expression and telomerase activity in both HEK293 and MCF-7 breast carcinoma cells transfected with two pmGENIE-3 construct targeting distinct regions of TERT. Importantly, this knockdown of expression was sufficient to abrogate telomerase function since telomeres were significantly shortened (3-4 Kb, P < 0.001) in both TERT-targeted cell lines following antibiotic selection of stable integrants. Together, these data show the capacity of the piggyBac nonviral delivery system to stably knockdown gene expression in mammalian cells and indicate the potential to develop novel tumor-targeting therapies.Molecular Therapy-Nucleic Acids (2013) 2, e137; doi:10.1038/mtna.2013.61; published online 3 December 2013.
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Affiliation(s)
- Jesse B Owens
- Department of Anatomy, Biochemistry, and Physiology Institute for Biogenesis Research, University of Hawaii, Honolulu, Hawaii, USA
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Owens JB, Mauro D, Stoytchev I, Bhakta MS, Kim MS, Segal DJ, Moisyadi S. Transcription activator like effector (TALE)-directed piggyBac transposition in human cells. Nucleic Acids Res 2013; 41:9197-207. [PMID: 23921635 PMCID: PMC3799441 DOI: 10.1093/nar/gkt677] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 12/13/2022] Open
Abstract
Insertional therapies have shown great potential for combating genetic disease and safer methods would undoubtedly broaden the variety of possible illness that can be treated. A major challenge that remains is reducing the risk of insertional mutagenesis due to random insertion by both viral and non-viral vectors. Targetable nucleases are capable of inducing double-stranded breaks to enhance homologous recombination for the introduction of transgenes at specific sequences. However, off-target DNA cleavages at unknown sites can lead to mutations that are difficult to detect. Alternatively, the piggyBac transposase is able perform all of the steps required for integration; therefore, cells confirmed to contain a single copy of a targeted transposon, for which its location is known, are likely to be devoid of aberrant genomic modifications. We aimed to retarget transposon insertions by comparing a series of novel hyperactive piggyBac constructs tethered to a custom transcription activator like effector DNA-binding domain designed to bind the first intron of the human CCR5 gene. Multiple targeting strategies were evaluated using combinations of both plasmid-DNA and transposase-protein relocalization to the target sequence. We demonstrated user-defined directed transposition to the CCR5 genomic safe harbor and isolated single-copy clones harboring targeted integrations.
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Affiliation(s)
- Jesse B. Owens
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Damiano Mauro
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Ilko Stoytchev
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Mital S. Bhakta
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Moon-Soo Kim
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - David J. Segal
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Stefan Moisyadi
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
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Meir YJJ, Lin A, Huang MF, Lin JR, Weirauch MT, Chou HC, Lin SJA, Wu SCY. A versatile, highly efficient, and potentially safer piggyBac transposon system for mammalian genome manipulations. FASEB J 2013; 27:4429-43. [PMID: 23896728 DOI: 10.1096/fj.12-223586] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The piggyBac transposon is one of the most attractive nonviral tools for mammalian genome manipulations. Given that piggybac mobilizes in a "cut-and-paste" fashion, integrant remobilization could potentially damage the host genome. Here, we report a novel piggyBac transposon system with a series of recombinant transposases. We found that the transposition activity of wild-type (PBase) and hyperactive (hyPBase) piggyBac transposases can be significantly increased by peptide fusions in a cell-type dependent fashion, with the greatest change typically seen in mouse embryonic stem (ES) cells. The two most potent recombinant transposases, TPLGMH and ThyPLGMH, give a 9- and 7-fold increase, respectively, in the number of integrants in HEK293 compared with Myc-tagged PBase (MycPBase), and both display 4-fold increase in generating induced pluripotential stem cells. Interestingly, ThyPLGMH but not TPLGMH shows improved chromosomal excision activity (2.5-fold). This unique feature of TPLGMH provides the first evidence that integration activity of a transposase can be drastically improved without increasing its remobilization activity. Transposition catalyzed by ThyPLGMH is more random and occurs further from CpG islands than that catalyzed by MycPBase or TPLGMH. Our transposon system diversifies the mammalian genetic toolbox and provides a spectrum of piggyBac transposases that is better suited to different experimental purposes.
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Affiliation(s)
- Yaa-Jyuhn James Meir
- 1S.C.-Y.W., Institute of Molecular Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan 333.
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PK-15 cells transfected with porcine CD163 by PiggyBac transposon system are susceptible to porcine reproductive and respiratory syndrome virus. J Virol Methods 2013; 193:383-90. [PMID: 23835031 DOI: 10.1016/j.jviromet.2013.06.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/18/2013] [Accepted: 06/26/2013] [Indexed: 01/12/2023]
Abstract
The PiggyBac (PB) transposon system is a non-viral DNA-transfer system in which a transposase directs integration of a PB transposon into a TTAA site in the genome. Transgenic expression of porcine CD163 is necessary and sufficient to confer non-permissive cells susceptible to infection with porcine reproductive and respiratory syndrome virus (PRRSV). Such permissive cells can be used as a tool for PRRSV cellular receptor and other studies. One of the problems in studying PRRSV is the lack of porcine cell lines. In this study, efficient transfection and expression of porcine CD163 in PK-15 cells by PB transposition was demonstrated. The stable PK-15CD163 cell line was used in PRRSV infection assays. The data indicated that the average PB transgene copy number per genome was approximately 10. In line with previous literature the integration of PB into the genome had a bias toward the TTAA chromosomal site. The PK-15CD163 cell line was susceptible to infection by different PRRSV strains and the virus grew to similar titers compared to the Marc-145 cell line. This simplification of PK-15CD163 cell line production will provide a valuable tool to facilitate PRRSV cellular receptor studies and to accelerate existing vectors for PK-15 cell-based gene transfer and expression.
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Abstract
Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. These chimeric nucleases are composed of programmable, sequence-specific DNA-binding modules linked to a nonspecific DNA cleavage domain. ZFNs and TALENs enable a broad range of genetic modifications by inducing DNA double-strand breaks that stimulate error-prone nonhomologous end joining or homology-directed repair at specific genomic locations. Here, we review achievements made possible by site-specific nuclease technologies and discuss applications of these reagents for genetic analysis and manipulation. In addition, we highlight the therapeutic potential of ZFNs and TALENs and discuss future prospects for the field, including the emergence of clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas-based RNA-guided DNA endonucleases.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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40
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78495111110.1016/j.tibtech.2013.04.004" />
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41
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Abstract
The piggyBac transposon system is a promising nonviral method to genetically modify T cells for immunotherapeutic applications. To evaluate the regulation and stability of transgene expression in human T cells modified with piggyBac-transposons, peripheral blood mononuclear cells were nucleofected with transposase and an enhanced green fluorescence protein (eGFP)-expressing transposon. Single-cell clones that were subsequently stimulated and expanded exhibited homogenous eGFP expression for >26 weeks in culture. CD3 stimulation of the T-cell receptor together with CD28-mediated costimulation resulted in an approximate 10-fold transient increase in eGFP expression, but immunomodulatory cytokines, including interferon-γ, interleukin-12, interleukin-4, and transforming growth factor-β, did not alter transgene expression in actively dividing, activated, or resting T cells. Epigenetic modification with 5-azacytidine or trichostatin-A increased transgene expression indicating that piggyBac-mediated transgene expression could be modulated by methylation or histone acetylation, respectively. We performed transposon copy number analysis of populations of stably transfected T cells, comparing transposon plasmids of 5.6 and 3.5 kb. The smaller vector achieved an average of 22 transposon copies per cell, whereas the larger vector achieved 1.6 copies/cell, implying that transposon copy number can be engineered to be low or high depending on the vector used. Our results provide important insight into the ability of piggyBac to achieve stable genetic modification of T cells for immunotherapy applications and how transgene expression might be regulated by TCR activation, cytokines, and epigenetic mechanisms.
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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.
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Gaj T, Gersbach CA, Barbas CF. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 2013; 31:397-405. [PMID: 23664777 DOI: 10.1016/j.tibtech.2013.04.004] [Citation(s) in RCA: 2321] [Impact Index Per Article: 211.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 04/13/2013] [Accepted: 04/13/2013] [Indexed: 12/11/2022]
Abstract
Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. These chimeric nucleases are composed of programmable, sequence-specific DNA-binding modules linked to a nonspecific DNA cleavage domain. ZFNs and TALENs enable a broad range of genetic modifications by inducing DNA double-strand breaks that stimulate error-prone nonhomologous end joining or homology-directed repair at specific genomic locations. Here, we review achievements made possible by site-specific nuclease technologies and discuss applications of these reagents for genetic analysis and manipulation. In addition, we highlight the therapeutic potential of ZFNs and TALENs and discuss future prospects for the field, including the emergence of clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas-based RNA-guided DNA endonucleases.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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44
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Hyperactive self-inactivating piggyBac for transposase-enhanced pronuclear microinjection transgenesis. Proc Natl Acad Sci U S A 2012; 109:19184-9. [PMID: 23093669 DOI: 10.1073/pnas.1216473109] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We have developed a unique method for mouse transgenesis. The transposase-enhanced pronuclear microinjection (PNI) technique described herein uses the hyperactive piggyBac transposase to insert a large transgene into the mouse genome. This procedure increased transgene integration efficiency by fivefold compared with conventional PNI or intracytoplasmic sperm injection-mediated transgenesis. Our data indicate that the transposase-enhanced PNI technique additionally requires fewer embryos to be microinjected than traditional methods to obtain transgenic animals. This transposase-mediated approach is also very efficient for single-cell embryo cytoplasmic injections, offering an easy-to-implement transgenesis method to the scientific community.
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