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Chow EWL, Song Y, Wang H, Xu X, Gao J, Wang Y. Genome-wide profiling of piggyBac transposon insertion mutants reveals loss of the F 1F 0 ATPase complex causes fluconazole resistance in Candida glabrata. Mol Microbiol 2024; 121:781-797. [PMID: 38242855 DOI: 10.1111/mmi.15229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/21/2024]
Abstract
Invasive candidiasis caused by non-albicans species has been on the rise, with Candida glabrata emerging as the second most common etiological agent. Candida glabrata possesses an intrinsically lower susceptibility to azoles and an alarming propensity to rapidly develop high-level azole resistance during treatment. In this study, we have developed an efficient piggyBac (PB) transposon-mediated mutagenesis system in C. glabrata to conduct genome-wide genetic screens and applied it to profile genes that contribute to azole resistance. When challenged with the antifungal drug fluconazole, PB insertion into 270 genes led to significant resistance. A large subset of these genes has a role in the mitochondria, including almost all genes encoding the subunits of the F1F0 ATPase complex. We show that deleting ATP3 or ATP22 results in increased azole resistance but does not affect susceptibility to polyenes and echinocandins. The increased azole resistance is due to increased expression of PDR1 that encodes a transcription factor known to promote drug efflux pump expression. Deleting PDR1 in the atp3Δ or atp22Δ mutant resulted in hypersensitivity to fluconazole. Our results shed light on the mechanisms contributing to azole resistance in C. glabrata. This PB transposon-mediated mutagenesis system can significantly facilitate future genome-wide genetic screens.
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Affiliation(s)
- Eve W L Chow
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science and Technology Research (A*STAR), Singapore, Singapore
| | - Yabing Song
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haitao Wang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science and Technology Research (A*STAR), Singapore, Singapore
| | - Xiaoli Xu
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science and Technology Research (A*STAR), Singapore, Singapore
| | - Jiaxin Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yue Wang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science and Technology Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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2
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Marie C, Scherman D. Antibiotic-Free Gene Vectors: A 25-Year Journey to Clinical Trials. Genes (Basel) 2024; 15:261. [PMID: 38540320 PMCID: PMC10970329 DOI: 10.3390/genes15030261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 06/15/2024] Open
Abstract
Until very recently, the major use, for gene therapy, specifically of linear or circular DNA, such as plasmids, was as ancillary products for viral vectors' production or as a genetic template for mRNA production. Thanks to targeted and more efficient physical or chemical delivery techniques and to the refinement of their structure, non-viral plasmid DNA are now under intensive consideration as pharmaceutical drugs. Plasmids traditionally carry an antibiotic resistance gene for providing the selection pressure necessary for maintenance in a bacterial host. Nearly a dozen different antibiotic-free gene vectors have now been developed and are currently assessed in preclinical assays and phase I/II clinical trials. Their reduced size leads to increased transfection efficiency and prolonged transgene expression. In addition, associating non-viral gene vectors and DNA transposons, which mediate transgene integration into the host genome, circumvents plasmid dilution in dividing eukaryotic cells which generate a loss of the therapeutic gene. Combining these novel molecular tools allowed a significantly higher yield of genetically engineered T and Natural Killer cells for adoptive immunotherapies due to a reduced cytotoxicity and increased transposition rate. This review describes the main progresses accomplished for safer, more efficient and cost-effective gene and cell therapies using non-viral approaches and antibiotic-free gene vectors.
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Affiliation(s)
- Corinne Marie
- Université Paris Cité, CNRS, Inserm, UTCBS, 75006 Paris, France;
- Chimie ParisTech, Université PSL, 75005 Paris, France
| | - Daniel Scherman
- Université Paris Cité, CNRS, Inserm, UTCBS, 75006 Paris, France;
- Fondation Maladies Rares, 75014 Paris, France
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3
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Ma Y, Sun W, Bai J, Gao F, Ma H, Liu H, Hu J, Xu C, Zhang X, Liu Z, Yuan T, Sun C, Huang Y, Wang R. Targeting blood brain barrier-Remote ischemic conditioning alleviates cognitive impairment in female APP/PS1 rats. CNS Neurosci Ther 2024; 30:e14613. [PMID: 38379185 PMCID: PMC10879645 DOI: 10.1111/cns.14613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/16/2023] [Accepted: 11/26/2023] [Indexed: 02/22/2024] Open
Abstract
AIMS Alzheimer's disease (AD) is a significant global health concern, and it is crucial that we find effective methods to prevent or slow down AD progression. Recent studies have highlighted the essential role of blood vessels in clearing Aβ, a protein that contributes to AD. Scientists are exploring blood biomarkers as a potential tool for future AD diagnosis. One promising method that may help prevent AD is remote ischemic conditioning (RIC). RIC involves using sub-lethal ischemic-reperfusion cycles on limbs. However, a comprehensive understanding of how RIC can prevent AD and its long-term effectiveness is still lacking. Further research is essential to fully comprehend the potential benefits of RIC in preventing AD. METHODS Female wild-type (WT) and APP/PS1 transgenic rats, aged 12 months, underwent ovariectomy and were subsequently assigned to WT, APP/PS1, and APP/PS1 + RIC groups. RIC was conducted five times a week for 4 weeks. The rats' depressive and cognitive behaviors were evaluated using force swimming, open-field tests, novel objective recognition, elevated plus maze, and Barnes maze tests. Evaluation of the neurovascular unit (NVU), synapses, vasculature, astrocytes, and microglia was conducted using immunofluorescence staining (IF), Western blot (WB), and transmission electron microscopy (TEM). Additionally, the cerebro-vasculature was examined using micro-CT, and cerebral blood flow (CBF) was measured using Speckle Doppler. Blood-brain barrier (BBB) permeability was determined by measuring the Evans blue leakage. Finally, Aβ levels in the rat frontal cortex were measured using WB, ELISA, or IF staining. RESULTS RIC enhanced memory-related protein expression and rescued depressive-like behavior and cognitive decline in APP/PS1 transgenic rats. Additionally, the intervention protected NVU in the rat frontal cortex, as evidenced by (1) increased expression of TJ (tight junction) proteins, pericyte marker PDGFRβ, and glucose transporter 1 (GLUT1), as well as decreased VCAM1; (2) mitigation of ultrastructure impairment in neuron, cerebral vascular, and astrocyte; (3) upregulation of A2 astrocyte phenotype markers and downregulation of A1 phenotype markers, indicating a shift toward a healthier phenotype. Correspondingly, RIC intervention alleviated neuroinflammation, as evidenced by the decreased Iba1 level, a microglia marker. Meanwhile, RIC intervention elevated CBF in frontal cortex of the rats. Notably, RIC intervention effectively suppressed Aβ toxicity, as demonstrated by the enhancement of α-secretase and attenuation of β-secretase (BACE1) and γ- secretase and Aβ1-42 and Aβ1-40 levels as well. CONCLUSION Chronic RIC intervention exerts vascular and neuroprotective roles, suggesting that RIC could be a promising therapeutic strategy targeting the BBB and NVU during AD development.
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Affiliation(s)
- Yuxuan Ma
- International Science & Technology Cooperation Base of GeriatricSchool of Public Health of North China University of Science and TechnologyTangshanHebeiChina
| | - Wuxiang Sun
- School of Basic Medical ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Jing Bai
- School of Basic Medical ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Fujia Gao
- International Science & Technology Cooperation Base of GeriatricSchool of Public Health of North China University of Science and TechnologyTangshanHebeiChina
| | - Haoran Ma
- International Science & Technology Cooperation Base of GeriatricSchool of Public Health of North China University of Science and TechnologyTangshanHebeiChina
| | - Huiyu Liu
- International Science & Technology Cooperation Base of GeriatricSchool of Public Health of North China University of Science and TechnologyTangshanHebeiChina
| | - Jiewei Hu
- School of Basic Medical ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Chao Xu
- International Science & Technology Cooperation Base of GeriatricSchool of Public Health of North China University of Science and TechnologyTangshanHebeiChina
| | - Xin Zhang
- International Science & Technology Cooperation Base of GeriatricSchool of Public Health of North China University of Science and TechnologyTangshanHebeiChina
| | - Zixuan Liu
- School of Basic Medical ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Tao Yuan
- International Science & Technology Cooperation Base of GeriatricSchool of Public Health of North China University of Science and TechnologyTangshanHebeiChina
| | - Chenxu Sun
- School of Basic Medical ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Yuanyuan Huang
- School of Basic Medical ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Ruimin Wang
- International Science & Technology Cooperation Base of GeriatricSchool of Public Health of North China University of Science and TechnologyTangshanHebeiChina
- School of Basic Medical ScienceNorth China University of Science and TechnologyTangshanHebeiChina
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4
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Guo M, Addy GA, Yang N, Asare E, Wu H, Saleh AA, Shi S, Gao B, Song C. PiggyBac Transposon Mining in the Small Genomes of Animals. BIOLOGY 2023; 13:24. [PMID: 38248455 PMCID: PMC10813416 DOI: 10.3390/biology13010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
TEs, including DNA transposons, are major contributors of genome expansions, and have played a very significant role in shaping the evolution of animal genomes, due to their capacity to jump from one genomic position to the other. In this study, we investigated the evolution landscapes of PB transposons, including their distribution, diversity, activity and structure organization in 79 species of small (compact) genomes of animals comprising both vertebrate and invertebrates. Overall, 212 PB transposon types were detected from almost half (37) of the total number of the small genome species (79) investigated. The detected PB transposon types, which were unevenly distributed in various genera and phyla, have been classified into seven distinct clades or families with good bootstrap support (>80%). The PB transposon types that were identified have a length ranging from 1.23 kb to 9.51 kb. They encode transposases of approximately ≥500 amino acids in length, and possess terminal inverted repeats (TIRs) ranging from 4 bp to 24 bp. Though some of the transposon types have long TIRs (528 bp), they still maintain the consistent and reliable 4 bp target site duplication (TSD) of TTAA. However, PiggyBac-2_Cvir transposon originating from the Crassostrea virginica species exhibits a unique TSD of TATG. The TIRs of the transposons in all the seven families display high divergence, with a highly conserved 5' end motif. The core transposase domains (DDD) were better conserved among the seven different families compared to the other protein domains, which were less prevalent in the vertebrate genome. The divergent evolution dynamics analysis also indicated that the majority of the PB transposon types identified in this study are either relatively young or old, with some being active. Additionally, numerous invasions of PB transposons were found in the genomes of both vertebrate and invertebrate animals. The data reveals that the PB superfamily is widely distributed in these species. PB transposons exhibit high diversity and activity in the small genomes of animals, and might play a crucial role in shaping the evolution of these small genomes of animals.
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Affiliation(s)
- Mengke Guo
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - George A. Addy
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Naisu Yang
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Emmanuel Asare
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Han Wu
- Department of Immunology, School of Medicine, Shenzhen University, Shenzhen 518060, China;
| | - Ahmed A. Saleh
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City 11865, Egypt
| | - Shasha Shi
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
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5
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Hua WK, Hsu JC, Chen YC, Chang PS, Wen KLK, Wang PN, Yang WC, Shen CN, Yu YS, Chen YC, Cheng IC, Wu SCY. Quantum pBac: An effective, high-capacity piggyBac-based gene integration vector system for unlocking gene therapy potential. FASEB J 2023; 37:e23108. [PMID: 37534940 DOI: 10.1096/fj.202201654r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/02/2023] [Accepted: 07/12/2023] [Indexed: 08/04/2023]
Abstract
Recent advances in gene therapy have brought novel treatment options for cancer. However, the full potential of this approach has yet to be unlocked due to the limited payload capacity of commonly utilized viral vectors. Virus-free DNA transposons, including piggyBac, have the potential to obviate these shortcomings. In this study, we improved a previously modified piggyBac system with superior transposition efficiency. We demonstrated that the internal domain sequences (IDS) within the 3' terminal repeat domain of hyperactive piggyBac (hyPB) donor vector contain dominant enhancer elements. Plasmid-free donor vector devoid of IDS was used in conjunction with a helper plasmid expressing Quantum PBase™ v2 to generate an optimal piggyBac system, Quantum pBac™ (qPB), for use in T cells. qPB outperformed hyPB in CD20/CD19 CAR-T production in terms of performance as well as yield of the CAR-T cells produced. Furthermore, qPB also produced CAR-T cells with lower donor-associated variabilities compared to lentiviral vector. Importantly, qPB yielded mainly CD8+ CAR-TSCM cells, and the qPB-produced CAR-T cells effectively eliminated CD20/CD19-expressing tumor cells both in vitro and in vivo. Our findings confirm qPB as a promising virus-free vector system with an enhanced payload capacity to incorporate multiple genes. This highly efficient and potentially safe system will be expected to further advance gene therapy applications.
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Affiliation(s)
- Wei-Kai Hua
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Jeff C Hsu
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Yi-Chun Chen
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Peter S Chang
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | | | - Po-Nan Wang
- Division of Hematology, Chang Gung Medical Foundation, Taipei City, Taiwan ROC
| | - Wei-Cheng Yang
- Biomedical Translation Research Center, Academia Sinica, Taipei City, Taiwan ROC
| | - Chia-Ning Shen
- Biomedical Translation Research Center, Academia Sinica, Taipei City, Taiwan ROC
- Genomics Research Center, Academia Sinica, Taipei City, Taiwan ROC
| | - Yi-Shan Yu
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Ying-Chun Chen
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - I-Cheng Cheng
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
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Luo W, Hickman AB, Genzor P, Ghirlando R, Furman C, Menshikh A, Haase A, Dyda F, Wilson M. Transposase N-terminal phosphorylation and asymmetric transposon ends inhibit piggyBac transposition in mammalian cells. Nucleic Acids Res 2022; 50:13128-13142. [PMID: 36537219 PMCID: PMC9825180 DOI: 10.1093/nar/gkac1191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/09/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
DNA transposon systems are widely used in mammalian cells for genetic modification experiments, but their regulation remains poorly understood. We used biochemical and cell-based assays together with AlphaFold modeling and rational protein redesign to evaluate aspects of piggyBac transposition including the previously unexplained role of the transposase N-terminus and the need for asymmetric transposon ends for cellular activity. We found that phosphorylation at predicted casein kinase II sites in the transposase N-terminus inhibits transposition, most likely by preventing transposase-DNA interactions. Deletion of the region containing these sites releases inhibition thereby enhancing activity. We also found that the N-terminal domain promotes transposase dimerization in the absence of transposon DNA. When the N-terminus is deleted, the transposase gains the ability to carry out transposition using symmetric transposon left ends. This novel activity is also conferred by appending a second C-terminal domain. When combined, these modifications together result in a transposase that is highly active when symmetric transposon ends are used. Our results demonstrate that transposase N-terminal phosphorylation and the requirement for asymmetric transposon ends both negatively regulate piggyBac transposition in mammalian cells. These novel insights into the mechanism and structure of the piggyBac transposase expand its potential use for genomic applications.
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Affiliation(s)
- Wentian Luo
- Department of Medicine, Division and Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pavol Genzor
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher M Furman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna Menshikh
- Department of Medicine, Division and Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Astrid Haase
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew H Wilson
- Department of Medicine, Division and Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Veterans Affairs, Nashville, TN 37212, USA
- Departments of Pharmacology and Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
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7
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Application of the Mutant Libraries for Candida albicans Functional Genomics. Int J Mol Sci 2022; 23:ijms232012307. [PMID: 36293157 PMCID: PMC9603287 DOI: 10.3390/ijms232012307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Candida albicans is a typical opportunistic pathogen in humans that causes serious health risks in clinical fungal infections. The construction of mutant libraries has made remarkable developments in the study of C. albicans molecular and cellular biology with the ongoing advancements of gene editing, which include the application of CRISPR-Cas9 and novel high-efficient transposon. Large-scale genetic screens and genome-wide functional analysis accelerated the investigation of new genetic regulatory mechanisms associated with the pathogenicity and resistance to environmental stress in C. albicans. More importantly, sensitivity screening based on C. albicans mutant libraries is critical for the target identification of novel antifungal compounds, which leads to the discovery of Sec7p, Tfp1p, Gwt1p, Gln4p, and Erg11p. This review summarizes the main types of C. albicans mutant libraries and interprets their applications in morphogenesis, biofilm formation, fungus-host interactions, antifungal drug resistance, and target identification.
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Leem JW, Jeon HJ, Ji Y, Park SM, Kwak Y, Park J, Kim KY, Kim SW, Kim YL. Edible Matrix Code with Photogenic Silk Proteins. ACS CENTRAL SCIENCE 2022; 8:513-526. [PMID: 35647284 PMCID: PMC9136975 DOI: 10.1021/acscentsci.1c01233] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 05/28/2023]
Abstract
Counterfeit medicines are a healthcare security problem, posing not only a direct threat to patient safety and public health but also causing heavy economic losses. Current anticounterfeiting methods are limited due to the toxicity of the constituent materials and the focus of secondary packaging level protections. We introduce an edible, imperceptible, and scalable matrix code of information representation and data storage for pharmaceutical products. This matrix code is digestible as it is composed of silk fibroin genetically encoded with fluorescent proteins produced by ecofriendly, sustainable silkworm farming. Three distinct fluorescence emission colors are incorporated into a multidimensional parameter space with a variable encoding capacity in a format of matrix arrays. This code is smartphone-readable to extract a digitized security key augmented by a deep neural network for overcoming fabrication imperfections and a cryptographic hash function for enhanced security. The biocompatibility, photostability, thermal stability, long-term reliability, and low bit error ratio of the code support the immediate feasibility for dosage-level anticounterfeit measures and authentication features. The edible code affixed to each medicine can serve as serialization, track and trace, and authentication at the dosage level, empowering every patient to play a role in combating illicit pharmaceuticals.
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Affiliation(s)
- Jung Woo Leem
- Weldon
School of Biomedical Engineering, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Hee-Jae Jeon
- Weldon
School of Biomedical Engineering, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Yuhyun Ji
- Weldon
School of Biomedical Engineering, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Sang Mok Park
- Weldon
School of Biomedical Engineering, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Yunsang Kwak
- Department
of Mechanical System Engineering, Kumoh
National Institute of Technology, 61 Daehak-ro, Gumi-si, Gyeongsangbuk-do 39177, Republic of Korea
| | - Jongwoo Park
- Department
of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Jeollabuk-do 55365, Republic of Korea
| | - Kee-Young Kim
- Department
of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Jeollabuk-do 55365, Republic of Korea
| | - Seong-Wan Kim
- Department
of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Jeollabuk-do 55365, Republic of Korea
| | - Young L. Kim
- Weldon
School of Biomedical Engineering, Purdue
University, West Lafayette, Indiana 47907, United States
- Purdue
University Center for Cancer Research, West Lafayette, Indiana 47907, United States
- Regenstrief
Center for Healthcare Engineering, West Lafayette, Indiana 47907, United States
- Purdue Quantum
Science and Engineering Institute, West Lafayette, Indiana 47907, United States
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9
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Dierick HA, Ben-Shahar Y, Raman B, Gabbiani F. Genetic and viral approaches to record or manipulate neurons in insects. CURRENT OPINION IN INSECT SCIENCE 2021; 48:79-88. [PMID: 34710643 PMCID: PMC8648980 DOI: 10.1016/j.cois.2021.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 05/11/2023]
Abstract
The development of genetically encoded tools to record and manipulate neurons in vivo has greatly increased our understanding of how neuronal activity affects behavior. Recent advances enable the use of these tools in species not typically considered genetically tractable. This progress is revolutionizing neuroscience in general, and insect neuroethology in particular. Here we cover the latest innovations and some of their applications in phylogenetically diverse insect species. We discuss the importance and implications of these approaches for both basic and translational research. We focus on genetically encoded and virally encoded tools used for calcium imaging, optogenetics, and synaptic silencing. Finally, we discuss potential future developments of universally applicable, modular, and user-friendly genetic toolkits for neuroethological studies of insect behavior.
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Affiliation(s)
- Herman A Dierick
- Dep. of Human and Molecular Genetics, Baylor College of Medicine, United States
| | | | - Baranidharan Raman
- Dep. of Bioengineering, Washington University in St. Louis, United States
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10
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Vierl F, Kaur M, Götz M. Non-codon Optimized PiggyBac Transposase Induces Developmental Brain Aberrations: A Call for in vivo Analysis. Front Cell Dev Biol 2021; 9:698002. [PMID: 34414186 PMCID: PMC8369470 DOI: 10.3389/fcell.2021.698002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
In this perspective article, we briefly review tools for stable gain-of-function expression to explore key fate determinants in embryonic brain development. As the piggyBac transposon system has the highest insert size, a seamless integration of the transposed sequence into the host genome, and can be delivered by transfection avoiding viral vectors causing an immune response, we explored its use in the murine developing forebrain. The original piggyBac transposase PBase or the mouse codon-optimized version mPB and the construct to insert, contained in the piggyBac transposon, were introduced by in utero electroporation at embryonic day 13 into radial glia, the neural stem cells, in the developing dorsal telencephalon, and analyzed 3 or 5 days later. When using PBase, we observed an increase in basal progenitor cells, often accompanied by folding aberrations. These effects were considerably ameliorated when using the piggyBac plasmid together with mPB. While size and strength of the electroporated region was not correlated to the aberrations, integration was essential and the positive correlation to the insert size implicates the frequency of transposition as a possible mechanism. We discuss this in light of the increase in transposing endogenous viral vectors during mammalian phylogeny and their role in neurogenesis and radial glial cells. Most importantly, we aim to alert the users of this system to the phenotypes caused by non-codon optimized PBase application in vivo.
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Affiliation(s)
- Franziska Vierl
- Institute for Stem Cell Research, Helmholtz Zentrum München, Munich, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany.,Graduate School of Systemic Neurosciences, Ludwig-Maximilians-Universität, Munich, Germany
| | - Manpreet Kaur
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Zentrum München, Munich, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany.,SyNergy, Munich Cluster for Systems Neurology, Ludwig-Maximilians-Universität, Munich, Germany
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Beckermann TM, Luo W, Wilson CM, Veach RA, Wilson MH. Cognate restriction of transposition by piggyBac-like proteins. Nucleic Acids Res 2021; 49:8135-8144. [PMID: 34232995 DOI: 10.1093/nar/gkab578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/16/2021] [Accepted: 06/26/2021] [Indexed: 11/14/2022] Open
Abstract
Mobile genetic elements have been harnessed for gene transfer for a wide variety of applications including generation of stable cell lines, recombinant protein production, creation of transgenic animals, and engineering cell and gene therapy products. The piggyBac transposon family includes transposase or transposase-like proteins from a variety of species including insect, bat and human. Recently, human piggyBac transposable element derived 5 (PGBD5) protein was reported to be able to transpose piggyBac transposons in human cells raising possible safety concerns for piggyBac-mediated gene transfer applications. We evaluated three piggyBac-like proteins across species including piggyBac (insect), piggyBat (bat) and PGBD5 (human) for their ability to mobilize piggyBac transposons in human cells. We observed a lack of cross-species transposition activity. piggyBac and piggyBat activity was restricted to their cognate transposons. PGBD5 was unable to mobilize piggyBac transposons based on excision, colony count and plasmid rescue analysis, and it was unable to bind piggyBac terminal repeats. Within the piggyBac family, we observed a lack of cross-species activity and found that PGBD5 was unable to bind, excise or integrate piggyBac transposons in human cells. Transposition activity appears restricted within species within the piggyBac family of mobile genetic elements.
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Affiliation(s)
- Thomas M Beckermann
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA
| | - Wentian Luo
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA
| | - Catherine M Wilson
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ruth Ann Veach
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA
| | - Matthew H Wilson
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA.,Departments of Pharmacology and Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
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12
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Sandoval-Villegas N, Nurieva W, Amberger M, Ivics Z. Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications of Sleeping Beauty, piggyBac and Tol2 for Genome Engineering. Int J Mol Sci 2021; 22:ijms22105084. [PMID: 34064900 PMCID: PMC8151067 DOI: 10.3390/ijms22105084] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/19/2023] Open
Abstract
Transposons are mobile genetic elements evolved to execute highly efficient integration of their genes into the genomes of their host cells. These natural DNA transfer vehicles have been harnessed as experimental tools for stably introducing a wide variety of foreign DNA sequences, including selectable marker genes, reporters, shRNA expression cassettes, mutagenic gene trap cassettes, and therapeutic gene constructs into the genomes of target cells in a regulated and highly efficient manner. Given that transposon components are typically supplied as naked nucleic acids (DNA and RNA) or recombinant protein, their use is simple, safe, and economically competitive. Thus, transposons enable several avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture comprising the generation of pluripotent stem cells, the production of germline-transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species and therapy of genetic disorders in humans. This review describes the molecular mechanisms involved in transposition reactions of the three most widely used transposon systems currently available (Sleeping Beauty, piggyBac, and Tol2), and discusses the various parameters and considerations pertinent to their experimental use, highlighting the state-of-the-art in transposon technology in diverse genetic applications.
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Affiliation(s)
| | | | | | - Zoltán Ivics
- Correspondence: ; Tel.: +49-6103-77-6000; Fax: +49-6103-77-1280
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13
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Schrevens S, Sanglard D. Hijacking Transposable Elements for Saturation Mutagenesis in Fungi. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:633876. [PMID: 37744130 PMCID: PMC10512250 DOI: 10.3389/ffunb.2021.633876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 09/26/2023]
Abstract
Transposable elements are present in almost all known genomes, these endogenous transposons have recently been referred to as the mobilome. They are now increasingly used in research in order to make extensive mutant libraries in different organisms. Fungi are an essential part of our lives on earth, they influence the availability of our food and they live inside our own bodies both as commensals and pathogenic organisms. Only few fungal species have been studied extensively, mainly due to the lack of appropriate molecular genetic tools. The use of transposon insertion libraries can however help to rapidly advance our knowledge of (conditional) essential genes, compensatory mutations and drug target identification in fungi. Here we give an overview of some recent developments in the use of different transposons for saturation mutagenesis in different fungi.
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Affiliation(s)
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
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Moscoso CG, Steer CJ. The Evolution of Gene Therapy in the Treatment of Metabolic Liver Diseases. Genes (Basel) 2020; 11:genes11080915. [PMID: 32785089 PMCID: PMC7463482 DOI: 10.3390/genes11080915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/02/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Monogenic metabolic disorders of hepatic origin number in the hundreds, and for many, liver transplantation remains the only cure. Liver-targeted gene therapy is an attractive treatment modality for many of these conditions, and there have been significant advances at both the preclinical and clinical stages. Viral vectors, including retroviruses, lentiviruses, adenovirus-based vectors, adeno-associated viruses and simian virus 40, have differing safety, efficacy and immunogenic profiles, and several of these have been used in clinical trials with variable success. In this review, we profile viral vectors and non-viral vectors, together with various payloads, including emerging therapies based on RNA, that are entering clinical trials. Genome editing technologies are explored, from earlier to more recent novel approaches that are more efficient, specific and safe in reaching their target sites. The various curative approaches for the multitude of monogenic hepatic metabolic disorders currently at the clinical development stage portend a favorable outlook for this class of genetic disorders.
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Affiliation(s)
- Carlos G. Moscoso
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Correspondence: (C.G.M.); (C.J.S.); Tel.: +1-612-625-8999 (C.G.M. & C.J.S.); Fax: +1-612-625-5620 (C.G.M. & C.J.S.)
| | - Clifford J. Steer
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Correspondence: (C.G.M.); (C.J.S.); Tel.: +1-612-625-8999 (C.G.M. & C.J.S.); Fax: +1-612-625-5620 (C.G.M. & C.J.S.)
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15
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Terzioğlu Kara E, Kiral FR, Öztürk Çolak A, Çelik A. Generation and characterization of inner photoreceptor-specific enhancer-trap lines using a novel piggyBac-Gal4 element in Drosophila. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 104:e21675. [PMID: 32285519 DOI: 10.1002/arch.21675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/17/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
The Drosophila inner photoreceptors R7 and R8 are responsible for color vision and their differentiation starts at the third instar larval stage. Only a handful of genes with R7 or R8-cell-specific expression are known. We performed an enhancer-trap screen using a novel piggyBac transposable element, pBGay, carrying a Gal4 sequence under the control of the P promoter to identify novel genes expressed specifically in R7 or R8 cells. From this screen, three lines were analyzed in detail: piggyBacAC109 and piggyBacAC783 are expressed in R8 cells and piggyBacAC887 is expressed in R7 cells at the third instar larval stage and pupal stages. Molecular analysis showed that the piggyBac elements were inserted into the first intron of CG14160 and CG7985 genes and the second intron of unzipped. We show the expression pattern in the developing eye imaginal disc, pupal retina as well as the adult retina. The photoreceptor-specific expression of these genes is reported for the first time and we propose that these lines are useful tools for studying the development of the visual system.
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Affiliation(s)
- Ece Terzioğlu Kara
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Ferdi Rıdvan Kiral
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
- Division of Neurobiology, Institute for Biology, Free University Berlin, Berlin, Germany
| | - Arzu Öztürk Çolak
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Arzu Çelik
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
- Center for Life Sciences and Technologies, Bogazici University, Istanbul, Turkey
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16
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Kandul NP, Liu J, Hsu AD, Hay BA, Akbari OS. A drug-inducible sex-separation technique for insects. Nat Commun 2020; 11:2106. [PMID: 32355156 PMCID: PMC7193620 DOI: 10.1038/s41467-020-16020-2] [Citation(s) in RCA: 13] [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: 12/19/2019] [Accepted: 04/07/2020] [Indexed: 11/16/2022] Open
Abstract
Here, we describe a drug-inducible genetic system for insect sex-separation that demonstrates proof-of-principle for positive sex selection in D. melanogaster. The system exploits the toxicity of commonly used broad-spectrum antibiotics geneticin and puromycin to kill the non-rescued sex. Sex-specific rescue is achieved by inserting sex-specific introns into the coding sequences of antibiotic-resistance genes. When raised on geneticin-supplemented food, the sex-sorter line establishes 100% positive selection for female progeny, while the food supplemented with puromycin positively selects 100% male progeny. Since the described system exploits conserved sex-specific splicing mechanisms and reagents, it has the potential to be adaptable to other insect species of medical and agricultural importance.
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Affiliation(s)
- Nikolay P Kandul
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92092, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92092, USA
| | - Alexander D Hsu
- Division of Biology and Biological Engineering, MC 156-29, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Bruce A Hay
- Division of Biology and Biological Engineering, MC 156-29, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92092, USA.
- Division of Biology and Biological Engineering, MC 156-29, California Institute of Technology, Pasadena, CA, 91125, USA.
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA, USA.
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17
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Wilson MH, Veach RA, Luo W, Welch RC, Roy S, Fissell WH. Genome Engineering Renal Epithelial Cells for Enhanced Volume Transport Function. Cell Mol Bioeng 2019; 13:17-26. [PMID: 32030105 DOI: 10.1007/s12195-019-00601-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/14/2019] [Indexed: 12/20/2022] Open
Abstract
Introduction Bioengineering an implantable artificial kidney (IAK) will require renal epithelial cells capable of reabsorption of salt and water. We used genome engineering to modify cells for improved Na+/H+ exchange and H2O reabsorption. The non-viral piggyBac transposon system enables genome engineering cells to stably overexpress one or more transgenes simultaneously. Methods We generated epitope-tagged human sodium hydrogen exchanger 3 (NHE3) and aquaporin-1 (AQP1) cDNA expressing piggyBac transposon vectors. Transgene expression was evaluated via western blot and immunofluorescence. Flow cytometry analysis was used to quantitate transporter expression in a library of genome engineered clones. Cell surface biotinylation was used evaluate surface protein localization. Blister formation assays were used to monitor cellular volumetric transport. Results piggyBac enabled stable transposon integration and overexpression of cumate-inducible NHE3 and/or constitutively expressing AQP1 in cultured renal (MDCK) epithelial cells. Cell surface delivery of NHE3 and AQP1 was confirmed using cell surface biotinylation assays. Flow cytometry of a library of MDCK clones revealed varying expression of AQP1 and NHE3. MDCK cells expressing AQP1 and cumate-inducible NHE3 demonstrated increased volumetric transport. Conclusions Our results demonstrate that renal epithelial cells an be genome engineered for enhanced volumetric transport that will be needed for an IAK device. Our results lay the foundation for future studies of genome engineering human kidney cells for renal tubule cell therapy.
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Affiliation(s)
- Matthew H Wilson
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave South, S-3223 MCN, Nashville, TN 37232 USA
- Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212 USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232 USA
| | - Ruth Ann Veach
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave South, S-3223 MCN, Nashville, TN 37232 USA
| | - Wentian Luo
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave South, S-3223 MCN, Nashville, TN 37232 USA
| | - Richard C Welch
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave South, S-3223 MCN, Nashville, TN 37232 USA
| | - Shuvo Roy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158 USA
| | - William H Fissell
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave South, S-3223 MCN, Nashville, TN 37232 USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232 USA
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18
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Vanslambrouck JM, Woodard LE, Suhaimi N, Williams FM, Howden SE, Wilson SB, Lonsdale A, Er PX, Li J, Maksimovic J, Oshlack A, Wilson MH, Little MH. Direct reprogramming to human nephron progenitor-like cells using inducible piggyBac transposon expression of SNAI2-EYA1-SIX1. Kidney Int 2019; 95:1153-1166. [PMID: 30827514 DOI: 10.1016/j.kint.2018.11.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 01/01/2023]
Abstract
All nephrons in the mammalian kidney arise from a transient nephron progenitor population that is lost close to the time of birth. The generation of new nephron progenitors and their maintenance in culture are central to the success of kidney regenerative strategies. Using a lentiviral screening approach, we previously generated a human induced nephron progenitor-like state in vitro using a pool of six transcription factors. Here, we sought to develop a more efficient approach for direct reprogramming of human cells that could be applied in vivo. PiggyBac transposons are a non-viral integrating gene delivery system that is suitable for in vivo use and allows for simultaneous delivery of multiple genes. Using an inducible piggyBac transposon system, we optimized a protocol for the direct reprogramming of HK2 cells to induced nephron progenitor-like cells with expression of only 3 transcription factors (SNAI2, EYA1, and SIX1). Culture in conditions supportive of the nephron progenitor state further increased the expression of nephron progenitor genes. The refined protocol was then applied to primary human renal epithelial cells, which integrated into developing nephron structures in vitro and in vivo. Such inducible reprogramming to nephron progenitor-like cells could facilitate direct cellular reprogramming for kidney regeneration.
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Affiliation(s)
- Jessica M Vanslambrouck
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia; Division of Genomics of Development and Disease, Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Lauren E Woodard
- Tennessee Valley Healthcare System, Department of Veterans Affairs, Nashville, Tennessee, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Norseha Suhaimi
- Division of Genomics of Development and Disease, Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Felisha M Williams
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sara E Howden
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia; Department of Pediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Sean B Wilson
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia
| | - Andrew Lonsdale
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia
| | - Pei X Er
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia
| | - Joan Li
- Division of Genomics of Development and Disease, Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Jovana Maksimovic
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia
| | - Alicia Oshlack
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia
| | - Matthew H Wilson
- Tennessee Valley Healthcare System, Department of Veterans Affairs, Nashville, Tennessee, USA; Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Melissa H Little
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia; Division of Genomics of Development and Disease, Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia; Department of Pediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia.
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19
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Candida albicans gains azole resistance by altering sphingolipid composition. Nat Commun 2018; 9:4495. [PMID: 30374049 PMCID: PMC6206040 DOI: 10.1038/s41467-018-06944-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/03/2018] [Indexed: 12/31/2022] Open
Abstract
Fungal infections by drug-resistant Candida albicans pose a global public health threat. However, the pathogen’s diploid genome greatly hinders genome-wide investigations of resistance mechanisms. Here, we develop an efficient piggyBac transposon-mediated mutagenesis system using stable haploid C. albicans to conduct genome-wide genetic screens. We find that null mutants in either gene FEN1 or FEN12 (encoding enzymes for the synthesis of very-long-chain fatty acids as precursors of sphingolipids) exhibit resistance to fluconazole, a first-line antifungal drug. Mass-spectrometry analyses demonstrate changes in cellular sphingolipid composition in both mutants, including substantially increased levels of several mannosylinositolphosphoceramides with shorter fatty-acid chains. Treatment with fluconazole induces similar changes in wild-type cells, suggesting a natural response mechanism. Furthermore, the resistance relies on a robust upregulation of sphingolipid biosynthesis genes. Our results shed light into the mechanisms underlying azole resistance, and the new transposon-mediated mutagenesis system should facilitate future genome-wide studies of C. albicans. The fungal pathogen Candida albicans is diploid, which hinders genome-wide studies. Here, Gao et al. present a piggyBac transposon-mediated mutagenesis system using stable haploid C. albicans strains, and use it to identify genes and mechanisms underlying azole resistance.
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20
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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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21
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Morellet N, Li X, Wieninger SA, Taylor JL, Bischerour J, Moriau S, Lescop E, Bardiaux B, Mathy N, Assrir N, Bétermier M, Nilges M, Hickman AB, Dyda F, Craig NL, Guittet E. Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase. Nucleic Acids Res 2018; 46:2660-2677. [PMID: 29385532 PMCID: PMC5861402 DOI: 10.1093/nar/gky044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 01/12/2018] [Accepted: 01/17/2018] [Indexed: 12/16/2022] Open
Abstract
The piggyBac transposase (PB) is distinguished by its activity and utility in genome engineering, especially in humans where it has highly promising therapeutic potential. Little is known, however, about the structure-function relationships of the different domains of PB. Here, we demonstrate in vitro and in vivo that its C-terminal Cysteine-Rich Domain (CRD) is essential for DNA breakage, joining and transposition and that it binds to specific DNA sequences in the left and right transposon ends, and to an additional unexpectedly internal site at the left end. Using NMR, we show that the CRD adopts the specific fold of the cross-brace zinc finger protein family. We determine the interaction interfaces between the CRD and its target, the 5'-TGCGT-3'/3'-ACGCA-5' motifs found in the left, left internal and right transposon ends, and use NMR results to propose docking models for the complex, which are consistent with our site-directed mutagenesis data. Our results provide support for a model of the PB/DNA interactions in the context of the transpososome, which will be useful for the rational design of PB mutants with increased activity.
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Affiliation(s)
- Nelly Morellet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Xianghong Li
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Silke A Wieninger
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Jennifer L Taylor
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julien Bischerour
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Séverine Moriau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Benjamin Bardiaux
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Nathalie Mathy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Nadine Assrir
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Mireille Bétermier
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Michael Nilges
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy L Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric Guittet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
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22
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Abstract
Fluid clearance from the respiratory system during developmental transitions is critically important for achieving optimal gas exchange in animals. During insect development from embryo to adult, airway clearance occurs episodically each time the molt is completed by performance of the ecdysis sequence, coordinated by a peptide-signaling cascade initiated by ecdysis-triggering hormone (ETH). We find that the neuropeptide Kinin (also known as Drosokinin or Leukokinin) is required for normal respiratory fluid clearance or "tracheal air-filling" in Drosophila larvae. Disruption of Kinin signaling leads to defective air-filling during all larval stages. Such defects are observed upon ablation or electrical silencing of Kinin neurons, as well as RNA silencing of the Kinin gene or the ETH receptor in Kinin neurons, indicating that ETH targets Kinin neurons to promote tracheal air-filling. A Kinin receptor mutant fly line (Lkrf02594 ) also exhibits tracheal air-filling defects in all larval stages. Targeted Kinin receptor silencing in tracheal epithelial cells using breathless or pickpocket (ppk) drivers compromises tracheal air-filling. On the other hand, promotion of Kinin signaling in vivo through peptide injection or Kinin neuron activation through Drosophila TrpA1 (dTrpA1) expression induces premature tracheal collapse and air-filling. Moreover, direct exposure of tracheal epithelial cells in vitro to Kinin leads to calcium mobilization in tracheal epithelial cells. Our findings strongly implicate the neuropeptide Kinin as an important regulator of airway clearance via intracellular calcium mobilization in tracheal epithelial cells of Drosophila.
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23
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Kasai Y, Matsuzaki K, Ikeda F, Yoshimitsu Y, Harayama S. Precise excision of a selectable marker gene in transgenic Coccomyxa strains by the piggyBac transposase. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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24
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Eldi P, Cooper TH, Liu L, Prow NA, Diener KR, Howley PM, Suhrbier A, Hayball JD. Production of a Chikungunya Vaccine Using a CHO Cell and Attenuated Viral-Based Platform Technology. Mol Ther 2017; 25:2332-2344. [PMID: 28720468 PMCID: PMC5628773 DOI: 10.1016/j.ymthe.2017.06.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/03/2017] [Accepted: 06/18/2017] [Indexed: 02/06/2023] Open
Abstract
Vaccinia-based systems have been extensively explored for the development of recombinant vaccines. Herein we describe an innovative vaccinia virus (VACV)-derived vaccine platform technology termed Sementis Copenhagen Vector (SCV), which was rendered multiplication-defective by targeted deletion of the essential viral assembly gene D13L. A SCV cell substrate line was developed for SCV vaccine production by engineering CHO cells to express D13 and the VACV host-range factor CP77, because CHO cells are routinely used for manufacture of biologics. To illustrate the utility of the platform technology, a SCV vaccine against chikungunya virus (SCV-CHIK) was developed and shown to be multiplication-defective in a range of human cell lines and in immunocompromised mice. A single vaccination of mice with SCV-CHIK induced antibody responses specific for chikungunya virus (CHIKV) that were similar to those raised following vaccination with a replication-competent VACV-CHIK and able to neutralize CHIKV. Vaccination also provided protection against CHIKV challenge, preventing both viremia and arthritis. Moreover, SCV retained capacity as an effective mouse smallpox vaccine. In summary, SCV represents a new and safe vaccine platform technology that can be manufactured in modified CHO cells, with pre-clinical evaluation illustrating utility for CHIKV vaccine design and construction.
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Affiliation(s)
- Preethi Eldi
- Experimental Therapeutics Laboratory, Hanson Institute and Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Tamara H Cooper
- Experimental Therapeutics Laboratory, Hanson Institute and Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Liang Liu
- Experimental Therapeutics Laboratory, Hanson Institute and Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Natalie A Prow
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Kerrilyn R Diener
- Experimental Therapeutics Laboratory, Hanson Institute and Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia; Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Paul M Howley
- Experimental Therapeutics Laboratory, Hanson Institute and Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia; Sementis Ltd., Melbourne, VIC 3000, Australia.
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - John D Hayball
- Experimental Therapeutics Laboratory, Hanson Institute and Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia; Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia.
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25
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Katayama H, Yasuchika K, Miyauchi Y, Kojima H, Yamaoka R, Kawai T, Yukie Yoshitoshi E, Ogiso S, Kita S, Yasuda K, Sasaki N, Fukumitsu K, Komori J, Ishii T, Uemoto S. Generation of non-viral, transgene-free hepatocyte like cells with piggyBac transposon. Sci Rep 2017; 7:44498. [PMID: 28295042 PMCID: PMC5353749 DOI: 10.1038/srep44498] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/08/2017] [Indexed: 12/12/2022] Open
Abstract
Somatic cells can be reprogrammed to induced hepatocyte-like cells (iHeps) by overexpressing certain defined factors in direct reprogramming techniques. Of the various methods to deliver genes into cells, typically used genome-integrating viral vectors are associated with integration-related adverse events such as mutagenesis, whereas non-integrating viral vectors have low efficiency, making viral vectors unsuitable for clinical application. Therefore, we focused on developing a transposon system to establish a non-viral reprogramming method. Transposons are unique DNA elements that can be integrated into and removed from chromosomes. PiggyBac, a type of transposon, has high transduction efficiency and cargo capacity, and the integrated transgene can be precisely excised in the presence of transposase. This feature enables the piggyBac vector to achieve efficient transgene expression and a transgene-free state, thus making it a promising method for cell reprogramming. Here, we attempted to utilize the piggyBac transposon system to generate iHeps by integrating a transgene consisting of Hnf4a and Foxa3, and successfully obtained functional iHeps. We then demonstrated removal of the transgene to obtain transgene-free iHeps, which still maintained hepatocyte functions. This non-viral, transgene-free reprogramming method using the piggyBac vector may facilitate clinical applications of iHeps in upcoming cell therapy.
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Affiliation(s)
- Hokahiro Katayama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kentaro Yasuchika
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuya Miyauchi
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidenobu Kojima
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryoya Yamaoka
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Kawai
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Elena Yukie Yoshitoshi
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Satoshi Ogiso
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sadahiko Kita
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsutaro Yasuda
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Naoya Sasaki
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Fukumitsu
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junji Komori
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takamichi Ishii
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinji Uemoto
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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26
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Wen Y, Liao G, Pritchard T, Zhao TT, Connelly JP, Pruett-Miller SM, Blanc V, Davidson NO, Madison BB. A stable but reversible integrated surrogate reporter for assaying CRISPR/Cas9-stimulated homology-directed repair. J Biol Chem 2017; 292:6148-6162. [PMID: 28228480 DOI: 10.1074/jbc.m117.777722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
The discovery and application of CRISPR/Cas9 technology for genome editing has greatly accelerated targeted mutagenesis in a variety of organisms. CRISPR/Cas9-mediated site-specific cleavage is typically exploited for the generation of insertions or deletions (indels) after aberrant dsDNA repair via the endogenous non-homology end-joining (NHEJ) pathway or, alternatively, for enhancing homology-directed repair to facilitate the generation of a specific mutation (or "knock-in"). However, there is a need for efficient cellular assays that can measure Cas9/guide RNA activity. Reliable methods for enriching and identifying desired mutants are also lacking. Here we describe a method using the Piggybac transposon for stable genomic integration of an H2B-GFP reporter or a hygromycin resistance gene for assaying Cas9 target cleavage and homology-directed repair. The H2B-GFP fusion protein provides increased stability and an obvious pattern of nuclear localization. This method, called SRIRACCHA (i.e. a stable, but reversible, integrated reporter for assaying CRISPR/Cas-stimulated HDR activity), enables the enrichment of mutants via selection of GFP-positive or hygromycin-resistant mammalian cells (immortalized or non-immortalized) as a surrogate for the modification of the endogenous target site. Currently available hyperactive Piggybac transposase mutants allow both delivery and removal of the surrogate reporters, with minimal risk of generating undesirable mutations. This assay permits rapid screening for efficient guide RNAs and the accelerated identification of mutant clones and is applicable to many cell types. We foresee the utility of this approach in contexts in which the maintenance of genomic integrity is essential, for example, when engineering cells for therapeutic purposes.
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Affiliation(s)
- Yahong Wen
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Grace Liao
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Thomas Pritchard
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Ting-Ting Zhao
- First Hospital of China Medical University, Department of Breast Surgery, Shenyang, China 110001
| | - Jon P Connelly
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University, Saint Louis, Missouri 63110, and
| | - Shondra M Pruett-Miller
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University, Saint Louis, Missouri 63110, and
| | - Valerie Blanc
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Nicholas O Davidson
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Blair B Madison
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110,
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27
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Allen SE, Nowacki M. Necessity Is the Mother of Invention: Ciliates, Transposons, and Transgenerational Inheritance. Trends Genet 2017; 33:197-207. [PMID: 28174020 DOI: 10.1016/j.tig.2017.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 01/01/2023]
Abstract
Ciliates are a fascinating model system for the study of the interaction between eukaryotic germlines and somatic lines, especially with regard to the invasion and defence against transposable elements. They separate their germline and somatic line into two nuclei within the same cell, and they silence transposons and repetitive elements by way of deleting them from their somatic genome. This large-scale deletion event uses a series of intricate sequence targeting pathways involving small RNAs and transposases, part of which consists of a transnuclear comparison between maternal soma and daughter germline. We present recent progress in this dynamic field, and argue that these DNA targeting pathways provide an optimal system for the transgenerational inheritance of acquired traits. Ciliates thus also demonstrate the evolutionary value of transposable elements, both as sources of sequence diversity and also as drivers of adaptive evolution by necessitating defensive systems.
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Affiliation(s)
- Sarah E Allen
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.
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28
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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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29
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Homology Requirements for Efficient, Footprintless Gene Editing at the CFTR Locus in Human iPSCs with Helper-dependent Adenoviral Vectors. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e372. [PMID: 27727248 PMCID: PMC5095686 DOI: 10.1038/mtna.2016.83] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/20/2016] [Indexed: 01/24/2023]
Abstract
Helper-dependent adenoviral vectors mediate high efficiency gene editing in induced pluripotent stem cells without needing a designer nuclease thereby avoiding off-target cleavage. Because of their large cloning capacity of 37 kb, helper-dependent adenoviral vectors with long homology arms are used for gene editing. However, this makes vector construction and recombinant analysis difficult. Conversely, insufficient homology may compromise targeting efficiency. Thus, we investigated the effect of homology length on helper-dependent adenoviral vector targeting efficiency at the cystic fibrosis transmembrane conductance regulator locus in induced pluripotent stem cells and found a positive correlation. With 23.8 and 21.4 kb of homology, the frequencies of targeted recombinants were 50–64.6% after positive selection for vector integration, and 97.4–100% after negative selection against random integrations. With 14.8 kb, the frequencies were 26.9–57.1% after positive selection and 87.5–100% after negative selection. With 9.6 kb, the frequencies were 21.4 and 75% after positive and negative selection, respectively. With only 5.6 kb, the frequencies were 5.6–16.7% after positive selection and 50% after negative selection, but these were more than high enough for efficient identification and isolation of targeted clones. Furthermore, we demonstrate helper-dependent adenoviral vector-mediated footprintless correction of cystic fibrosis transmembrane conductance regulator mutations through piggyBac excision of the selectable marker. However, low frequencies (≤ 1 × 10−3) necessitated negative selection for piggyBac-excision product isolation.
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30
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Yang D, Liao R, Zheng Y, Sun L, Xu T. Analysis of PBase Binding Profile Indicates an Insertion Target Selection Mechanism Dependent on TTAA, But Not Transcriptional Activity. Int J Biol Sci 2016; 12:1074-82. [PMID: 27570481 PMCID: PMC4997051 DOI: 10.7150/ijbs.15589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/15/2016] [Indexed: 12/20/2022] Open
Abstract
Transposons and retroviruses are important pathogenic agents and tools for mutagenesis and transgenesis. Insertion target selection is a key feature for a given transposon or retrovirus. The piggyBac (PB) transposon is highly active in mice and human cells, which has a much better genome-wide distribution compared to the retrovirus and P-element. However, the underlying reason is not clear. Utilizing a tagged functional PB transposase (PBase), we were able to conduct genome-wide profiling for PBase binding sites in the mouse genome. We have shown that PBase binding mainly depends on the distribution of the tetranucleotide TTAA, which is not affected by the presence of PB DNA. Furthermore, PBase binding is negatively influenced by the methylation of CG sites in the genome. Analysis of a large collection of PB insertions in mice has revealed an insertion profile similar to the PBase binding profile. Interestingly, this profile is not correlated with transcriptional active genes in the genome or transcriptionally active regions within a transcriptional unit. This differs from what has been previously shown for P-element and retroviruses insertions. Our study provides an explanation for PB's genome-wide insertion distribution and also suggests that PB target selection relies on a new mechanism independent of active transcription and open chromatin structure.
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Affiliation(s)
- Dong Yang
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433; 2. Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06536
| | - Ruiqi Liao
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433
| | - Yun Zheng
- 3. Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Ling Sun
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433
| | - Tian Xu
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433; 2. Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06536
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31
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Chen F, Becker A, LoTurco J. Overview of Transgenic Glioblastoma and Oligoastrocytoma CNS Models and Their Utility in Drug Discovery. ACTA ACUST UNITED AC 2016; 72:14.37.1-14.37.12. [PMID: 26995546 DOI: 10.1002/0471141755.ph1437s72] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many animal models have been developed to investigate the sources of central nervous system (CNS) tumor heterogeneity. Reviewed in this unit is a recently developed CNS tumor model using the piggyBac transposon system delivered by in utero electroporation, in which sources of tumor heterogeneity can be conveniently studied. Their applications for studying CNS tumors and drug discovery are also reviewed. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Fuyi Chen
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Conn.,Current address: Department of Neurology, Yale School of Medicine, New Haven, Conn
| | - Albert Becker
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Joseph LoTurco
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Conn
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32
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Abstract
The piggyBac transposon was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and dissimilarity to the other DNA transposon families, the piggyBac transposon was not recognized as a member of a large transposon superfamily for a long time. Initially, the piggyBac transposon was thought to be a rare transposon. This view, however, has now been completely revised as a number of fully sequenced genomes have revealed the presence of piggyBac-like repetitive elements. The isolation of active copies of the piggyBac-like elements from several distinct species further supported this revision. This includes the first isolation of an active mammalian DNA transposon identified in the bat genome. To date, the piggyBac transposon has been deeply characterized and it represents a number of unique characteristics. In general, all members of the piggyBac superfamily use TTAA as their integration target sites. In addition, the piggyBac transposon shows precise excision, i.e., restoring the sequence to its preintegration state, and can transpose in a variety of organisms such as yeasts, malaria parasites, insects, mammals, and even in plants. Biochemical analysis of the chemical steps of transposition revealed that piggyBac does not require DNA synthesis during the actual transposition event. The broad host range has attracted researchers from many different fields, and the piggyBac transposon is currently the most widely used transposon system for genetic manipulations.
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33
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Zhao S, Jiang E, Chen S, Gu Y, Shangguan AJ, Lv T, Luo L, Yu Z. PiggyBac transposon vectors: the tools of the human gene encoding. Transl Lung Cancer Res 2016; 5:120-5. [PMID: 26958506 DOI: 10.3978/j.issn.2218-6751.2016.01.05] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A transposon is a DNA segment, which is able to change its relative position within the entire genome of a cell. The piggyBac (PB) transposon is a movable genetic element that efficiently transposes between vectors and chromosomes through a "cut-and-paste" mechanism. During transposition, the PB transposase recognizes transposon-specific inverted terminal repeats (ITRs) sequences located on both ends of the transposon vector and eight efficiently moves the contents from its original positions and efficiently integrates them into TTAA chromosomal sites. PB has drawn much attention because of its transposition efficiency, safety and stability. Due to its priorities, PB can be used as a new genetic vehicle, a new tool for oncogene screening and a new method for gene therapy. PB has created a new outlook for human gene encoding.
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Affiliation(s)
- Shuang Zhao
- 1 Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China ; 2 Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing 210002, China ; 3 Shanghai Medical College of Fudan University, Shanghai 20032, China ; 4 Weinberg College of Arts and Sciences at Northwestern University, Evanston, Illinois 60204, USA ; 5 Department of Respiratory Medicine, 6 Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing 210002, China
| | - Enze Jiang
- 1 Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China ; 2 Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing 210002, China ; 3 Shanghai Medical College of Fudan University, Shanghai 20032, China ; 4 Weinberg College of Arts and Sciences at Northwestern University, Evanston, Illinois 60204, USA ; 5 Department of Respiratory Medicine, 6 Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing 210002, China
| | - Shuangshuang Chen
- 1 Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China ; 2 Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing 210002, China ; 3 Shanghai Medical College of Fudan University, Shanghai 20032, China ; 4 Weinberg College of Arts and Sciences at Northwestern University, Evanston, Illinois 60204, USA ; 5 Department of Respiratory Medicine, 6 Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing 210002, China
| | - Yuan Gu
- 1 Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China ; 2 Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing 210002, China ; 3 Shanghai Medical College of Fudan University, Shanghai 20032, China ; 4 Weinberg College of Arts and Sciences at Northwestern University, Evanston, Illinois 60204, USA ; 5 Department of Respiratory Medicine, 6 Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing 210002, China
| | - Anna Junjie Shangguan
- 1 Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China ; 2 Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing 210002, China ; 3 Shanghai Medical College of Fudan University, Shanghai 20032, China ; 4 Weinberg College of Arts and Sciences at Northwestern University, Evanston, Illinois 60204, USA ; 5 Department of Respiratory Medicine, 6 Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing 210002, China
| | - Tangfeng Lv
- 1 Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China ; 2 Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing 210002, China ; 3 Shanghai Medical College of Fudan University, Shanghai 20032, China ; 4 Weinberg College of Arts and Sciences at Northwestern University, Evanston, Illinois 60204, USA ; 5 Department of Respiratory Medicine, 6 Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing 210002, China
| | - Liguo Luo
- 1 Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China ; 2 Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing 210002, China ; 3 Shanghai Medical College of Fudan University, Shanghai 20032, China ; 4 Weinberg College of Arts and Sciences at Northwestern University, Evanston, Illinois 60204, USA ; 5 Department of Respiratory Medicine, 6 Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing 210002, China
| | - Zhenghong Yu
- 1 Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing 210002, China ; 2 Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing 210002, China ; 3 Shanghai Medical College of Fudan University, Shanghai 20032, China ; 4 Weinberg College of Arts and Sciences at Northwestern University, Evanston, Illinois 60204, USA ; 5 Department of Respiratory Medicine, 6 Department of Cardiothoracic Surgery, Jinling Hospital, Nanjing 210002, China
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Pyykkö I, Zou J, Schrott-Fischer A, Glueckert R, Kinnunen P. An Overview of Nanoparticle Based Delivery for Treatment of Inner Ear Disorders. Methods Mol Biol 2016; 1427:363-415. [PMID: 27259938 DOI: 10.1007/978-1-4939-3615-1_21] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nanoparticles offer new possibilities for inner ear treatment as they can carry a variety of drugs, protein, and nucleic acids to inner ear. Nanoparticles are equipped with several functions such as targetability, immuno-transparency, biochemical stability, and ability to be visualized in vivo and in vitro. A group of novel peptides can be attached to the surface of nanoparticles that will enhance the cell entry, endosomal escape, and nuclear targeting. Eight different types of nanoparticles with different payload carrying strategies are available now. The transtympanic delivery of nanoparticles indicates that, depending on the type of nanoparticle, different migration pathways into the inner ear can be employed, and that optimal carriers can be designed according to the intended cargo. The use of nanoparticles as drug/gene carriers is especially attractive in conjunction with cochlear implantation or even as an inclusion in the implant as a drug/gene reservoir.
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Affiliation(s)
- Ilmari Pyykkö
- Department of Otolaryngology, University of Tampere and University Hospital of Tampere, Tampere, 33014, Finland. .,Hearing and Balance Research Unit, Field of Otolaryngology, School of Medicine, University of Tampere, Medisiinarinkatu 3, Tampere, 33520, Finland.
| | - Jing Zou
- BECS, Department of Biomedical Engineering and Computational Science, Aalto University, Aalto, 02150, Espoo, Finland
| | - Annelies Schrott-Fischer
- Department of Otolaryngology, Medical University of Innsbruck, Anichstrasse 35, Innsbruck, 6020, Austria
| | - Rudolf Glueckert
- Department of Otolaryngology, Medical University of Innsbruck, Anichstrasse 35, Innsbruck, 6020, Austria
| | - Paavo Kinnunen
- BECS, Department of Biomedical Engineering and Computational Science, Aalto University, Aalto, Finland
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Hou X, Du Y, Deng Y, Wu J, Cao G. Sleeping Beauty transposon system for genetic etiological research and gene therapy of cancers. Cancer Biol Ther 2015; 16:8-16. [PMID: 25455252 DOI: 10.4161/15384047.2014.986944] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Carcinogenesis is etiologically associated with somatic mutations of critical genes. Recently, a number of somatic mutations and key molecules have been found to be involved in functional networks affecting cancer progression. Suitable animal models are required to validate cancer-promoting or -inhibiting capacities of these mutants and molecules. Sleeping Beauty transposon system consists of a transposon that carries gene(s) of interest and a transposase that recognizes, excises, and reinserts genes in given location of the genome. It can create both gain-of-function and loss-of-function mutations, thus being frequently chosen to investigate the etiological mechanisms and gene therapy for cancers in animal models. In this review, we summarized current advances of Sleeping Beauty transposon system in revealing molecular mechanism of cancers and improving gene therapy. Understanding molecular mechanisms by which driver mutations contribute to carcinogenesis and metastasis may pave the way for the development of innovative prophylactic and therapeutic strategies against malignant diseases.
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Key Words
- 7, 12-dimethylbenzanthracene/12-O-tetradecanoylphorbol-13-acetate
- Alb-Cre, Albumin promoter-Cre
- CAG promoter, CMV enhancer/chicken β-actin promoter
- CAR, chimeric antigen receptor
- CIS, common insertion site
- CMV, chimeric cytomegalovirus
- CRC, colorectal cancer
- Cre, cyclization recombination enzyme
- DDE, Asp, Asp, Glu
- DMBA/TPA
- DR, direct orientation
- Fah, fumarylacetoacetate hydrolase gene
- GWAS, gnome wide analysis study
- HBV, Hepatitis B Virus
- HBx, HBV X protein
- HCC, hepatocellular carcinoma
- IRs, inverted repeat sequences
- LsL, loxP-stop-loxP
- MPNSTs, malignant peripheral nerve sheath tumor
- MSCV, murine stem cell virus
- PAI, Pro, Ala, Ile
- PBMCs, peripheral blood mononuclear cells
- RED, Arg, Glu, Asp
- RosaSBaseLsL, Cre-inducible SBase allele
- Rtl1, Retrotransposon-like 1
- SB, Sleeping Beauty
- SBase, Sleeping Beauty transposase
- Sleeping Beauty transposon system
- StatinAE, angiostatin-endostatin fusion gene
- Trp53, transformation related protein 53
- animal model
- driver
- gene function
- gene therapy
- malignant diseases
- sgRNA, single guide RNA
- shp53, short hairpin RNA against the Trp53 gene
- somatic mutation
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Affiliation(s)
- Xiaomei Hou
- a Department of Epidemiology ; Second Military Medical University ; Shanghai , China
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Cunningham SC, Siew SM, Hallwirth CV, Bolitho C, Sasaki N, Garg G, Michael IP, Hetherington NA, Carpenter K, de Alencastro G, Nagy A, Alexander IE. Modeling correction of severe urea cycle defects in the growing murine liver using a hybrid recombinant adeno-associated virus/piggyBac transposase gene delivery system. Hepatology 2015; 62:417-28. [PMID: 26011400 DOI: 10.1002/hep.27842] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/07/2015] [Indexed: 12/17/2022]
Abstract
UNLABELLED Liver-targeted gene therapy based on recombinant adeno-associated viral vectors (rAAV) shows promising therapeutic efficacy in animal models and adult-focused clinical trials. This promise, however, is not directly translatable to the growing liver, where high rates of hepatocellular proliferation are accompanied by loss of episomal rAAV genomes and subsequently a loss in therapeutic efficacy. We have developed a hybrid rAAV/piggyBac transposon vector system combining the highly efficient liver-targeting properties of rAAV with stable piggyBac-mediated transposition of the transgene into the hepatocyte genome. Transposition efficiency was first tested using an enhanced green fluorescent protein expression cassette following delivery to newborn wild-type mice, with a 20-fold increase in stably gene-modified hepatocytes observed 4 weeks posttreatment compared to traditional rAAV gene delivery. We next modeled the therapeutic potential of the system in the context of severe urea cycle defects. A single treatment in the perinatal period was sufficient to confer robust and stable phenotype correction in the ornithine transcarbamylase-deficient Spf(ash) mouse and the neonatal lethal argininosuccinate synthetase knockout mouse. Finally, transposon integration patterns were analyzed, revealing 127,386 unique integration sites which conformed to previously published piggyBac data. CONCLUSION Using a hybrid rAAV/piggyBac transposon vector system, we achieved stable therapeutic protection in two urea cycle defect mouse models; a clinically conceivable early application of this technology in the management of severe urea cycle defects could be as a bridging therapy while awaiting liver transplantation; further improvement of the system will result from the development of highly human liver-tropic capsids, the use of alternative strategies to achieve transient transposase expression, and engineered refinements in the safety profile of piggyBac transposase-mediated integration.
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Affiliation(s)
- Sharon C Cunningham
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,University of Sydney Medical School, Sydney, New South Wales, Australia
| | - Susan M Siew
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Christine Bolitho
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Natsuki Sasaki
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Gagan Garg
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Department of Chemistry and Biomolecular Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Iacovos P Michael
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Nicola A Hetherington
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Kevin Carpenter
- Biochemical Genetics, The Children's Hospital at Westmead, Westmead, Sydney, New South Wales, Australia
| | - Gustavo de Alencastro
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Institute of Medical Science and Department of Obstetrics & Gynaecology, University of Toronto, Toronto, Ontario, Canada.,Department of Obstetrics & Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Paediatrics and Child Health, The University of Sydney, Sydney, New South Wales, Australia
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Caro LN, Li Z, Balo AR, Van Eps N, Rini JM, Ernst OP. Rapid and facile recombinant expression of bovine rhodopsin in HEK293S GnTI(-) cells using a PiggyBac inducible system. Methods Enzymol 2015; 556:307-30. [PMID: 25857788 DOI: 10.1016/bs.mie.2015.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Rhodopsin is a class A G protein-coupled receptor (GPCR) that provides important insights into the structure and function of the GPCR superfamily. Bovine rhodopsin is widely used as a model for GPCRs and was the first GPCR whose X-ray crystal structure was solved. One of the advantages of rhodopsin is that it is abundant in native tissue, and as a result, milligram quantities can be purified from the retinal rod cells of bovine eyes. Nonetheless, the study of GPCR conformation and dynamics, e.g., by electron paramagnetic resonance or (19)F nuclear magnetic resonance spectroscopy, typically requires mutagenesis to enable site-directed labeling of the protein. Mutations are also of great importance as they can stabilize the receptor and can be necessary to study different receptor conformations. Recombinant production of rhodopsins for biophysical studies has been achieved in different systems, including mammalian, insect, and yeast cells in culture, and from Drosophila melanogaster and Caenorhabditis elegans tissue. The piggyBac (PB) transposon system is used for gene delivery into a variety of cell types (e.g., HEK293 and CHO cells, fibroblasts, stem cells) and living organisms (e.g., honeybees, pigs, chicken, mice). Recently, the PB transposon has been described as an efficient tool for inducible protein expression in HEK293T and HEK293S N-acetylglucosaminyltransferase I-deficient (GnTI(-)) cells. This chapter describes a protocol for using the PB-based system for inducible expression of bovine rhodopsin in HEK293S GnTI(-) cells. Using this protocol, we expressed and purified 26 rhodopsin mutants to be used for site-directed spin labeling.
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Affiliation(s)
- Lydia N Caro
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Zhijie Li
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Aidin R Balo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - James M Rini
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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Sato M, Inada E, Saitoh I, Matsumoto Y, Ohtsuka M, Miura H, Nakamura S, Sakurai T, Watanabe S. A combination of targeted toxin technology and the piggyBac-mediated gene transfer system enables efficient isolation of stable transfectants in nonhuman mammalian cells. Biotechnol J 2014; 10:143-53. [PMID: 25345906 DOI: 10.1002/biot.201400283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 11/22/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022]
Abstract
Isolation of cells harboring exogenous DNA is typically achieved by the introduction of plasmids, but its efficiency remains still low. In this study, we developed a novel strategy to obtain stable transfectants efficiently. Porcine embryonic fibroblasts were transfected with two plasmids: (i) pTransIEnd, which comprises the ubiquitous promoter, the piggyBac (PB) transposase gene, an internal ribosomal entry site, the Clostridium perfringens-derived endo-β-galactosidase C (EndoGalC) gene, and a poly(A) tail and (ii) a PB-based plasmid, termed pT-EGFP, which contains enhanced green fluorescent protein (EGFP) expression unit flanked by PB acceptor sites. The PB transposase can accelerate the chromosomal integration of transposon vectors. EndoGalC expression results in removal of a cell surface α-Gal epitope, which is specifically recognized by Bandeiraea simplicifolia isolectin-B4 (IB4). Four days after transfection, cells were treated with IB4SAP (IB4 conjugated to saporin, which eliminates any α-Gal epitope-expressing cells) for a short period, followed by standard culture for approximately 10 days. Several colonies emerged, most of which were positive for EGFP expression and lacked TransIEnd. These results indicated that the proposed approach is useful and efficient for obtaining stable transfectants without the use of drug-resistance genes, and offers a novel route for gene manipulation in cultured nonhuman mammalian cells.
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Affiliation(s)
- Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, Kagoshima, Japan.
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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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Martinez-Fernandez A, Nelson TJ, Reyes S, Alekseev AE, Secreto F, Perez-Terzic C, Beraldi R, Sung HK, Nagy A, Terzic A. iPS cell-derived cardiogenicity is hindered by sustained integration of reprogramming transgenes. ACTA ACUST UNITED AC 2014; 7:667-76. [PMID: 25077947 DOI: 10.1161/circgenetics.113.000298] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Nuclear reprogramming inculcates pluripotent capacity by which de novo tissue differentiation is enabled. Yet, introduction of ectopic reprogramming factors may desynchronize natural developmental schedules. This study aims to evaluate the effect of imposed transgene load on the cardiogenic competency of induced pluripotent stem (iPS) cells. METHODS AND RESULTS Targeted inclusion and exclusion of reprogramming transgenes (c-MYC, KLF4, OCT4, and SOX2) was achieved using a drug-inducible and removable cassette according to the piggyBac transposon/transposase system. Pulsed transgene overexpression, before iPS cell differentiation, hindered cardiogenic outcomes. Delayed in counterparts with maintained integrated transgenes, transgene removal enabled proficient differentiation of iPS cells into functional cardiac tissue. Transgene-free iPS cells generated reproducible beating activity with robust expression of cardiac α-actinin, connexin 43, myosin light chain 2a, α/β-myosin heavy chain, and troponin I. Although operational excitation-contraction coupling was demonstrable in the presence or absence of transgenes, factor-free derivatives exhibited an expedited maturing phenotype with canonical responsiveness to adrenergic stimulation. CONCLUSIONS A disproportionate stemness load, caused by integrated transgenes, affects the cardiogenic competency of iPS cells. Offload of transgenes in engineered iPS cells ensures integrity of cardiac developmental programs, underscoring the value of nonintegrative nuclear reprogramming for derivation of competent cardiogenic regenerative biologics.
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Affiliation(s)
- Almudena Martinez-Fernandez
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.)
| | - Timothy J Nelson
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.)
| | - Santiago Reyes
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.)
| | - Alexey E Alekseev
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.)
| | - Frank Secreto
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.)
| | - Carmen Perez-Terzic
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.)
| | - Rosanna Beraldi
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.)
| | - Hoon-Ki Sung
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.)
| | - Andras Nagy
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.)
| | - Andre Terzic
- From the Center for Regenerative Medicine (A.M.-F., T.J.N., S.R., A.E.A., A.T.), Marriott Heart Disease Research Program, Division of Cardiovascular Diseases (A.M.-F., S.R., A.E.A., A.T.), and Department of Physical Medicine and Rehabilitation (C.P.-T.), General Internal Medicine and Transplant Center (T.J.N., F.S., R.B.), Mayo Clinic, Rochester, MN; and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada (H.-K.S., A.N.).
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Swart EC, Wilkes CD, Sandoval PY, Arambasic M, Sperling L, Nowacki M. Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion. Nucleic Acids Res 2014; 42:8970-83. [PMID: 25016527 PMCID: PMC4132734 DOI: 10.1093/nar/gku619] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
During the development of the somatic genome from the Paramecium germline genome the bulk of the copies of ∼45 000 unique, internal eliminated sequences (IESs) are deleted. IES targeting is facilitated by two small RNA (sRNA) classes: scnRNAs, which relay epigenetic information from the parental nucleus to the developing nucleus, and iesRNAs, which are produced and used in the developing nucleus. Why only certain IESs require sRNAs for their removal has been enigmatic. By analyzing the silencing effects of three genes: PGM (responsible for DNA excision), DCL2/3 (scnRNA production) and DCL5 (iesRNA production), we identify key properties required for IES elimination. Based on these results, we propose that, depending on the exact combination of their lengths and end bases, some IESs are less efficiently recognized or excised and have a greater requirement for targeting by scnRNAs and iesRNAs. We suggest that the variation in IES retention following silencing of DCL2/3 is not primarily due to scnRNA density, which is comparatively uniform relative to IES retention, but rather the genetic properties of IESs. Taken together, our analyses demonstrate that in Paramecium the underlying genetic properties of developmentally deleted DNA sequences are essential in determining the sensitivity of these sequences to epigenetic control.
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Affiliation(s)
- Estienne C Swart
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Cyril Denby Wilkes
- CNRS UPR3404 Centre de Génétique Moléculaire, 1 avenue de la Terrasse, Gif-sur-Yvette F-91198 cedex, France Université Paris-Sud, Département de Biologie, Orsay, F-91405, France
| | - Pamela Y Sandoval
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Miroslav Arambasic
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Linda Sperling
- CNRS UPR3404 Centre de Génétique Moléculaire, 1 avenue de la Terrasse, Gif-sur-Yvette F-91198 cedex, France Université Paris-Sud, Département de Biologie, Orsay, F-91405, France
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
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Chen F, Maher BJ, LoTurco JJ. piggyBac transposon-mediated cellular transgenesis in mammalian forebrain by in utero electroporation. Cold Spring Harb Protoc 2014; 2014:741-9. [PMID: 24987137 DOI: 10.1101/pdb.prot073650] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In utero electroporation (IUE) is an effective transfection method for delivering plasmid DNA into neural progenitor cells and neurons of mammalian neocortex in vivo. Although IUE is effective at delivering multiple DNA plasmids into populations of cells, unfortunately plasmids delivered into neural progenitor cells remain largely episomal and often get inactivated or lost after cell division. This results in a form of "birthdate" labeling in which only the cell types that do not undergo a second cell division continue to express the transfected plasmids. This limits the application of IUE with standard plasmids and precludes its use in experiments where manipulating or labeling the complete cell lineage of a progenitor is desired. To circumvent this episomal loss of plasmid in IUE, we have used a binary piggyBac transposon system to induce nonviral genomic integration of transgenes. These transgenes do not appear to inactivate after cell division, and this results in stable somatic cellular transgenesis of neurons and glia. Like standard IUE, the system can be used with multiple combinations of plasmids to achieve multicolor labeling and both loss-of-function and gain-of-function manipulations. In this protocol, we describe the method for delivering a binary piggyBac transposon plasmid system by IUE.
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Affiliation(s)
- Fuyi Chen
- Department of Physiology and Neurobiology, University of Connecticut Storrs, Connecticut 06269
| | - Brady J Maher
- Department of Physiology and Neurobiology, University of Connecticut Storrs, Connecticut 06269
| | - Joseph J LoTurco
- Department of Physiology and Neurobiology, University of Connecticut Storrs, Connecticut 06269
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Abstract
Recent years have challenged the view that adult somatic cells reach a state of terminal differentiation. Although the ultimate example of this, somatic cell nuclear transfer, has not proven feasible in human beings, dedifferentiation of mature cell types to a more primitive state, direct reprogramming from one mature state to another, and the reprogramming of any adult cell type to a pluripotent state via enforced expression of key transcription factors now all have been shown. The implications of these findings for kidney disease include the re-creation of key renal cell types from more readily available and expandable somatic cell sources. The feasibility of such an approach recently was shown with the dedifferentiation of proximal tubule cells to nephrogenic mesenchyme. In this review, we examine the technical and clinical challenges that remain to such an approach and how new reprogramming approaches also may be useful for kidney disease.
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Affiliation(s)
- Minoru Takasato
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Jessica M Vanslambrouck
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Melissa H Little
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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Anderson CD, Urschitz J, Khemmani M, Owens JB, Moisyadi S, Shohet RV, Walton CB. Ultrasound directs a transposase system for durable hepatic gene delivery in mice. ULTRASOUND IN MEDICINE & BIOLOGY 2013; 39:2351-61. [PMID: 24035623 PMCID: PMC3838570 DOI: 10.1016/j.ultrasmedbio.2013.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 05/15/2023]
Abstract
Our aim was to evaluate the delivery of transposase-based vectors by ultrasound targeted microbubble destruction (UTMD) in mice. DNA vectors were attached to cationic lipid microbubbles (1-3 μm in diameter), injected intravenously and delivered to the liver by destruction of the carrier bubbles with ultrasound in burst mode at 1.0 MHz, 20-μs pulse duration, 10-Hz pulse repetition frequency and ∼1.3-MPa acoustic peak negative pressure. We evaluated the expression and genomic integration of conventional (pcDNA3) and piggyBac transposase-based (pmGENIE) reporter vectors. In vivo, we observed UTMD-mediated liver-specific expression of pmGENIE for an average of 24 d, compared with 4 d with pcDNA3. Reporter expression was located predominately near blood vessels initially, whereas expression after 3 d was more evenly distributed through the parenchyma of the liver. We confirmed random genomic integration for pmGENIE in vitro; however, integration events for pmGENIE in vivo were targeted to specific areas of chromosome 14. Our results suggest that a combination of UTMD and non-viral DNA transposase vectors can mediate weeks of hepatic-specific gene transfer in vivo, and analyses performed by non-restrictive linear amplification-mediated (nrLAM) polymerase chain reaction, cloning and sequencing identify an unexpected tropism for integration within a specific sequence on chromosome 14 in mice. UTMD delivery of transgenes may be useful for the treatment of hepatic gene deficiency disorders.
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Affiliation(s)
- Cynthia D Anderson
- Department of Cellular and Molecular Biology; John A. Burns School of Medicine, Honolulu, HI 96813
| | - Johann Urschitz
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI 96813
| | - Mark Khemmani
- Department of Medicine, John A. Burns School of Medicine, Honolulu, HI 96813
| | - Jesse B Owens
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI 96813
| | - Stefan Moisyadi
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI 96813
- Manoa Biosciences
| | - Ralph V Shohet
- Department of Medicine, John A. Burns School of Medicine, Honolulu, HI 96813
| | - Chad B Walton
- Department of Medicine, John A. Burns School of Medicine, Honolulu, HI 96813
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Shin S, Kim BY, Jeon HY, Lee A, Lee S, Sung SH, Park CS, Lee CK, Kong H, Song Y, Kim K. Expression system for production of bioactive compounds, recombinant human adiponectin, in the silk glands of transgenic silkworms. Arch Pharm Res 2013; 37:645-51. [PMID: 24272890 DOI: 10.1007/s12272-013-0298-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/12/2013] [Indexed: 12/16/2022]
Abstract
Adiponectin is an adipocyte hormone involved in glucose and lipid metabolism. The aim of this study was to develop a human adiponectin expression system in transgenic silkworm using a human adiponectin expression vector. The silk gland of the silkworm is a highly specialized organ that has the wonderful ability to synthesize and secrete silk protein. To express human adiponectin in the silk gland of transgenic silkworm, targeting vectors pB-A3-adiponectin-IRES-RFP and pB-Ser1-adiponectin-IRES-RFP were constructed and then introduced into the silkworm pupa. The transgenic silkworms were verified by PCR and then generated. The level of adiponectin in the transgenic silkworm was 6-10 ng/50 mg of freeze-dried powder, and western blotting using an antibody against human adiponectin demonstrated a specific band with a molecular weight of 30 kDa in the silkworm. These results showed that human adiponectin introduced into the silkworm genome was expressed successfully on a large-scale.
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Affiliation(s)
- Seulmee Shin
- College of Pharmacy, Sahmyook University, Hwarangro-815, Nowon-gu, Seoul, 139-742, Korea
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Solodushko V, Bitko V, Fouty B. Minimal piggyBac vectors for chromatin integration. Gene Ther 2013; 21:1-9. [PMID: 24131979 DOI: 10.1038/gt.2013.52] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/16/2013] [Accepted: 08/27/2013] [Indexed: 01/22/2023]
Abstract
We describe novel transposon piggyBac vectors engineered to deliver transgenes as efficiently as currently available piggyBac systems, but with significantly less helper DNA co-delivered into the host genome. To generate these plasmids, we identified a previously unreported aspect of transposon biology, that the full-length terminal domains required for successful plasmid-to-chromatin transgene delivery can be removed from the transgene delivery cassette to other parts of the plasmid without significantly impairing transposition efficiency. This is achieved by including in the same plasmid, an additional helper piggyBac sequence that contains both long terminal domains, but is modified to prevent its transposition into the host genome. This design decreases the size of the required terminal domains within the delivered gene cassette of the piggyBac vector from about 1500 to just 98 base pairs. By removing these sequences from the delivered gene cassette, they are no longer incorporated into the host genome which may reduce the risk of target cell transformation.
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Affiliation(s)
- V Solodushko
- 1] Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, USA [2] Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, USA
| | - V Bitko
- NanoBio Corporation, Ann Arbor, MI, USA
| | - B Fouty
- 1] Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, USA [2] Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, USA [3] Department of Internal Medicine University of South Alabama School of Medicine, Mobile, AL, USA
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Palavesam A, Esnault C, O’Brochta DA. Post-integration silencing of piggyBac transposable elements in Aedes aegypti. PLoS One 2013; 8:e68454. [PMID: 23861905 PMCID: PMC3701635 DOI: 10.1371/journal.pone.0068454] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/30/2013] [Indexed: 12/04/2022] Open
Abstract
The piggyBac transposon, originating in the genome of the Lepidoptera Trichoplusia ni, has a broad host range, making it useful for the development of a number of transposon-based functional genomic technologies including gene vectors, enhancer-, gene- and protein-traps. While capable of being used as a vector for the creation of transgenic insects and insect cell lines, piggyBac has very limited mobility once integrated into the genome of the yellow fever mosquito, Aedes aegypti. A transgenic Aedes aegypti cell line (AagPB8) was created containing three integrated piggyBac elements and the remobilization potential of the elements was tested. The integrated piggyBac elements in AagPB8 were transpositionally silent in the presence of functional transposase, which was shown to be capable of catalyzing the movement of plasmid-borne piggyBac elements in the same cells. The structural integrity of one of the integrated elements along with the quality of element-flanking DNA, which is known to influence transposition rates, were tested in D. melanogaster. The element was found to be structurally intact, capable of transposition and excision in the soma and germ-line of Drosophila melanogaster, and in a DNA sequence context highly conducive to element movement in Drosophila melanogaster. These data show that transpositional silencing of integrated piggyBac elements in the genome of Aedes aegypti appears to be a function of higher scale genome organization or perhaps epigenetic factors, and not due to structural defects or suboptimal integration sites.
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Affiliation(s)
- Azhahianambi Palavesam
- Department of Entomology, The Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
| | - Caroline Esnault
- Department of Entomology, The Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
| | - David A. O’Brochta
- Department of Entomology, The Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- * E-mail:
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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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Chen L, Stuart L, Ohsumi TK, Burgess S, Varshney GK, Dastur A, Borowsky M, Benes C, Lacy-Hulbert A, Schmidt EV. Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics. BMC Cancer 2013; 13:93. [PMID: 23442791 PMCID: PMC3598783 DOI: 10.1186/1471-2407-13-93] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/19/2013] [Indexed: 11/16/2022] Open
Abstract
Background The development of resistance to chemotherapies represents a significant barrier to successful cancer treatment. Resistance mechanisms are complex, can involve diverse and often unexpected cellular processes, and can vary with both the underlying genetic lesion and the origin or type of tumor. For these reasons developing experimental strategies that could be used to understand, identify and predict mechanisms of resistance in different malignant cells would be a major advance. Methods Here we describe a gain-of-function forward genetic approach for identifying mechanisms of resistance. This approach uses a modified piggyBac transposon to generate libraries of mutagenized cells, each containing transposon insertions that randomly activate nearby gene expression. Genes of interest are identified using next-gen high-throughput sequencing and barcode multiplexing is used to reduce experimental cost. Results Using this approach we successfully identify genes involved in paclitaxel resistance in a variety of cancer cell lines, including the multidrug transporter ABCB1, a previously identified major paclitaxel resistance gene. Analysis of co-occurring transposons integration sites in single cell clone allows for the identification of genes that might act cooperatively to produce drug resistance a level of information not accessible using RNAi or ORF expression screening approaches. Conclusion We have developed a powerful pipeline to systematically discover drug resistance in mammalian cells in vitro. This cost-effective approach can be readily applied to different cell lines, to identify canonical or context specific resistance mechanisms. Its ability to probe complex genetic context and non-coding genomic elements as well as cooperative resistance events makes it a good complement to RNAi or ORF expression based screens.
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Affiliation(s)
- Li Chen
- Center for Molecular Therapeutics, Center for Cancer Research, Massachusetts General Hospital, and Harvard Medical School, CNY 149-Rm7308, Thirteenth St. Charlestown, MA 02129, USA.
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Design and Application of Synthetic Biology Devices for Therapy. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00009-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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