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Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401797. [PMID: 38728624 PMCID: PMC11267366 DOI: 10.1002/advs.202401797] [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: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
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Affiliation(s)
- Yongfeng Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Mudi Meng Honors CollegeChina Pharmaceutical UniversityNanjing210009China
| | - Jianping Kong
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Gongyu Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Zhaoxing Li
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
| | - Yibei Xiao
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
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2
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Bhatti JS, Khullar N, Mishra J, Kaur S, Sehrawat A, Sharma E, Bhatti GK, Selman A, Reddy PH. Stem cells in the treatment of Alzheimer's disease - Promises and pitfalls. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166712. [PMID: 37030521 DOI: 10.1016/j.bbadis.2023.166712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
Abstract
Alzheimer's disease (AD) is the most widespread form of neurodegenerative disorder that causes memory loss and multiple cognitive issues. The underlying mechanisms of AD include the build-up of amyloid-β and phosphorylated tau, synaptic damage, elevated levels of microglia and astrocytes, abnormal microRNAs, mitochondrial dysfunction, hormonal imbalance, and age-related neuronal loss. However, the etiology of AD is complex and involves a multitude of environmental and genetic factors. Currently, available AD medications only alleviate symptoms and do not provide a permanent cure. Therefore, there is a need for therapies that can prevent or reverse cognitive decline, brain tissue loss, and neural instability. Stem cell therapy is a promising treatment for AD because stem cells possess the unique ability to differentiate into any type of cell and maintain their self-renewal. This article provides an overview of the pathophysiology of AD and existing pharmacological treatments. This review article focuses on the role of various types of stem cells in neuroregeneration, the potential challenges, and the future of stem cell-based therapies for AD, including nano delivery and gaps in stem cell technology.
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Affiliation(s)
- Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Jayapriya Mishra
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Satinder Kaur
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Abhishek Sehrawat
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Eva Sharma
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India
| | - Ashley Selman
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA.
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3
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Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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4
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Bire S, Dusserre Y, Bigot Y, Mermod N. PiggyBac transposase and transposon derivatives for gene transfer targeting the ribosomal DNA loci of CHO cells. J Biotechnol 2021; 341:103-112. [PMID: 34560160 DOI: 10.1016/j.jbiotec.2021.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022]
Abstract
Integrative non-viral vectors such as transposons engineered to mediate targeted gene transfer into safe harbor sites in the genome may be a promising approach for the production of therapeutic proteins or for gene therapy in an efficient and secure way. In this context, we designed and evaluated two strategies for targeting the nuclear ribosomal DNA (rDNA) loci. One approach relied on the co-location of the transposase and transposon near transcriptionally active rDNA copies using a nucleolar localization signal (NoLS). Another one consisted of targeting the 18S-coding region in the rDNA loci using a NoLS-FokI-dCas9 endonuclease to perform targeted transgene knock-in. We show that integration into the rDNA of Chinese hamster ovary (CHO) cells can be achieved at a high frequency using the piggyBac transposon system, indicating that the rDNA is highly accessible for transposition. Consistently, rDNA-targeted transposition events were most frequently obtained when both the piggyBac transposon DNA and the transposase were nucleoli-targeted, yielding cells displaying stable and homogeneous expression of the transgene. This approach thus provides an alternative strategy to improve targeted transgene delivery and protein expression using CHO cells.
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Affiliation(s)
- Solenne Bire
- Institute of Biotechnology and Department of Fundamental Microbiology, Center for Biotechnology UNIL-EPFL, University of Lausanne, Lausanne, Switzerland
| | - Yves Dusserre
- Institute of Biotechnology and Department of Fundamental Microbiology, Center for Biotechnology UNIL-EPFL, University of Lausanne, Lausanne, Switzerland
| | - Yves Bigot
- UMR INRAE 0085, CNRS 7247, Physiologie de la Reproduction et des Comportements, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Nicolas Mermod
- Institute of Biotechnology and Department of Fundamental Microbiology, Center for Biotechnology UNIL-EPFL, University of Lausanne, Lausanne, Switzerland.
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5
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Guo C, Fordjour FK, Tsai SJ, Morrell JC, Gould SJ. Choice of selectable marker affects recombinant protein expression in cells and exosomes. J Biol Chem 2021; 297:100838. [PMID: 34051235 PMCID: PMC8258971 DOI: 10.1016/j.jbc.2021.100838] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/14/2021] [Accepted: 05/25/2021] [Indexed: 11/19/2022] Open
Abstract
Transgenic mammalian cells are used for numerous research, pharmaceutical, industrial, and clinical purposes, and dominant selectable markers are often used to enable the selection of transgenic cell lines. Using HEK293 cells, we show here that the choice of selectable marker gene has a significant impact on both the level of recombinant protein expression and the cell-to-cell variability in recombinant protein expression. Specifically, we observed that cell lines generated with the NeoR or BsdR selectable markers and selected in the antibiotics G418 or blasticidin, respectively, displayed the lowest level of recombinant protein expression as well as the greatest cell-to-cell variability in transgene expression. In contrast, cell lines generated with the BleoR marker and selected in zeocin yielded cell lines that expressed the highest levels of linked recombinant protein, approximately 10-fold higher than those selected using the NeoR or BsdR markers, as well as the lowest cell-to-cell variability in recombinant protein expression. Intermediate yet still-high levels of expression were observed in cells generated with the PuroR- or HygR-based vectors and that were selected in puromycin or hygromycin, respectively. Similar results were observed in the African green monkey cell line COS7. These data indicate that each combination of selectable marker and antibiotic establishes a threshold below which no cell can survive and that these thresholds vary significantly between different selectable markers. Moreover, we show that choice of selectable marker also affects recombinant protein expression in cell-derived exosomes, consistent with the hypothesis that exosome protein budding is a stochastic rather than determinative process.
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Affiliation(s)
- Chenxu Guo
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore Maryland, USA
| | - Francis K Fordjour
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore Maryland, USA
| | - Shang Jui Tsai
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore Maryland, USA
| | - James C Morrell
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore Maryland, USA
| | - Stephen J Gould
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore Maryland, USA.
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6
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piggyBac-Based Non-Viral In Vivo Gene Delivery Useful for Production of Genetically Modified Animals and Organs. Pharmaceutics 2020; 12:pharmaceutics12030277. [PMID: 32204422 PMCID: PMC7151002 DOI: 10.3390/pharmaceutics12030277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 11/17/2022] Open
Abstract
In vivo gene delivery involves direct injection of nucleic acids (NAs) into tissues, organs, or tail-veins. It has been recognized as a useful tool for evaluating the function of a gene of interest (GOI), creating models for human disease and basic research targeting gene therapy. Cargo frequently used for gene delivery are largely divided into viral and non-viral vectors. Viral vectors have strong infectious activity and do not require the use of instruments or reagents helpful for gene delivery but bear immunological and tumorigenic problems. In contrast, non-viral vectors strictly require instruments (i.e., electroporator) or reagents (i.e., liposomes) for enhanced uptake of NAs by cells and are often accompanied by weak transfection activity, with less immunological and tumorigenic problems. Chromosomal integration of GOI-bearing transgenes would be ideal for achieving long-term expression of GOI. piggyBac (PB), one of three transposons (PB, Sleeping Beauty (SB), and Tol2) found thus far, has been used for efficient transfection of GOI in various mammalian cells in vitro and in vivo. In this review, we outline recent achievements of PB-based production of genetically modified animals and organs and will provide some experimental concepts using this system.
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7
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Tipanee J, Di Matteo M, Tulalamba W, Samara-Kuko E, Keirsse J, Van Ginderachter JA, Chuah MK, VandenDriessche T. Validation of miR-20a as a Tumor Suppressor Gene in Liver Carcinoma Using Hepatocyte-Specific Hyperactive piggyBac Transposons. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:1309-1329. [PMID: 32160703 PMCID: PMC7036702 DOI: 10.1016/j.omtn.2020.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 02/07/2023]
Abstract
We established a semi-high-throughput in vivo screening platform using hyperactive piggyBac (hyPB) transposons (designated as PB-miR) to identify microRNAs (miRs) that inhibit hepatocellular carcinoma (HCC) development in vivo, following miR overexpression in hepatocytes. PB-miRs encoding six different miRs from the miR-17-92 cluster and nine miRs from outside this cluster were transfected into mouse livers that were chemically induced to develop HCC. In this slow-onset HCC model, miR-20a significantly inhibited HCC. Next, we developed a more aggressive HCC model by overexpression of oncogenic Harvey rat sarcoma viral oncogene homolog (HRASG12V) and c-MYC oncogenes that accelerated HCC development after only 6 weeks. The tumor suppressor effect of miR-20a could be demonstrated even in this rapid-onset HRASG12V/c-MYC HCC model, consistent with significantly prolonged survival and decreased HCC tumor burden. Comprehensive RNA expression profiling of 95 selected genes typically associated with HCC development revealed differentially expressed genes and functional pathways that were associated with miR-20a-mediated HCC suppression. To our knowledge, this is the first study establishing a direct causal relationship between miR-20a overexpression and liver cancer inhibition in vivo. Moreover, these results demonstrate that hepatocyte-specific hyPB transposons are an efficient platform to screen and identify miRs that affect overall survival and HCC tumor regression.
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Affiliation(s)
- Jaitip Tipanee
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mario Di Matteo
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium; Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, 3000 Leuven, Belgium
| | - Warut Tulalamba
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Ermira Samara-Kuko
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Jiri Keirsse
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium; Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jo A Van Ginderachter
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium; Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marinee Khim Chuah
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium; Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, 3000 Leuven, Belgium.
| | - Thierry VandenDriessche
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, 1090 Brussels, Belgium; Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, 3000 Leuven, Belgium.
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8
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Siew SM, Cunningham SC, Zhu E, Tay SS, Venuti E, Bolitho C, Alexander IE. Prevention of Cholestatic Liver Disease and Reduced Tumorigenicity in a Murine Model of PFIC Type 3 Using Hybrid AAV-piggyBac Gene Therapy. Hepatology 2019; 70:2047-2061. [PMID: 31099022 DOI: 10.1002/hep.30773] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 05/06/2019] [Indexed: 12/14/2022]
Abstract
Recombinant adeno-associated viral (rAAV) vectors are highly promising vehicles for liver-targeted gene transfer, with therapeutic efficacy demonstrated in preclinical models and clinical trials. Progressive familial intrahepatic cholestasis type 3 (PFIC3), an inherited juvenile-onset, cholestatic liver disease caused by homozygous mutation of the ABCB4 gene, may be a promising candidate for rAAV-mediated liver-targeted gene therapy. The Abcb4-/- mice model of PFIC3, with juvenile mice developing progressive cholestatic liver injury due to impaired biliary phosphatidylcholine excretion, resulted in cirrhosis and liver malignancy. Using a conventional rAAV strategy, we observed markedly blunted rAAV transduction in adult Abcb4-/- mice with established liver disease, but not in disease-free, wild-type adults or in homozygous juveniles prior to liver disease onset. However, delivery of predominantly nonintegrating rAAV vectors to juvenile mice results in loss of persistent transgene expression due to hepatocyte proliferation in the growing liver. Conclusion: A hybrid vector system, combining the high transduction efficiency of rAAV with piggyBac transposase-mediated somatic integration, was developed to facilitate stable human ABCB4 expression in vivo and to correct juvenile-onset chronic liver disease in a murine model of PFIC3. A single dose of hybrid vector at birth led to life-long restoration of bile composition, prevention of biliary cirrhosis, and a substantial reduction in tumorigenesis. This powerful hybrid rAAV-piggyBac transposon vector strategy has the capacity to mediate lifelong phenotype correction and reduce the tumorigenicity of progressive familial intrahepatic cholestasis type 3 and, with further refinement, the potential for human clinical translation.
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Affiliation(s)
- Susan M Siew
- Department of Gastroenterology and James Fairfax Institute of Pediatric Nutrition, Sydney Children's Hospitals Network, Westmead, Australia
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Sharon C Cunningham
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Szun S Tay
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Elena Venuti
- Department of Gastroenterology and James Fairfax Institute of Pediatric Nutrition, Sydney Children's Hospitals Network, Westmead, Australia
| | - Christine Bolitho
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
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9
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Li L, Liang J, Luo H, Tam KM, Tse ECM, Li Y. A new chemical approach for proximity labelling of chromatin-associated RNAs and proteins with visible light irradiation. Chem Commun (Camb) 2019; 55:12340-12343. [DOI: 10.1039/c9cc06251c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new nucleus-localized singlet oxygen generator was designed and synthesized.
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Affiliation(s)
- Lan Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Jiying Liang
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Hao Luo
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - K. Ming Tam
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Edmund C. M. Tse
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
| | - Ying Li
- Department of Chemistry
- The University of Hong Kong
- Hong Kong, SAR
- Hong Kong
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10
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Kirk JM, Kim SO, Inoue K, Smola MJ, Lee DM, Schertzer MD, Wooten JS, Baker AR, Sprague D, Collins DW, Horning CR, Wang S, Chen Q, Weeks KM, Mucha PJ, Calabrese JM. Functional classification of long non-coding RNAs by k-mer content. Nat Genet 2018; 50:1474-1482. [PMID: 30224646 PMCID: PMC6262761 DOI: 10.1038/s41588-018-0207-8] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 07/24/2018] [Indexed: 12/30/2022]
Abstract
The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called kmers. We found that lncRNAs of related function often had similar kmer profiles despite lacking linear homology, and that kmer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. Kmer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.
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Affiliation(s)
- Jessime M Kirk
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan O Kim
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Kaoru Inoue
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Matthew J Smola
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Ribometrix, Durham, NC, USA
| | - David M Lee
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Megan D Schertzer
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joshua S Wooten
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison R Baker
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Harvard Medical School, Ph.D. Program in Biological and Biomedical Sciences, Boston, MA, USA
| | - Daniel Sprague
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David W Collins
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher R Horning
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shuo Wang
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qidi Chen
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Peter J Mucha
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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11
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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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12
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Thompson DB, Aboulhouda S, Hysolli E, Smith CJ, Wang S, Castanon O, Church GM. The Future of Multiplexed Eukaryotic Genome Engineering. ACS Chem Biol 2018; 13:313-325. [PMID: 29241002 PMCID: PMC5880278 DOI: 10.1021/acschembio.7b00842] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multiplex genome editing is the simultaneous introduction of multiple distinct modifications to a given genome. Though in its infancy, maturation of this field will facilitate powerful new biomedical research approaches and will enable a host of far-reaching biological engineering applications, including new therapeutic modalities and industrial applications, as well as "genome writing" and de-extinction efforts. In this Perspective, we focus on multiplex editing of large eukaryotic genomes. We describe the current state of multiplexed genome editing, the current limits of our ability to multiplex edits, and provide perspective on the many applications that fully realized multiplex editing technologies would enable in higher eukaryotic genomes. We offer a broad look at future directions, covering emergent CRISPR-based technologies, advances in intracellular delivery, and new DNA assembly approaches that may enable future genome editing on a massively multiplexed scale.
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Affiliation(s)
- David B. Thompson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Soufiane Aboulhouda
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Eriona Hysolli
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Cory J. Smith
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Stan Wang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Oscar Castanon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau, France
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
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13
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Bire S, Ishac N, Rouleux-Bonnin F. In Vitro Synthesis, Delivery, and Bioavailability of Exogenous mRNA in Gene Transfer Mediated by PiggyBac Transposition. Methods Mol Biol 2017; 1428:187-217. [PMID: 27236801 DOI: 10.1007/978-1-4939-3625-0_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nowadays, nonviral gene transfer is currently of great importance for introducing exogenous genes into genomes and for ensuring that transgene expression is suitable for therapeutic and bioproduction purposes. The piggyBac transposon-based system is particularly interesting since it is easy to engineer and has a large cargo capacity, up to 100 kb. In its setup, the system requires only the piggyBac transposase protein and the transgene delineated by the two piggyBac-specific inverted terminal repeats. Usually the source of transposase is carried by a DNA plasmid. However, the principal drawback of this method is the lasting presence of the transposase, due to episomal persistence or possible integration of the transposase gene vector into the cell's genome. This can lead to genotoxic effects such as multiple genomic integration events and remobilization of the transposon vector once it has been integrated. One alternative to improve the safety of the system is to deliver the transposase as in vitro-synthesized messenger RNA in order to define a very narrow expression window during which a one-shot transposition process would occur. Issues that can be encountered when working on mRNA cell transfer are related to the quality of the synthetic mRNA, the system used to introduce mRNA into the cells and the bioavailability of the mRNA molecules. Here we describe a method to produce mRNA, verify its quality, determine which transfecting reagents can be used and how this mRNA is available to promote the transposition process in HeLa cells. Additionally, we illustrate this method in stromal mesenchymal cell lines in order to support hematopoiesis.
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Affiliation(s)
- Solenne Bire
- LBTM, Institute of Biotechnology, UNIL-EPFL, Station 6, Lausanne, 1015, Switzerland
| | - Nicole Ishac
- LNOX, GICC UMR CNRS 7292, UFR de Médecine, Bâtiment Dutrochet, 10 Boulevard Tonnellé, Tours, 37032, France
| | - Florence Rouleux-Bonnin
- LNOX, GICC UMR CNRS 7292, UFR de Médecine, Bâtiment Dutrochet, 10 Boulevard Tonnellé, Tours, 37032, France.
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14
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Tipanee J, VandenDriessche T, Chuah MK. Transposons: Moving Forward from Preclinical Studies to Clinical Trials. Hum Gene Ther 2017; 28:1087-1104. [DOI: 10.1089/hum.2017.128] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Jaitip Tipanee
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
| | - Thierry VandenDriessche
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Marinee K. Chuah
- Department of Gene Therapy and Regenerative Medicine, Free University of Brussels (VUB), Brussels, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
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15
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Ma Y, Yue J, Zhang Y, Shi C, Odenwald M, Liang WG, Wei Q, Goel A, Gou X, Zhang J, Chen SY, Tang WJ, Turner JR, Yang F, Liang H, Qin H, Wu X. ACF7 regulates inflammatory colitis and intestinal wound response by orchestrating tight junction dynamics. Nat Commun 2017; 8:15375. [PMID: 28541346 PMCID: PMC5458510 DOI: 10.1038/ncomms15375] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/16/2017] [Indexed: 12/12/2022] Open
Abstract
In the intestinal epithelium, the aberrant regulation of cell/cell junctions leads to intestinal barrier defects, which may promote the onset and enhance the severity of inflammatory bowel disease (IBD). However, it remains unclear how the coordinated behaviour of cytoskeletal network may contribute to cell junctional dynamics. In this report, we identified ACF7, a crosslinker of microtubules and F-actin, as an essential player in this process. Loss of ACF7 leads to aberrant microtubule organization, tight junction stabilization and impaired wound closure in vitro. With the mouse genetics approach, we show that ablation of ACF7 inhibits intestinal wound healing and greatly increases susceptibility to experimental colitis in mice. ACF7 level is also correlated with development and progression of ulcerative colitis (UC) in human patients. Together, our results reveal an important molecular mechanism whereby coordinated cytoskeletal dynamics contributes to cell adhesion regulation during intestinal wound repair and the development of IBD. The cytoskeleton plays a key role in cell/cell junction formation, but how the coordinated behaviour of the cytoskeleton contributes is not known. Here the authors show that actin-microtubule crosslinker ACF7 plays a key role in tight junction stabilization and wound healing in intestinal epithelium.
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Affiliation(s)
- Yanlei Ma
- Department of GI surgery, Shanghai Tenth People's Hospital Affiliated with Tongji University, 301 Yanchang Road, Shanghai 200072, China.,The University of Chicago, Ben May Department for Cancer Research, Chicago, Illinois 60637, USA.,State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China, Guanxi Normal University, Guilin 541004, China
| | - Jiping Yue
- The University of Chicago, Ben May Department for Cancer Research, Chicago, Illinois 60637, USA
| | - Yao Zhang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Chenzhang Shi
- Department of GI surgery, Shanghai Tenth People's Hospital Affiliated with Tongji University, 301 Yanchang Road, Shanghai 200072, China
| | - Matt Odenwald
- Pritzker School of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Wenguang G Liang
- The University of Chicago, Ben May Department for Cancer Research, Chicago, Illinois 60637, USA
| | - Qing Wei
- Department of Pathology, Shanghai Tenth People's Hospital Affiliated with Tongji University, 301 Yanchang Road, Shanghai 200072, China
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Scott &White Research Institute and Charles A. Sammons Cancer Center, Texas, USA
| | - Xuewen Gou
- The University of Chicago, Ben May Department for Cancer Research, Chicago, Illinois 60637, USA
| | - Jamie Zhang
- The University of Chicago, Ben May Department for Cancer Research, Chicago, Illinois 60637, USA
| | - Shao-Yu Chen
- Department of Pharmacology and Toxicology, University of Louisville Health Science Center, Louisville, Kentucky 40292, USA
| | - Wei-Jen Tang
- The University of Chicago, Ben May Department for Cancer Research, Chicago, Illinois 60637, USA
| | - Jerrold R Turner
- Departments of Pathology and Medicine (GI), Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Feng Yang
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China, Guanxi Normal University, Guilin 541004, China
| | - Hong Liang
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China, Guanxi Normal University, Guilin 541004, China
| | - Huanlong Qin
- Department of GI surgery, Shanghai Tenth People's Hospital Affiliated with Tongji University, 301 Yanchang Road, Shanghai 200072, China
| | - Xiaoyang Wu
- The University of Chicago, Ben May Department for Cancer Research, Chicago, Illinois 60637, USA
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16
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Denduluri SK, Scott B, Lamplot JD, Yin L, Yan Z, Wang Z, Ye J, Wang J, Wei Q, Mohammed MK, Haydon RC, Kang RW, He TC, Athiviraham A, Ho SH, Shi LL. Immortalized Mouse Achilles Tenocytes Demonstrate Long-Term Proliferative Capacity While Retaining Tenogenic Properties. Tissue Eng Part C Methods 2016; 22:280-9. [PMID: 26959762 DOI: 10.1089/ten.tec.2015.0244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Investigating the cellular processes underlying tendon healing can allow researchers to improve long-term outcomes after injury. However, conducting meaningful studies to uncover the injury healing mechanism at cellular and molecular levels remains challenging. This is due to the inherent difficulty in isolating, culturing, and expanding sufficient primary tenocytes, due to their limited proliferative capacity and short lifespan. In this study, we sought to establish a novel line of immortalized mouse Achilles tenocytes (iMATs) with primary tenocyte properties, but increased proliferative capacity suitable for extensive in vitro experimentation. We show that isolated primary mouse Achilles tenocytes (pMATs) can be effectively immortalized using a piggyBac transposon expressing SV40 large T antigen flanked by FLP recombination target site (FRT). The resulting iMATs exhibit markedly greater proliferation and survival, which can be reversed with FLP recombinase. Furthermore, iMATs express the same set of tendon-specific markers as that of primary cells, although in lower levels, and respond similarly to exogenous stimulation with bone morphogenetic protein 13 (BMP13) as has been previously reported with pMATs. Taken together, our results suggest that iMATs acquire long-term proliferative capacity while maintaining tenogenic properties. We believe that iMATs are a suitable model for studying not only the native cellular processes involved in injury and healing, but also potential therapeutic agents that may augment the stability of tendon repair.
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Affiliation(s)
- Sahitya K Denduluri
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Bryan Scott
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Joseph D Lamplot
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Liangjun Yin
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois.,2 Ministry of Education Key Laboratory of Diagnostic Medicine, The Affiliated Hospitals of Chongqing Medical University , Chongqing, China
| | - Zhengjian Yan
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois.,2 Ministry of Education Key Laboratory of Diagnostic Medicine, The Affiliated Hospitals of Chongqing Medical University , Chongqing, China
| | - Zhongliang Wang
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois.,2 Ministry of Education Key Laboratory of Diagnostic Medicine, The Affiliated Hospitals of Chongqing Medical University , Chongqing, China
| | - Jixing Ye
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Jing Wang
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois.,2 Ministry of Education Key Laboratory of Diagnostic Medicine, The Affiliated Hospitals of Chongqing Medical University , Chongqing, China
| | - Qiang Wei
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois.,2 Ministry of Education Key Laboratory of Diagnostic Medicine, The Affiliated Hospitals of Chongqing Medical University , Chongqing, China
| | - Maryam K Mohammed
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Rex C Haydon
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Richard W Kang
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Tong-Chuan He
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Aravind Athiviraham
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Sherwin H Ho
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
| | - Lewis L Shi
- 1 Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Pritzker School of Medicine , Chicago, Illinois
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17
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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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18
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Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. PLoS Pathog 2016; 12:e1005763. [PMID: 27467575 PMCID: PMC4965013 DOI: 10.1371/journal.ppat.1005763] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/21/2016] [Indexed: 01/22/2023] Open
Abstract
A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal chemistry programs. The data for all of these assays are presented and analyzed to show how outstanding leads for many indications can be selected. These results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications. Another lesson is that when multiple screens from different groups are run on the same library, results can be integrated quickly to select the most valuable starting points for subsequent medicinal chemistry efforts. Malaria leads to the loss of over 440,000 lives annually; accelerating research to discover new candidate drugs is a priority. Medicines for Malaria Venture (MMV) has distilled over 25,000 compounds that kill malaria parasites in vitro into a group of 400 representative compounds, called the "Malaria Box". These Malaria Box sets were distributed free-of-charge to research laboratories in 30 different countries that work on a wide variety of pathogens. Fifty-five groups compiled >290 assay results for this paper describing the many activities of the Malaria Box compounds. The collective results suggest a potential mechanism of action for over 130 compounds against malaria and illuminate the most promising compounds for further malaria drug development research. Excitingly some of these compounds also showed outstanding activity against other disease agents including fungi, bacteria, other single-cellular parasites, worms, and even human cancer cells. The results have ignited over 30 drug development programs for a variety of diseases. This open access effort was so successful that MMV has begun to distribute another set of compounds with initial activity against a wider range of infectious agents that are of public health concern, called the Pathogen Box, available now to scientific labs all over the world (www.PathogenBox.org).
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19
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Abrusán G, Yant SR, Szilágyi A, Marsh JA, Mátés L, Izsvák Z, Barabás O, Ivics Z. Structural Determinants of Sleeping Beauty Transposase Activity. Mol Ther 2016; 24:1369-77. [PMID: 27401040 DOI: 10.1038/mt.2016.110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022] Open
Abstract
Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold.
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Affiliation(s)
- György Abrusán
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.,Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Stephen R Yant
- Department of Pediatrics and Genetics, Stanford University School of Medicine, Stanford, California, USA.,Present address: Gilead Sciences Inc., Foster City, California, USA
| | - András Szilágyi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Lajos Mátés
- Instistute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | | | - Orsolya Barabás
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
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20
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Yue J, Zhang Y, Liang WG, Gou X, Lee P, Liu H, Lyu W, Tang WJ, Chen SY, Yang F, Liang H, Wu X. In vivo epidermal migration requires focal adhesion targeting of ACF7. Nat Commun 2016; 7:11692. [PMID: 27216888 PMCID: PMC5476826 DOI: 10.1038/ncomms11692] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/19/2016] [Indexed: 11/09/2022] Open
Abstract
Turnover of focal adhesions allows cell retraction, which is essential for cell migration. The mammalian spectraplakin protein, ACF7 (Actin-Crosslinking Factor 7), promotes focal adhesion dynamics by targeting of microtubule plus ends towards focal adhesions. However, it remains unclear how the activity of ACF7 is regulated spatiotemporally to achieve focal adhesion-specific guidance of microtubule. To explore the potential mechanisms, we resolve the crystal structure of ACF7’s NT (amino-terminal) domain, which mediates F-actin interactions. Structural analysis leads to identification of a key tyrosine residue at the calponin homology (CH) domain of ACF7, whose phosphorylation by Src/FAK (focal adhesion kinase) complex is essential for F-actin binding of ACF7. Using skin epidermis as a model system, we further demonstrate that the phosphorylation of ACF7 plays an indispensable role in focal adhesion dynamics and epidermal migration in vitro and in vivo. Together, our findings provide critical insights into the molecular mechanisms underlying coordinated cytoskeletal dynamics during cell movement. The spectraplakin protein ACF7 binds to actin at focal adhesions and targets microtubule plus ends to focal adhesions, promoting their disassembly. Here the authors reveal that ACF7 is phosphorylated by Src/FAK, and this regulates actin binding and focal adhesion dynamics in vitro and in vivo.
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Affiliation(s)
- Jiping Yue
- Ben May Department for Cancer Research, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Yao Zhang
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China, Guanxi Normal University, Guilin 541004, China
| | - Wenguang G Liang
- Ben May Department for Cancer Research, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Xuewen Gou
- Ben May Department for Cancer Research, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Philbert Lee
- Ben May Department for Cancer Research, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Han Liu
- Ben May Department for Cancer Research, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Wanqing Lyu
- Ben May Department for Cancer Research, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Wei-Jen Tang
- Ben May Department for Cancer Research, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Shao-Yu Chen
- Department of Pharmacology and Toxicology, University of Louisville Health Science Center, Louisville, Kentucky 40292, USA
| | - Feng Yang
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China, Guanxi Normal University, Guilin 541004, China
| | - Hong Liang
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Science and Technology of China, Guanxi Normal University, Guilin 541004, China
| | - Xiaoyang Wu
- Ben May Department for Cancer Research, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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21
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Abstract
Genome editing in large animals has tremendous practical applications, from more accurate models for medical research through improved animal welfare and production efficiency. Although genetic modification in large animals has a 30 year history, until recently technical issues limited its utility. The original methods - pronuclear injection and integrating viruses - were plagued with problems associated with low efficiency, silencing, poor regulation of gene expression, and variability associated with random integration. With the advent of site specific nucleases such as TALEN and CRISPR/Cas9, precision editing became possible. When used on their own, these can be used to truncate or knockout genes through non-homologous end joining (NHEJ) with relatively high efficiency. When used with a template containing desired gene edits, these can be used to allow insertion of any desired changes to the genome through homologous recombination (HR) with substantially lower efficiency. Consideration must be given to the issues of marker sets and off-target effects. Somatic cell nuclear transfer is most commonly used to create animals from gene edited cells, but direct zygote injection and use of spermatogonial stem cells are alternatives under development. In developing gene editing projects, priority must be given to understanding the potential for off-target or unexpected effects of planned edits, which have been common in the past. Because of the increasing technical sophistication with which it can be accomplished, genome editing is poised to revolutionize large animal genetics, but attention must be paid to the underlying biology in order to maximize benefit.
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Affiliation(s)
- James West
- AgGenetics, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - W Warren Gill
- AgGenetics, Nashville, TN; School of Agribusiness and Agriscience, Middle Tennessee State University, Murfreesboro, TN
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22
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Basu S, Tan YL, Taylor EJR, Laue ED, Lee SF. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localisation Microscopy. Methods Mol Biol 2016; 1431:235-63. [PMID: 27283313 DOI: 10.1007/978-1-4939-3631-1_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-molecule localisation microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal 'snapshots' of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination and protein labelling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analysing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Edward J R Taylor
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Steven F Lee
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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23
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Skipper KA, Mikkelsen JG. Delivering the Goods for Genome Engineering and Editing. Hum Gene Ther 2015; 26:486-97. [DOI: 10.1089/hum.2015.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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24
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Wu Y, Feng G, Song J, Zhang Y, Yu Y, Huang L, Zheng L, Deng F. TrAmplification of Human Dental Follicle Cells by piggyBac Transposon - Mediated Reversible Immortalization System. PLoS One 2015; 10:e0130937. [PMID: 26172849 PMCID: PMC4501788 DOI: 10.1371/journal.pone.0130937] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/27/2015] [Indexed: 11/18/2022] Open
Abstract
Dental follicle cells (DFCs) are the precursor cells of periodontium. Under certain differentiation conditions, DFCs can be induced to differentiate into chondrogenic, osteogenic and adipogenic cells. However, DFCs has limited lifespan in vitro, so it's difficult to harvest enough cells for basic research and translational application. pMPH86 is a piggyBac transposon-mediated vector which contains SV40 T-Ag cassette that can be removed by flippase recognition target (FRT) recombinase. Here we demonstrated the pMPH86 can effectively amplify human DFCs through reversible immortalization. The immortalized DFCs (iDFCs) exhibit higher proliferate activity, which can be reversed to its original level before immortalization when deimmortalized by FLP recombinase. The iDFCs and deimmortalized DFCs (dDFCs) express most DFC markers and maintain multiple differentiation potential in vitro as they can be induced by BMP9 to differentiate into chondrogenic, osteogenic and adipogenic cells evidenced by gene expression and protein marker. We also proved telomerase activity of iDFCs are significantly increased and maintained at a high level, while the telomerase activity of primary DFCs was relatively low and decreased with every passage. After SV40 T-Ag was removed to deimmortalize the cells, telomerase activity was reduced to its original level before immortalization and decreased with passages just the same as primary DFCs. These results suggest that piggyBac immortalization system could be a potential strategy to amplify primary cells, which is critical for regenerative research and further clinical application.
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Affiliation(s)
- Yan Wu
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, P. R. China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Chongqing, P. R. China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, P. R. China
| | - Ge Feng
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, P. R. China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Chongqing, P. R. China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, P. R. China
| | - Jinlin Song
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, P. R. China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Chongqing, P. R. China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, P. R. China
| | - Yuanyuan Zhang
- Wake Forest Institute for Regenerative Medicine (WFIRM), Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Yong Yu
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, P. R. China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Chongqing, P. R. China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, P. R. China
| | - Lan Huang
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, P. R. China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Chongqing, P. R. China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, P. R. China
| | - Leilei Zheng
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, P. R. China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Chongqing, P. R. China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, P. R. China
| | - Feng Deng
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, P. R. China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Chongqing, P. R. China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, P. R. China
- * E-mail:
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25
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Chen X, Cui J, Yan Z, Zhang H, Chen X, Wang N, Shah P, Deng F, Zhao C, Geng N, Li M, Denduluri SK, Haydon RC, Luu HH, Reid RR, He TC. Sustained high level transgene expression in mammalian cells mediated by the optimized piggyBac transposon system. Genes Dis 2015; 2:96-105. [PMID: 25815368 PMCID: PMC4372205 DOI: 10.1016/j.gendis.2014.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Sustained, high level transgene expression in mammalian cells is desired in many cases for studying gene functions. Traditionally, stable transgene expression has been accomplished by using retroviral or lentiviral vectors. However, such viral vector-mediated transgene expression is often at low levels and can be reduced over time due to low copy numbers and/or chromatin remodeling repression. The piggyBac transposon has emerged as a promising non-viral vector system for efficient gene transfer into mammalian cells. Despite its inherent advantages over lentiviral and retroviral systems, piggyBac system has not been widely used, at least in part due to their limited manipulation flexibilities. Here, we seek to optimize piggyBac-mediated transgene expression and generate a more efficient, user-friendly piggyBac system. By engineering a panel of versatile piggyBac vectors and constructing recombinant adenoviruses expressing piggyBac transposase (PBase), we demonstrate that adenovirus-mediated PBase expression significantly enhances the integration efficiency and expression level of transgenes in mesenchymal stem cells and osteosarcoma cells, compared to that obtained from co-transfection of the CMV-PBase plasmid. We further determine the drug selection timeline to achieve optimal stable transgene expression. Moreover, we demonstrate that the transgene copy number of piggyBac-mediated integration is approximately 10 times higher than that mediated by retroviral vectors. Using the engineered tandem expression vector, we show that three transgenes can be simultaneously expressed in a single vector with high efficiency. Thus, these results strongly suggest that the optimized piggyBac system is a valuable tool for making stable cell lines with sustained, high transgene expression.
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Affiliation(s)
- Xiang Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Department of Pediatric Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Jing Cui
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Ministry of Education Key Laboratory of Diagnostic Medicine, and The Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Zhengjian Yan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Ministry of Education Key Laboratory of Diagnostic Medicine, and The Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Hongmei Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Ministry of Education Key Laboratory of Diagnostic Medicine, and The Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Xian Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Department of Laboratory Medicine, the Affiliated Hospitals of Qingdao University, Qingdao, China
| | - Ning Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Departments of Oncology, Cell Biology and Laboratory Medicine, Third Military Medical University, Chongqing, China
| | - Palak Shah
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Fang Deng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Departments of Oncology, Cell Biology and Laboratory Medicine, Third Military Medical University, Chongqing, China
| | - Chen Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Departments of Oncology, Cell Biology and Laboratory Medicine, Third Military Medical University, Chongqing, China
| | - Nisha Geng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Melissa Li
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Sahitya K Denduluri
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Rex C Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Section of Plastic & Reconstructive Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA ; Ministry of Education Key Laboratory of Diagnostic Medicine, and The Affiliated Hospitals of Chongqing Medical University, Chongqing, China
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26
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Ovchinnikov DA, Sun J, Wolvetang EJ. Generation of Footprint-Free Induced Pluripotent Stem Cells from Human Fibroblasts Using Episomal Plasmid Vectors. Methods Mol Biol 2015; 1330:37-45. [PMID: 26621587 DOI: 10.1007/978-1-4939-2848-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human induced pluripotent stem cells (hiPSCs) have provided novel insights into the etiology of disease and are set to transform regenerative medicine and drug screening over the next decade. The generation of human iPSCs free of a genetic footprint of the reprogramming process is crucial for the realization of these potential uses. Here we describe in detail the generation of human iPSC from control and disease-carrying individuals' fibroblasts using episomal plasmids.
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Affiliation(s)
- Dmitry A Ovchinnikov
- Stem Cell Engineering Group, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Corner College and Cooper Rds (Building 75), St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jane Sun
- Stem Cell Engineering Group, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Corner College and Cooper Rds (Building 75), St. Lucia, Brisbane, QLD, 4072, Australia
| | - Ernst J Wolvetang
- Stem Cell Engineering Group, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Corner College and Cooper Rds (Building 75), St. Lucia, Brisbane, QLD, 4072, Australia.
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27
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Palazzo A, Moschetti R, Caizzi R, Marsano RM. The Drosophila mojavensis Bari3 transposon: distribution and functional characterization. Mob DNA 2014; 5:21. [PMID: 25093043 PMCID: PMC4120734 DOI: 10.1186/1759-8753-5-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/13/2014] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Bari-like transposons belong to the Tc1-mariner superfamily, and they have been identified in several genomes of the Drosophila genus. This transposon's family has been used as paradigm to investigate the complex dynamics underlying the persistence and structural evolution of transposable elements (TEs) within a genome. Three structural Bari variants have been identified so far and can be distinguished based on the organization of their terminal inverted repeats. Bari3 is the last discovered member of this family identified in Drosophila mojavensis, a recently emerged species of the Repleta group of the genus Drosophila. RESULTS We studied the insertion pattern of Bari3 in different D. mojavensis populations and found evidence of recent transposition activity. Analysis of the transposase domains unveiled the presence of a functional nuclear localization signal, as well as a functional binding domain. Using luciferase-based assays, we investigated the promoter activity of Bari3 as well as the interaction of its transposase with its left terminus. The results suggest that Bari3 is transposition-competent. Finally we demonstrated transposase transcript processing when the transposase gene is overexpressed in vivo and in vitro. CONCLUSIONS Bari3 displays very similar structural and functional features with its close relative, Bari1. Our results strongly suggest that Bari3 is an independent element that has generated genomic diversity in D. mojavensis. It can autonomously transcribe its transposase gene, which in turn can localize in the nucleus and bind the terminal inverted repeats of the transposon. Nevertheless, the identification of an unpredicted spliced form of the Bari3 transposase transcript allows us to hypothesize a control mechanism of its mobility based on mRNA processing. These results will aid the studies on the Bari family of transposons, which is intriguing for its widespread diffusion in Drosophilids coupled with a structural diversity generated during the evolution of Bari-like elements in their host genomes.
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Affiliation(s)
- Antonio Palazzo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - Roberta Moschetti
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - Ruggiero Caizzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - René Massimiliano Marsano
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
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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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29
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Wang N, Zhang W, Cui J, Zhang H, Chen X, Li R, Wu N, Chen X, Wen S, Zhang J, Yin L, Deng F, Liao Z, Zhang Z, Zhang Q, Yan Z, Liu W, Ye J, Deng Y, Wang Z, Qiao M, Luu HH, Haydon RC, Shi LL, Liang H, He TC. The piggyBac transposon-mediated expression of SV40 T antigen efficiently immortalizes mouse embryonic fibroblasts (MEFs). PLoS One 2014; 9:e97316. [PMID: 24845466 PMCID: PMC4028212 DOI: 10.1371/journal.pone.0097316] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 04/19/2014] [Indexed: 12/29/2022] Open
Abstract
Mouse embryonic fibroblasts (MEFs) are mesenchymal stem cell (MSC)-like multipotent progenitor cells and can undergo self-renewal and differentiate into to multiple lineages, including bone, cartilage and adipose. Primary MEFs have limited life span in culture, which thus hampers MEFs’ basic research and translational applications. To overcome this challenge, we investigate if piggyBac transposon-mediated expression of SV40 T antigen can effectively immortalize mouse MEFs and that the immortalized MEFs can maintain long-term cell proliferation without compromising their multipotency. Using the piggyBac vector MPH86 which expresses SV40 T antigen flanked with flippase (FLP) recognition target (FRT) sites, we demonstrate that mouse embryonic fibroblasts (MEFs) can be efficiently immortalized. The immortalized MEFs (piMEFs) exhibit an enhanced proliferative activity and maintain long-term cell proliferation, which can be reversed by FLP recombinase. The piMEFs express most MEF markers and retain multipotency as they can differentiate into osteogenic, chondrogenic and adipogenic lineages upon BMP9 stimulation in vitro. Stem cell implantation studies indicate that piMEFs can form bone, cartilage and adipose tissues upon BMP9 stimulation, whereas FLP-mediated removal of SV40 T antigen diminishes the ability of piMEFs to differentiate into these lineages, possibly due to the reduced expansion of progenitor populations. Our results demonstrate that piggyBac transposon-mediated expression of SV40 T can effectively immortalize MEFs and that the reversibly immortalized piMEFs not only maintain long-term cell proliferation but also retain their multipotency. Thus, the high transposition efficiency and the potential footprint-free natures may render piggyBac transposition an effective and safe strategy to immortalize progenitor cells isolated from limited tissue supplies, which is essential for basic and translational studies.
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Affiliation(s)
- Ning Wang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Wenwen Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
- Department of Laboratory Medicine, the Affiliated Hospital, Binzhou Medical University, Yantai, Shandong, China
| | - Jing Cui
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Hongmei Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Xiang Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Ruidong Li
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Ningning Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Xian Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Sheng Wen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Junhui Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Liangjun Yin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Fang Deng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Department of Cell Biology, Third Military Medical University, Chongqing, China
| | - Zhan Liao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Department of Orthopaedic Surgery, Xiang-Ya Hospital of Central South University, Changsha, China
| | - Zhonglin Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Department of Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qian Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Zhengjian Yan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Wei Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Jixing Ye
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- School of Bioengineering, Chongqing University, Chongqing, China
| | - Youlin Deng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Zhongliang Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Min Qiao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Lewis L. Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Houjie Liang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
- * E-mail: (HL); (TCH)
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
- * E-mail: (HL); (TCH)
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30
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Wen S, Zhang H, Li Y, Wang N, Zhang W, Yang K, Wu N, Chen X, Deng F, Liao Z, Zhang J, Zhang Q, Yan Z, Liu W, Zhang Z, Ye J, Deng Y, Zhou G, Luu HH, Haydon RC, Shi LL, He TC, Wei G. Characterization of constitutive promoters for piggyBac transposon-mediated stable transgene expression in mesenchymal stem cells (MSCs). PLoS One 2014; 9:e94397. [PMID: 24714676 PMCID: PMC3979777 DOI: 10.1371/journal.pone.0094397] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 03/15/2014] [Indexed: 01/23/2023] Open
Abstract
Multipotent mesenchymal stem cells (MSCs) can undergo self-renewal and give rise to multi-lineages under given differentiation cues. It is frequently desirable to achieve a stable and high level of transgene expression in MSCs in order to elucidate possible molecular mechanisms through which MSC self-renewal and lineage commitment are regulated. Retroviral or lentiviral vector-mediated gene expression in MSCs usually decreases over time. Here, we choose to use the piggyBac transposon system and conduct a systematic comparison of six commonly-used constitutive promoters for their abilities to drive RFP or firefly luciferase expression in somatic HEK-293 cells and MSC iMEF cells. The analyzed promoters include three viral promoters (CMV, CMV-IVS, and SV40), one housekeeping gene promoter (UbC), and two composite promoters of viral and housekeeping gene promoters (hEFH and CAG-hEFH). CMV-derived promoters are shown to drive the highest transgene expression in HEK-293 cells, which is however significantly reduced in MSCs. Conversely, the composite promoter hEFH exhibits the highest transgene expression in MSCs whereas its promoter activity is modest in HEK-293 cells. The reduced transgene expression driven by CMV promoters in MSCs may be at least in part caused by DNA methylation, or to a lesser extent histone deacetlyation. However, the hEFH promoter is not significantly affected by these epigenetic modifications. Taken together, our results demonstrate that the hEFH composite promoter may be an ideal promoter to drive long-term and high level transgene expression using the piggyBac transposon vector in progenitor cells such as MSCs.
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Affiliation(s)
- Sheng Wen
- Stem Cell Biology and Therapy Laboratory of Ministry of Education Key Laboratory for Pediatrics, Chongqing Stem Cell Therapy and Engineering Center, and Department of Urology, The Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Hongmei Zhang
- Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, and the Affiliated Hospital of Stomatology, Chongqing Medical University, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Yasha Li
- Stem Cell Biology and Therapy Laboratory of Ministry of Education Key Laboratory for Pediatrics, Chongqing Stem Cell Therapy and Engineering Center, and Department of Urology, The Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ning Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Departments of Cell Biology and Oncology of the Affiliated Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - Wenwen Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals, Chongqing Medical University, Chongqing, China
| | - Ke Yang
- Stem Cell Biology and Therapy Laboratory of Ministry of Education Key Laboratory for Pediatrics, Chongqing Stem Cell Therapy and Engineering Center, and Department of Urology, The Children's Hospital of Chongqing Medical University, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Ningning Wu
- Stem Cell Biology and Therapy Laboratory of Ministry of Education Key Laboratory for Pediatrics, Chongqing Stem Cell Therapy and Engineering Center, and Department of Urology, The Children's Hospital of Chongqing Medical University, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals, Chongqing Medical University, Chongqing, China
| | - Xian Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals, Chongqing Medical University, Chongqing, China
| | - Fang Deng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Departments of Cell Biology and Oncology of the Affiliated Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - Zhan Liao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Department of Orthopaedic Surgery, the Affiliated Xiang-Ya Hospital of Central South University, Changsha, China
| | - Junhui Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals, Chongqing Medical University, Chongqing, China
| | - Qian Zhang
- Stem Cell Biology and Therapy Laboratory of Ministry of Education Key Laboratory for Pediatrics, Chongqing Stem Cell Therapy and Engineering Center, and Department of Urology, The Children's Hospital of Chongqing Medical University, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Zhengjian Yan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals, Chongqing Medical University, Chongqing, China
| | - Wei Liu
- Stem Cell Biology and Therapy Laboratory of Ministry of Education Key Laboratory for Pediatrics, Chongqing Stem Cell Therapy and Engineering Center, and Department of Urology, The Children's Hospital of Chongqing Medical University, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Zhonglin Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Department of Surgery, the Affiliated Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jixing Ye
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- School of Bioengineering, Chongqing University, Chongqing, China
| | - Youlin Deng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals, Chongqing Medical University, Chongqing, China
| | - Guolin Zhou
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Lewis L. Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, Illinois, United States of America
| | - Tong-Chuan He
- Stem Cell Biology and Therapy Laboratory of Ministry of Education Key Laboratory for Pediatrics, Chongqing Stem Cell Therapy and Engineering Center, and Department of Urology, The Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals, Chongqing Medical University, Chongqing, China
- * E-mail: (TCH); (GW)
| | - Guanghui Wei
- Stem Cell Biology and Therapy Laboratory of Ministry of Education Key Laboratory for Pediatrics, Chongqing Stem Cell Therapy and Engineering Center, and Department of Urology, The Children's Hospital of Chongqing Medical University, Chongqing, China
- * E-mail: (TCH); (GW)
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Mossine VV, Waters JK, Hannink M, Mawhinney TP. piggyBac transposon plus insulators overcome epigenetic silencing to provide for stable signaling pathway reporter cell lines. PLoS One 2013; 8:e85494. [PMID: 24376882 PMCID: PMC3869926 DOI: 10.1371/journal.pone.0085494] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 12/04/2013] [Indexed: 12/28/2022] Open
Abstract
Genetically modified hematopoietic progenitors represent an important testing platform for a variety of cell-based therapies, pharmaceuticals, diagnostics and other applications. Stable expression of a transfected gene of interest in the cells is often obstructed by its silencing. DNA transposons offer an attractive non-viral alternative of transgene integration into the host genome, but their broad applicability to leukocytes and other "transgene unfriendly" cells has not been fully demonstrated. Here we assess stability of piggyBac transposon-based reporter expression in murine prostate adenocarcinoma TRAMP-C2, human monocyte THP-1 and erythroleukemia K562 cell lines, along with macrophages and dendritic cells (DCs) that have differentiated from the THP-1 transfects. The most efficient and stable reporter activity was observed for combinations of the transposon inverted terminal repeats and one 5'- or two cHS4 core insulators flanking a green fluorescent protein reporter construct, with no detectable silencing over 10 months of continuous cell culture in absence of any selective pressure. In monocytic THP-1 cells, the functional activity of luciferase reporters for NF-κB, Nrf2, or HIF-1α has not decreased over time and was retained following differentiation into macrophages and DCs, as well. These results imply pB as a versatile tool for gene integration in monocytic cells in general, and as a convenient access route to DC-based signaling pathway reporters suitable for high-throughput assays, in particular.
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Affiliation(s)
- Valeri V. Mossine
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
- Experiment Station Chemical Labs, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
| | - James K. Waters
- Experiment Station Chemical Labs, University of Missouri, Columbia, Missouri, United States of America
| | - Mark Hannink
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Thomas P. Mawhinney
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
- Experiment Station Chemical Labs, University of Missouri, Columbia, Missouri, United States of America
- Department of Child Health, University of Missouri, Columbia, Missouri, United States of America
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32
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Skipper KA, Andersen PR, Sharma N, Mikkelsen JG. DNA transposon-based gene vehicles - scenes from an evolutionary drive. J Biomed Sci 2013; 20:92. [PMID: 24320156 PMCID: PMC3878927 DOI: 10.1186/1423-0127-20-92] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/27/2013] [Indexed: 12/12/2022] Open
Abstract
DNA transposons are primitive genetic elements which have colonized living organisms from plants to bacteria and mammals. Through evolution such parasitic elements have shaped their host genomes by replicating and relocating between chromosomal loci in processes catalyzed by the transposase proteins encoded by the elements themselves. DNA transposable elements are constantly adapting to life in the genome, and self-suppressive regulation as well as defensive host mechanisms may assist in buffering ‘cut-and-paste’ DNA mobilization until accumulating mutations will eventually restrict events of transposition. With the reconstructed Sleeping Beauty DNA transposon as a powerful engine, a growing list of transposable elements with activity in human cells have moved into biomedical experimentation and preclinical therapy as versatile vehicles for delivery and genomic insertion of transgenes. In this review, we aim to link the mechanisms that drive transposon evolution with the realities and potential challenges we are facing when adapting DNA transposons for gene transfer. We argue that DNA transposon-derived vectors may carry inherent, and potentially limiting, traits of their mother elements. By understanding in detail the evolutionary journey of transposons, from host colonization to element multiplication and inactivation, we may better exploit the potential of distinct transposable elements. Hence, parallel efforts to investigate and develop distinct, but potent, transposon-based vector systems will benefit the broad applications of gene transfer. Insight and clever optimization have shaped new DNA transposon vectors, which recently debuted in the first DNA transposon-based clinical trial. Learning from an evolutionary drive may help us create gene vehicles that are safer, more efficient, and less prone for suppression and inactivation.
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Affiliation(s)
| | | | | | - Jacob Giehm Mikkelsen
- Department of Biomedicine, Aarhus University, Wilh, Meyers Allé 4, DK-8000, Aarhus C, Denmark.
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Bire S, Ley D, Casteret S, Mermod N, Bigot Y, Rouleux-Bonnin F. Optimization of the piggyBac transposon using mRNA and insulators: toward a more reliable gene delivery system. PLoS One 2013; 8:e82559. [PMID: 24312663 PMCID: PMC3849487 DOI: 10.1371/journal.pone.0082559] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/23/2013] [Indexed: 12/23/2022] Open
Abstract
Integrating and expressing stably a transgene into the cellular genome remain major challenges for gene-based therapies and for bioproduction purposes. While transposon vectors mediate efficient transgene integration, expression may be limited by epigenetic silencing, and persistent transposase expression may mediate multiple transposition cycles. Here, we evaluated the delivery of the piggyBac transposase messenger RNA combined with genetically insulated transposons to isolate the transgene from neighboring regulatory elements and stabilize expression. A comparison of piggyBac transposase expression from messenger RNA and DNA vectors was carried out in terms of expression levels, transposition efficiency, transgene expression and genotoxic effects, in order to calibrate and secure the transposition-based delivery system. Messenger RNA reduced the persistence of the transposase to a narrow window, thus decreasing side effects such as superfluous genomic DNA cleavage. Both the CTF/NF1 and the D4Z4 insulators were found to mediate more efficient expression from a few transposition events. We conclude that the use of engineered piggyBac transposase mRNA and insulated transposons offer promising ways of improving the quality of the integration process and sustaining the expression of transposon vectors.
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Affiliation(s)
- Solenne Bire
- GICC, UMR CNRS 7292, Université François Rabelais, Tours, France
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
- PRC, UMR INRA-CNRS 7247, Centre INRA Val de Loire, Nouzilly, France
| | - Déborah Ley
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | - Sophie Casteret
- PRC, UMR INRA-CNRS 7247, Centre INRA Val de Loire, Nouzilly, France
| | - Nicolas Mermod
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | - Yves Bigot
- PRC, UMR INRA-CNRS 7247, Centre INRA Val de Loire, Nouzilly, France
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Pyykkö I, Zou J, Zhang Y, Zhang W, Feng H, Kinnunen P. Nanoparticle based inner ear therapy. World J Otorhinolaryngol 2013; 3:114-133. [DOI: 10.5319/wjo.v3.i4.114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 08/22/2013] [Accepted: 10/18/2013] [Indexed: 02/06/2023] Open
Abstract
Synthetic nanoparticles can be used to carry drugs, genes, small interfering RNA (siRNA) and growth factors into the inner ear, to repair, restore and induce cellular regeneration. Nanoparticles (NPs) have been developed which are targetable to selected tissue, traceable in vivo, and equipped with controlled drug/gene release. The NPs are coated with a ‘stealth’ layer, and decorated with targeting ligands, markers, transfection agents and endosomal escape peptides. As payloads, genes such as the BDNF-gene, Math1-gene and Prestin-gene have been constructed and delivered in vitro. Short-hairpin RNA has been used in vitro to silence the negative regulator of Math1, the inhibitors of differentiation and DNA binding. In order to facilitate the passage of cargo from the middle ear to the inner ear, the oval window transports gadolinium chelate more efficiently than the round window and is the key element in introducing therapeutic agents into the vestibule and cochlea. Depending upon the type of NPs, different migration and cellular internalization pathways are employed, and optimal carriers should be designed depending on the cargo. The use of NPs as drug/gene/siRNA carriers is fascinating and can also be used as an intraoperative adjunct to cochlear implantation to attract the peripheral processes of the cochlear nerve.
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35
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Cai Y, Bak RO, Krogh LB, Staunstrup NH, Moldt B, Corydon TJ, Schrøder LD, Mikkelsen JG. DNA transposition by protein transduction of the piggyBac transposase from lentiviral Gag precursors. Nucleic Acids Res 2013; 42:e28. [PMID: 24270790 PMCID: PMC3936723 DOI: 10.1093/nar/gkt1163] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
DNA transposon-based vectors have emerged as gene vehicles with a wide biomedical and therapeutic potential. So far, genomic insertion of such vectors has relied on the co-delivery of genetic material encoding the gene-inserting transposase protein, raising concerns related to persistent expression, insertional mutagenesis and cytotoxicity. This report describes potent DNA transposition achieved by direct delivery of transposase protein. By adapting integrase-deficient lentiviral particles (LPs) as carriers of the hyperactive piggyBac transposase protein (hyPBase), we demonstrate rates of DNA transposition that are comparable with the efficiency of a conventional plasmid-based strategy. Embedded in the Gag polypeptide, hyPBase is robustly incorporated into LPs and liberated from the viral proteins by the viral protease during particle maturation. We demonstrate lentiviral co-delivery of the transposase protein and vector RNA carrying the transposon sequence, allowing robust DNA transposition in a variety of cell types. Importantly, this novel delivery method facilitates a balanced cellular uptake of hyPBase, as shown by confocal microscopy, and allows high-efficiency production of clones harboring a single transposon insertion. Our findings establish engineered LPs as a new tool for transposase delivery. We believe that protein transduction methods will increase applicability and safety of DNA transposon-based vector technologies.
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Affiliation(s)
- Yujia Cai
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark and Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
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Owens JB, Mauro D, Stoytchev I, Bhakta MS, Kim MS, Segal DJ, Moisyadi S. Transcription activator like effector (TALE)-directed piggyBac transposition in human cells. Nucleic Acids Res 2013; 41:9197-207. [PMID: 23921635 PMCID: PMC3799441 DOI: 10.1093/nar/gkt677] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 12/13/2022] Open
Abstract
Insertional therapies have shown great potential for combating genetic disease and safer methods would undoubtedly broaden the variety of possible illness that can be treated. A major challenge that remains is reducing the risk of insertional mutagenesis due to random insertion by both viral and non-viral vectors. Targetable nucleases are capable of inducing double-stranded breaks to enhance homologous recombination for the introduction of transgenes at specific sequences. However, off-target DNA cleavages at unknown sites can lead to mutations that are difficult to detect. Alternatively, the piggyBac transposase is able perform all of the steps required for integration; therefore, cells confirmed to contain a single copy of a targeted transposon, for which its location is known, are likely to be devoid of aberrant genomic modifications. We aimed to retarget transposon insertions by comparing a series of novel hyperactive piggyBac constructs tethered to a custom transcription activator like effector DNA-binding domain designed to bind the first intron of the human CCR5 gene. Multiple targeting strategies were evaluated using combinations of both plasmid-DNA and transposase-protein relocalization to the target sequence. We demonstrated user-defined directed transposition to the CCR5 genomic safe harbor and isolated single-copy clones harboring targeted integrations.
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Affiliation(s)
- Jesse B. Owens
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Damiano Mauro
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Ilko Stoytchev
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Mital S. Bhakta
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Moon-Soo Kim
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - David J. Segal
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
| | - Stefan Moisyadi
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA, Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA and Manoa BioSciences, Honolulu, HI 96819, USA
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37
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Torella JP, Boehm CR, Lienert F, Chen JH, Way JC, Silver PA. Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic Acids Res 2013; 42:681-9. [PMID: 24078086 PMCID: PMC3874176 DOI: 10.1093/nar/gkt860] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminator parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.
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Affiliation(s)
- Joseph P Torella
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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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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Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon. Proc Natl Acad Sci U S A 2012; 110:234-9. [PMID: 23248290 DOI: 10.1073/pnas.1217548110] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A revelation of the genomic age has been the contributions of the mobile DNA segments called transposable elements to chromosome structure, function, and evolution in virtually all organisms. Substantial fractions of vertebrate genomes derive from transposable elements, being dominated by retroelements that move via RNA intermediates. Although many of these elements have been inactivated by mutation, several active retroelements remain. Vertebrate genomes also contain substantial quantities and a high diversity of cut-and-paste DNA transposons, but no active representative of this class has been identified in mammals. Here we show that a cut-and-paste element called piggyBat, which has recently invaded the genome of the little brown bat (Myotis lucifugus) and is a member of the piggyBac superfamily, is active in its native form in transposition assays in bat and human cultured cells, as well as in the yeast Saccharomyces cerevisiae. Our study suggests that some DNA transposons are still actively shaping some mammalian genomes and reveals an unprecedented opportunity to study the mechanism, regulation, and genomic impact of cut-and-paste transposition in a natural mammalian host.
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