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Ranjan V, Leighton G, Yan C, Arango M, Lustig J, Corona R, Guo JT, Nesmelov Y, Ivics Z, Nesmelova I. DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain. Nucleic Acids Res 2025; 53:gkae1188. [PMID: 39657726 PMCID: PMC11754664 DOI: 10.1093/nar/gkae1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/08/2024] [Accepted: 11/14/2024] [Indexed: 12/12/2024] Open
Abstract
DNA transposons have emerged as promising tools in both gene therapy and functional genomics. In particular, the Sleeping Beauty (SB) DNA transposon has advanced into clinical trials due to its ability to stably integrate DNA sequences of choice into eukaryotic genomes. The efficiency of the DNA transposon system depends on the interaction between the transposon DNA and the transposase enzyme that facilitates gene transfer. In this study, we assess the DNA-binding capabilities of variants of the SB transposase and demonstrate that the structural stability of the primary DNA-recognition subdomain, PAI, affects SB DNA-binding affinity and transposition activity. This fundamental understanding of the structure-function relationship of the SB transposase will assist the design of improved transposases for gene therapy applications.
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Affiliation(s)
- Venkatesh V Ranjan
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
- Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Gage O Leighton
- Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC 27599, USA
| | - Chenbo Yan
- Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Maria Arango
- Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Janna Lustig
- Division of Hematology, Gene and Cell Therapy, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany
| | - Rosario I Corona
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Jun-Tao Guo
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Yuri E Nesmelov
- Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Zoltán Ivics
- Division of Hematology, Gene and Cell Therapy, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany
| | - Irina V Nesmelova
- Department of Physics and Optical Science, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
- School of Data Science, University of North Carolina at Charlotte, Charlotte, 9201 University City Blvd., NC 28223, USA
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2
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Ochmann MT, Miskey C, Botezatu L, Sandoval-Villegas N, Diem T, Ivics Z. A novel hyperactive variant of the Sleeping Beauty transposase facilitates non-viral genome engineering. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102381. [PMID: 39654540 PMCID: PMC11626015 DOI: 10.1016/j.omtn.2024.102381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 10/31/2024] [Indexed: 12/12/2024]
Abstract
The Sleeping Beauty (SB) transposon system is a useful tool for genetic applications, including gene therapy. We discovered a hyperactive variant of the SB100X transposase, called SB200X. This mutant, resulting from a specific amino acid replacement (Q124C), showed an ∼2-fold increase in transposition activity in various human and murine cells. Other amino acid replacements in position 124 also led to a hyperactive phenotype. Position 124 is located at the very edge of the linker region that connects the DNA-binding and catalytic domains of the transposase. Consistent with a role of the linker in an autoregulatory mechanism called overproduction inhibition (OPI) in the monophyletic group of mariner transposases, we show that the hyperactivity of Q124C manifests at high concentrations of the transposase, suggesting a partial resistance of SB200X to OPI. We demonstrate that the hyperactive phenotype of Q124C can be combined with features of other useful mutations in the SB transposase. Namely, Q124C improves the transposition efficiency of the previously described K248R variant, while maintaining or even slightly improving its safer genome-wide integration profile. The SB200X transposase could enhance the utility of SB transposon-mediated genome engineering in preclinical and clinical applications.
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Affiliation(s)
- Matthias Thomas Ochmann
- Research Center, Division of Hematology, Cell and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Csaba Miskey
- Research Center, Division of Hematology, Cell and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Lacramioara Botezatu
- Research Center, Division of Hematology, Cell and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Nicolás Sandoval-Villegas
- Research Center, Division of Hematology, Cell and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Tanja Diem
- Research Center, Division of Hematology, Cell and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Zoltán Ivics
- Research Center, Division of Hematology, Cell and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
- Institute of Clinical Immunology, University of Leipzig, 04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany
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3
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Zhang T, Tan S, Tang N, Li Y, Zhang C, Sun J, Guo Y, Gao H, Cai Y, Sun W, Wang C, Fu L, Ma H, Wu Y, Hu X, Zhang X, Gee P, Yan W, Zhao Y, Chen Q, Guo B, Wang H, Zhang YE. Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox. Cell 2024; 187:3741-3760.e30. [PMID: 38843831 DOI: 10.1016/j.cell.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 03/11/2024] [Accepted: 05/02/2024] [Indexed: 07/14/2024]
Abstract
Experimental studies on DNA transposable elements (TEs) have been limited in scale, leading to a lack of understanding of the factors influencing transposition activity, evolutionary dynamics, and application potential as genome engineering tools. We predicted 130 active DNA TEs from 102 metazoan genomes and evaluated their activity in human cells. We identified 40 active (integration-competent) TEs, surpassing the cumulative number (20) of TEs found previously. With this unified comparative data, we found that the Tc1/mariner superfamily exhibits elevated activity, potentially explaining their pervasive horizontal transfers. Further functional characterization of TEs revealed additional divergence in features such as insertion bias. Remarkably, in CAR-T therapy for hematological and solid tumors, Mariner2_AG (MAG), the most active DNA TE identified, largely outperformed two widely used vectors, the lentiviral vector and the TE-based vector SB100X. Overall, this study highlights the varied transposition features and evolutionary dynamics of DNA TEs and increases the TE toolbox diversity.
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Affiliation(s)
- Tongtong Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Tang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yuanqing Li
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenze Zhang
- National Key Laboratory of Efficacy and Mechanism on Chinese Medicine for Metabolic Diseases, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jing Sun
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyan Guo
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Gao
- Rengene Biotechnology Co., Ltd., Beijing 100036, China
| | - Yujia Cai
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Sun
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chenxin Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Liangzheng Fu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yachao Wu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoxuan Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuechun Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Peter Gee
- MaxCyte Inc., Rockville, MD 20850, USA
| | - Weihua Yan
- Cold Spring Biotech Corp., Beijing 100031, China
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Baocheng Guo
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Haoyi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Shao W, Yao Y, Yang L, Li X, Ge T, Zheng Y, Zhu Q, Ge S, Gu X, Jia R, Song X, Zhuang A. Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy. Exp Hematol Oncol 2024; 13:37. [PMID: 38570883 PMCID: PMC10988985 DOI: 10.1186/s40164-024-00504-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Adoptive immunotherapy in the T cell landscape exhibits efficacy in cancer treatment. Over the past few decades, genetically modified T cells, particularly chimeric antigen receptor T cells, have enabled remarkable strides in the treatment of hematological malignancies. Besides, extensive exploration of multiple antigens for the treatment of solid tumors has led to clinical interest in the potential of T cells expressing the engineered T cell receptor (TCR). TCR-T cells possess the capacity to recognize intracellular antigen families and maintain the intrinsic properties of TCRs in terms of affinity to target epitopes and signal transduction. Recent research has provided critical insight into their capability and therapeutic targets for multiple refractory solid tumors, but also exposes some challenges for durable efficacy. In this review, we describe the screening and identification of available tumor antigens, and the acquisition and optimization of TCRs for TCR-T cell therapy. Furthermore, we summarize the complete flow from laboratory to clinical applications of TCR-T cells. Last, we emerge future prospects for improving therapeutic efficacy in cancer world with combination therapies or TCR-T derived products. In conclusion, this review depicts our current understanding of TCR-T cell therapy in solid neoplasms, and provides new perspectives for expanding its clinical applications and improving therapeutic efficacy.
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Affiliation(s)
- Weihuan Shao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiaoran Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Tongxin Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yue Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Qiuyi Zhu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Xin Song
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
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Vela J, Mora P, Montiel EE, Rico-Porras JM, Sanllorente O, Amoasii D, Lorite P, Palomeque T. Exploring horizontal transfer of mariner transposable elements among ants and aphids. Gene 2024; 899:148144. [PMID: 38195050 DOI: 10.1016/j.gene.2024.148144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Aphids and ants are mutualistic species with a close space-time relationship, which may facilitate the occurrence of horizontal transfer events between these insect groups. Myrmar-like mariner elements were previously isolated from two ant (Myrmica ruginodis and Tapinoma ibericum) and two aphid species (Aphis fabae and Aphis hederae). The aim of this work is to determine the presence of Myrmar-like mariner elements in new ant and aphid species, as well as to analyze the likelihood of horizontal transfer events between these taxa. To accomplish this, the Myrmar-like element has been isolated from five aphid species and six ant species. Among these new analyzed species, full-length Myrmar-like mariner elements with very high sequence similarity have been isolated from the aphids Aphis nerii, Aphis spiraecola, Brachycaudus cardui, and Rhopalosiphum maidis as well as from the ants Lasius grandis and Lasius niger, even though aphids and ants belong to two insect orders (Hemiptera and Hymenoptera) that have evolved independently for at least 300 million-years. Both Lasius species establish frequent mutualistic relationships with multiple aphid species, including A. nerii, A. spiraecola, and B. cardui. The study of the putative protein encoded by them and the phylogenetic analysis suggests that they could be active transposons shared by aphids and ants through horizontal transfer events. Additionally, mariner elements with internal deletion were found in several aphids and one ant species, showing a high degree of sequence similarity among them. The characteristics of these elements with internal deletion suggest a complex origin involving various evolutionary processes, possibly including also horizontal transfer events. Myrmar-like elements have also been isolated from the other ant species, although without similarity with the aphid mariner sequences. Myrmar-like elements are also present in phylogenetically distant insect species, as well as in one crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the probable occurrence of horizontal transfer events.
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Affiliation(s)
- Jesús Vela
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Eugenia E Montiel
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - José M Rico-Porras
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Olivia Sanllorente
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Daniela Amoasii
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
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Kovač A, Miskey C, Ivics Z. Sleeping Beauty Transposon Insertions into Nucleolar DNA by an Engineered Transposase Localized in the Nucleolus. Int J Mol Sci 2023; 24:14978. [PMID: 37834425 PMCID: PMC10573994 DOI: 10.3390/ijms241914978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Transposons are nature's gene delivery vehicles that can be harnessed for experimental and therapeutic purposes. The Sleeping Beauty (SB) transposon shows efficient transposition and long-term transgene expression in human cells, and is currently under clinical development for gene therapy. SB transposition occurs into the human genome in a random manner, which carries a risk of potential genotoxic effects associated with transposon integration. Here, we evaluated an experimental strategy to manipulate SB's target site distribution by preferentially compartmentalizing the SB transposase to the nucleolus, which contains repetitive ribosomal RNA (rRNA) genes. We generated a fusion protein composed of the nucleolar protein nucleophosmin (B23) and the SB100X transposase, which was found to retain almost full transposition activity as compared to unfused transposase and to be predominantly localized to nucleoli in transfected human cells. Analysis of transposon integration sites generated by B23-SB100X revealed a significant enrichment into the p-arms of chromosomes containing nucleolus organizing regions (NORs), with preferential integration into the p13 and p11.2 cytobands directly neighboring the NORs. This bias in the integration pattern was accompanied by an enrichment of insertions into nucleolus-associated chromatin domains (NADs) at the periphery of nucleolar DNA and into lamina-associated domains (LADs). Finally, sub-nuclear targeting of the transposase resulted in preferential integration into chromosomal domains associated with the Upstream Binding Transcription Factor (UBTF) that plays a critical role in the transcription of 47S rDNA gene repeats of the NORs by RNA Pol I. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.
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Affiliation(s)
| | | | - Zoltán Ivics
- Transposition and Genome Engineering, Research Centre of the Division of Hematology, Gene and Cell Therapy, Paul Ehrlich Institute, Paul Ehrlich Str. 51–59, D-63225 Langen, Germany; (A.K.); (C.M.)
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7
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Harmening N, Johnen S, Izsvák Z, Ivics Z, Kropp M, Bascuas T, Walter P, Kreis A, Pajic B, Thumann G. Enhanced Biosafety of the Sleeping Beauty Transposon System by Using mRNA as Source of Transposase to Efficiently and Stably Transfect Retinal Pigment Epithelial Cells. Biomolecules 2023; 13:biom13040658. [PMID: 37189405 DOI: 10.3390/biom13040658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
Neovascular age-related macular degeneration (nvAMD) is characterized by choroidal neovascularization (CNV), which leads to retinal pigment epithelial (RPE) cell and photoreceptor degeneration and blindness if untreated. Since blood vessel growth is mediated by endothelial cell growth factors, including vascular endothelial growth factor (VEGF), treatment consists of repeated, often monthly, intravitreal injections of anti-angiogenic biopharmaceuticals. Frequent injections are costly and present logistic difficulties; therefore, our laboratories are developing a cell-based gene therapy based on autologous RPE cells transfected ex vivo with the pigment epithelium derived factor (PEDF), which is the most potent natural antagonist of VEGF. Gene delivery and long-term expression of the transgene are enabled by the use of the non-viral Sleeping Beauty (SB100X) transposon system that is introduced into the cells by electroporation. The transposase may have a cytotoxic effect and a low risk of remobilization of the transposon if supplied in the form of DNA. Here, we investigated the use of the SB100X transposase delivered as mRNA and showed that ARPE-19 cells as well as primary human RPE cells were successfully transfected with the Venus or the PEDF gene, followed by stable transgene expression. In human RPE cells, secretion of recombinant PEDF could be detected in cell culture up to one year. Non-viral ex vivo transfection using SB100X-mRNA in combination with electroporation increases the biosafety of our gene therapeutic approach to treat nvAMD while ensuring high transfection efficiency and long-term transgene expression in RPE cells.
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Affiliation(s)
- Nina Harmening
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Zoltan Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Martina Kropp
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Thais Bascuas
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Peter Walter
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Andreas Kreis
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Bojan Pajic
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
- Eye Clinic ORASIS, Swiss Eye Research Foundation, 5734 Reinach, Switzerland
- Faculty of Sciences, Department of Physics, University of Novi Sad, Trg Dositeja Obradovica 4, 21000 Novi Sad, Serbia
- Faculty of Medicine of the Military Medical Academy, University of Defense, 11000 Belgrade, Serbia
| | - Gabriele Thumann
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
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8
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Pszenny V, Tjhin E, Alves‐Ferreira EV, Spada S, Bouamr F, Nair V, Ganesan S, Grigg ME. Using the Sleeping Beauty (SB) Transposon to Generate Stable Cells Producing Enveloped Virus-Like Particles (eVLPs) Pseudotyped with SARS-CoV-2 Proteins for Vaccination. Curr Protoc 2022; 2:e575. [PMID: 36300895 PMCID: PMC9874545 DOI: 10.1002/cpz1.575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Sleeping Beauty (SB) transposon system is an efficient non-viral tool for gene transfer into a variety of cells, including human cells. Through a cut-and-paste mechanism, your favorite gene (YFG) is integrated into AT-rich regions within the genome, providing stable long-term expression of the transfected gene. The SB system is evolving and has become a powerful tool for gene therapy. There are no safety concerns using this system, the handling is easy, and the time required to obtain a stable cell line is significantly reduced compared to other systems currently available. Here, we present a novel application of this system to generate, within 8 days, a stable producer HEK293T cell line capable of constitutively delivering enveloped virus-like particles (eVLPs) for vaccination. We provide step-by-step protocols for generation of the SB transposon constructs, transfection procedures, and validation of the produced eVLPs. We next describe a method to pseudotype the constitutively produced eVLPs using the Spike protein derived from the SARS-CoV-2 virus (by coating the eVLP capsid with the heterologous antigen). We also describe optimization methods to scale up the production of pseudotyped eVLPs in a laboratory setting (from 100 µg to 5 mg). © Published 2022. This article is a U.S. Government work and is in the public domain in the USA. Basic Protocol 1: Generation of the SB plasmids Basic Protocol 2: Generation of a stable HEK293T cell line constitutively secreting MLV-based eVLPs Basic Protocol 3: Evaluation of the SB constructs by immunofluorescence assay Basic Protocol 4: Validation of eVLPs by denaturing PAGE and western blot Alternate Protocol 1: Analysis of SARS-CoV-2 Spike protein oligomerization using blue native gel electrophoresis and western blot Alternate Protocol 2: Evaluation of eVLP quality by electron microscopy (negative staining) Basic Protocol 5: Small-scale production of eVLPs Alternate Protocol 3: Large-scale production of eVLPs (up to about 1 to 3 mg VLPs) Alternate Protocol 4: Large-scale production of eVLPs (up to about 3 to 5 mg VLPs) Support Protocol: Quantification of total protein concentration by Bradford assay.
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Affiliation(s)
- Viviana Pszenny
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
| | - Erick Tjhin
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
| | - Eliza V.C. Alves‐Ferreira
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
| | - Stephanie Spada
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
| | - Fadila Bouamr
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
| | - Vinod Nair
- Microscopy Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthHamiltonMontana
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
| | - Michael E. Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
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9
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Sántha M. Biologia futura: animal testing in drug development-the past, the present and the future. Biol Futur 2021; 71:443-452. [PMID: 34554463 DOI: 10.1007/s42977-020-00050-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/04/2020] [Indexed: 12/26/2022]
Abstract
Animal experiments have served to improve our knowledge on diseases and treatment approaches since ancient times. Today, animal experiments are widely used in medical, biomedical and veterinary research, and are essential means of drug development and preclinical testing, including toxicology and safety studies. Recently, great efforts have been made to replace animal experiments with in vitro organoid culture methods and in silico predictions, in agreement with the 3R strategy to "reduce, refine and replace" animals in experimental testing, as outlined by the European Commission. Here we present a mini-review on the development of animal testing, as well as on alternative in vitro and in silico methods, that may at least partly replace animal experiments in the near future.
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Affiliation(s)
- Miklós Sántha
- Institute of Biochemistry, ELKH Biological Research Centre, 62. Temesvári Ave, Szeged, 6726, Hungary.
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10
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Sandoval-Villegas N, Nurieva W, Amberger M, Ivics Z. Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications of Sleeping Beauty, piggyBac and Tol2 for Genome Engineering. Int J Mol Sci 2021; 22:ijms22105084. [PMID: 34064900 PMCID: PMC8151067 DOI: 10.3390/ijms22105084] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/19/2023] Open
Abstract
Transposons are mobile genetic elements evolved to execute highly efficient integration of their genes into the genomes of their host cells. These natural DNA transfer vehicles have been harnessed as experimental tools for stably introducing a wide variety of foreign DNA sequences, including selectable marker genes, reporters, shRNA expression cassettes, mutagenic gene trap cassettes, and therapeutic gene constructs into the genomes of target cells in a regulated and highly efficient manner. Given that transposon components are typically supplied as naked nucleic acids (DNA and RNA) or recombinant protein, their use is simple, safe, and economically competitive. Thus, transposons enable several avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture comprising the generation of pluripotent stem cells, the production of germline-transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species and therapy of genetic disorders in humans. This review describes the molecular mechanisms involved in transposition reactions of the three most widely used transposon systems currently available (Sleeping Beauty, piggyBac, and Tol2), and discusses the various parameters and considerations pertinent to their experimental use, highlighting the state-of-the-art in transposon technology in diverse genetic applications.
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Affiliation(s)
| | | | | | - Zoltán Ivics
- Correspondence: ; Tel.: +49-6103-77-6000; Fax: +49-6103-77-1280
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11
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Magnani CF, Gaipa G, Lussana F, Belotti D, Gritti G, Napolitano S, Matera G, Cabiati B, Buracchi C, Borleri G, Fazio G, Zaninelli S, Tettamanti S, Cesana S, Colombo V, Quaroni M, Cazzaniga G, Rovelli A, Biagi E, Galimberti S, Calabria A, Benedicenti F, Montini E, Ferrari S, Introna M, Balduzzi A, Valsecchi MG, Dastoli G, Rambaldi A, Biondi A. Sleeping Beauty-engineered CAR T cells achieve antileukemic activity without severe toxicities. J Clin Invest 2020; 130:6021-6033. [PMID: 32780725 PMCID: PMC7598053 DOI: 10.1172/jci138473] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/29/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUNDChimeric antigen receptor (CAR) T cell immunotherapy has resulted in complete remission (CR) and durable response in highly refractory patients. However, logistical complexity and high costs of manufacturing autologous viral products limit CAR T cell availability.METHODSWe report the early results of a phase I/II trial in B cell acute lymphoblastic leukemia (B-ALL) patients relapsed after allogeneic hematopoietic stem cell transplantation (HSCT) using donor-derived CD19 CAR T cells generated with the Sleeping Beauty (SB) transposon and differentiated into cytokine-induced killer (CIK) cells.RESULTSThe cellular product was produced successfully for all patients from the donor peripheral blood (PB) and consisted mostly of CD3+ lymphocytes with 43% CAR expression. Four pediatric and 9 adult patients were infused with a single dose of CAR T cells. Toxicities reported were 2 grade I and 1 grade II cytokine-release syndrome (CRS) cases at the highest dose in the absence of graft-versus-host disease (GVHD), neurotoxicity, or dose-limiting toxicities. Six out of 7 patients receiving the highest doses achieved CR and CR with incomplete blood count recovery (CRi) at day 28. Five out of 6 patients in CR were also minimal residual disease negative (MRD-). Robust expansion was achieved in the majority of the patients. CAR T cells were measurable by transgene copy PCR up to 10 months. Integration site analysis showed a positive safety profile and highly polyclonal repertoire in vitro and at early time points after infusion.CONCLUSIONSB-engineered CAR T cells expand and persist in pediatric and adult B-ALL patients relapsed after HSCT. Antileukemic activity was achieved without severe toxicities.TRIAL REGISTRATIONClinicalTrials.gov NCT03389035.FUNDINGThis study was supported by grants from the Fondazione AIRC per la Ricerca sul Cancro (AIRC); Cancer Research UK (CRUK); the Fundación Científica de la Asociación Española Contra el Cáncer (FC AECC); Ministero Della Salute; Fondazione Regionale per la Ricerca Biomedica (FRRB).
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Affiliation(s)
- Chiara F. Magnani
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Giuseppe Gaipa
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Federico Lussana
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Daniela Belotti
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
- Department of Pediatrics, University of Milano–Bicocca, Milan, Italy
| | - Giuseppe Gritti
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Sara Napolitano
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Giada Matera
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Benedetta Cabiati
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Chiara Buracchi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Gianmaria Borleri
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Grazia Fazio
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | | | - Sarah Tettamanti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Stefania Cesana
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Valentina Colombo
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Michele Quaroni
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Giovanni Cazzaniga
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Attilio Rovelli
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Ettore Biagi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Stefania Galimberti
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre, Department of Medicine and Surgery, University of Milano–Bicocca, Milan, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET)/IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET)/IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET)/IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Ferrari
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Martino Introna
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
- USS Centro di Terapia Cellulare “G. Lanzani,” Bergamo, Italy
| | - Adriana Balduzzi
- Department of Pediatrics, University of Milano–Bicocca, Milan, Italy
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Maria Grazia Valsecchi
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre, Department of Medicine and Surgery, University of Milano–Bicocca, Milan, Italy
| | - Giuseppe Dastoli
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Alessandro Rambaldi
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
- Department of Oncology and Hematology, University of Milan, Milan, Italy
| | - Andrea Biondi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
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12
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Carducci F, Barucca M, Canapa A, Carotti E, Biscotti MA. Mobile Elements in Ray-Finned Fish Genomes. Life (Basel) 2020; 10:E221. [PMID: 32992841 PMCID: PMC7599744 DOI: 10.3390/life10100221] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.
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Affiliation(s)
| | | | | | | | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (F.C.); (M.B.); (A.C.); (E.C.)
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13
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Amberger M, Ivics Z. Latest Advances for the Sleeping Beauty Transposon System: 23 Years of Insomnia but Prettier than Ever: Refinement and Recent Innovations of the Sleeping Beauty Transposon System Enabling Novel, Nonviral Genetic Engineering Applications. Bioessays 2020; 42:e2000136. [PMID: 32939778 DOI: 10.1002/bies.202000136] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/29/2020] [Indexed: 12/13/2022]
Abstract
The Sleeping Beauty transposon system is a nonviral DNA transfer tool capable of efficiently mediating transposition-based, stable integration of DNA sequences of choice into eukaryotic genomes. Continuous refinements of the system, including the emergence of hyperactive transposase mutants and novel approaches in vectorology, greatly improve upon transposition efficiency rivaling viral-vector-based methods for stable gene insertion. Current developments, such as reversible transgenesis and proof-of-concept RNA-guided transposition, further expand on possible applications in the future. In addition, innate advantages such as lack of preferential integration into genes reduce insertional mutagenesis-related safety concerns while comparably low manufacturing costs enable widespread implementation. Accordingly, the system is recognized as a powerful and versatile tool for genetic engineering and is playing a central role in an ever-expanding number of gene and cell therapy clinical trials with the potential to become a key technology to meet the growing demand for advanced therapy medicinal products.
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Affiliation(s)
- Maximilian Amberger
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, D-63225, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, D-63225, Germany
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14
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Moscoso CG, Potz KR, Tan S, Jacobson PA, Berger KM, Steer CJ. Precision medicine, agriculture, and genome editing: science and ethics. Ann N Y Acad Sci 2019; 1465:59-75. [PMID: 31721233 DOI: 10.1111/nyas.14266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/16/2019] [Indexed: 01/20/2023]
Abstract
The era of precision medicine has generated advances in various fields of science and medicine with the potential for a paradigm shift in healthcare delivery that will ultimately lead to an individualized approach to medicine. Such timely topics were explored in 2018 at a workshop held at the Third International Conference on One Medicine One Science (iCOMOS), in Minneapolis, Minnesota. A broad range of scientists and regulatory experts provided detailed insights into the challenges and opportunities associated with precision medicine and gene editing. There was a general consensus that advances in studying the genomic traits driving differential pharmacogenomics will undoubtedly enhance individualized treatments for a wide variety of diseases. Ethical considerations, societal implications, approaches for prioritizing safe and secure use of treatment modalities, and the advent of high-throughput computing and analysis of large, complex datasets were discussed. Large biobanks, such as the All of Us Research Program and the Veterans Affairs Million Veterans Program, can aid studies of various conditions in massive cohorts of patients. As the applications of precision medicine continue to mature, the full potential and promise of these individualized approaches will continue to yield important advances in transplant medicine, oncology, public health, agriculture, pharmacology, and bioinformatics.
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Affiliation(s)
- Carlos G Moscoso
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Kelly R Potz
- College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - Shaoyuan Tan
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | | | - Clifford J Steer
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota.,Department of Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, Minnesota
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15
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Querques I, Mades A, Zuliani C, Miskey C, Alb M, Grueso E, Machwirth M, Rausch T, Einsele H, Ivics Z, Hudecek M, Barabas O. A highly soluble Sleeping Beauty transposase improves control of gene insertion. Nat Biotechnol 2019; 37:1502-1512. [PMID: 31685959 PMCID: PMC6894935 DOI: 10.1038/s41587-019-0291-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/13/2019] [Indexed: 12/21/2022]
Abstract
The Sleeping Beauty (SB) transposon system is an efficient non-viral gene transfer tool in mammalian cells but its broad use has been hampered by uncontrolled transposase gene activity from DNA vectors, posing a risk for genome instability, and by the inability to use transposase protein directly. Here, we used rational protein design based on the crystal structure of the hyperactive SB100X variant to create an SB transposase (hsSB) with enhanced solubility and stability. We demonstrate that hsSB can be delivered with transposon DNA to genetically modify cell lines and embryonic, hematopoietic and induced pluripotent stem cells (iPSCs), overcoming uncontrolled transposase activity. We used hsSB to generate chimeric antigen receptor (CAR) T-cells, which exhibit potent anti-tumor activity in vitro and in xenograft mice. We found that hsSB spontaneously penetrates cells, enabling modification of iPSCs and generation of CAR-T cells without the use of transfection reagents. Titration of hsSB to modulate genomic integration frequency achieved as few as two integrations per genome.
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Affiliation(s)
- Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Mades
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Miriam Alb
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Esther Grueso
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Markus Machwirth
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Tobias Rausch
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Michael Hudecek
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany.
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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16
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Romero MA, Mumford PW, Roberson PA, Osburn SC, Parry HA, Kavazis AN, Gladden LB, Schwartz TS, Baker BA, Toedebusch RG, Childs TE, Booth FW, Roberts MD. Five months of voluntary wheel running downregulates skeletal muscle LINE-1 gene expression in rats. Am J Physiol Cell Physiol 2019; 317:C1313-C1323. [PMID: 31618076 DOI: 10.1152/ajpcell.00301.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transposable elements (TEs) are mobile DNA and constitute approximately half of the human genome. LINE-1 (L1) is the only active autonomous TE in the mammalian genome and has been implicated in a number of diseases as well as aging. We have previously reported that skeletal muscle L1 expression is lower following acute and chronic exercise training in humans. Herein, we used a rodent model of voluntary wheel running to determine whether long-term exercise training affects markers of skeletal muscle L1 regulation. Selectively bred high-running female Wistar rats (n = 11 per group) were either given access to a running wheel (EX) or not (SED) at 5 wk of age, and these conditions were maintained until 27 wk of age. Thereafter, mixed gastrocnemius tissue was harvested and analyzed for L1 mRNA expression and DNA content along with other L1 regulation markers. We observed significantly (P < 0.05) lower L1 mRNA expression, higher L1 DNA methylation, and less L1 DNA in accessible chromatin regions in EX versus SED rats. We followed these experiments with 3-h in vitro drug treatments in L6 myotubes to mimic transient exercise-specific signaling events. The AMP-activated protein kinase (AMPK) agonist 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR; 4 mM) significantly decreased L1 mRNA expression in L6 myotubes. However, this effect was not facilitated through increased L1 DNA methylation. Collectively, these data suggest that long-term voluntary wheel running downregulates skeletal muscle L1 mRNA, and this may occur through chromatin modifications. Enhanced AMPK signaling with repetitive exercise bouts may also decrease L1 mRNA expression, although the mechanism of action remains unknown.
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Affiliation(s)
| | | | | | | | - Hailey A Parry
- School of Kinesiology, Auburn University, Auburn, Alabama
| | | | | | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Brent A Baker
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | - Ryan G Toedebusch
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Thomas E Childs
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Frank W Booth
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama.,Edward Via College of Osteopathic Medicine-Auburn Campus, Auburn, Alabama
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17
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Ramakrishnan M, Zhou MB, Pan CF, Hänninen H, Tang DQ, Vinod KK. Nuclear export signal (NES) of transposases affects the transposition activity of mariner-like elements Ppmar1 and Ppmar2 of moso bamboo. Mob DNA 2019; 10:35. [PMID: 31452694 PMCID: PMC6699137 DOI: 10.1186/s13100-019-0179-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/14/2019] [Indexed: 11/10/2022] Open
Abstract
Ppmar1 and Ppmar2 are two active mariner-like elements (MLEs) cloned from moso bamboo (Phyllostachys edulis (Carrière) J. Houz) genome possessing transposases that harbour nuclear export signal (NES) domain, but not any nuclear localization signal (NLS) domain. To understand the functions of NES in transposon activity, we have conducted two experiments, fluorescence and excision frequency assays in the yeast system. For this, by site-directed mutagenesis, three NES mutants were developed from each of the MLE. In the fluorescence assay, the mutants, NES-1, 2 and 3 along with the wild types (NES-0) were fused with fluorescent proteins, enhanced yellow fluorescent protein (EYFP) and enhanced cyan fluorescent protein (ECFP) were co-transformed into yeast system. To differentiate protein localisation under the NES influence, ECFP alone was fused to wild and mutant NES domains either on N- or C-terminal and not to EYFP. Fluorescence assay revealed that blue fluorescence of ECFP was more intense than the red fluorescence of the EYFP in the yeast cell matrix. Further, ECFP had a wider localisation in the cellular matrix, but EYFP was largely located in the nucleus. The NES-1 domain was related to the comparatively high spread of ECFP, while NES-2 and NES-3 indicated a low spread, implying that NES activity on nuclear export increased when the NES is made leucine-rich, while the signalling activity was reduced when the leucine content was lowered in the NES domain. In the transposon excision assay, the mutant and wild type NES of both the Ppmar elements were integrated into an Ade2 vector, and within the Ade2 gene. Co-transformation of the vector together with non-autonomous Ppmar transposons and NES-lacking transposases was used to assess the differential excision frequencies of the mutants NES domains. In both the MLEs, NES-1 had the highest excision suppression, which was less than half of the excision frequency of the wild type. NES-2 and NES-3 elements showed, up to three times increase in transposon excision than the wild types. The results suggested that NES is an important regulator of nuclear export of transposase in Ppmar elements and the mutation of the NES domains can either increase or decrease the export signalling. We speculate that in moso bamboo, NESs regulates the transposition activity of MLEs to maintain the genome integrity.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 Zhejiang Province People’s Republic of China
| | - Ming-Bing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 Zhejiang Province People’s Republic of China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin’an, Hangzhou, 311300 Zhejiang Province People’s Republic of China
| | - Chun-Fang Pan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 Zhejiang Province People’s Republic of China
| | - Heikki Hänninen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 Zhejiang Province People’s Republic of China
| | - Ding-Qin Tang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 Zhejiang Province People’s Republic of China
| | - Kunnummal Kurungara Vinod
- Division of Genetics, Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai, Tamil Nadu 612101 India
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Palazzo A, Lorusso P, Miskey C, Walisko O, Gerbino A, Marobbio CMT, Ivics Z, Marsano RM. Transcriptionally promiscuous "blurry" promoters in Tc1/ mariner transposons allow transcription in distantly related genomes. Mob DNA 2019; 10:13. [PMID: 30988701 PMCID: PMC6446368 DOI: 10.1186/s13100-019-0155-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/26/2019] [Indexed: 12/04/2022] Open
Abstract
Background We have recently described a peculiar feature of the promoters in two Drosophila Tc1-like elements, Bari1 and Bari3. The AT-richness and the presence of weak core-promoter motifs make these promoters, that we have defined “blurry”, able to activate transcription of a reporter gene in cellular systems as diverse as fly, human, yeast and bacteria. In order to clarify whether the blurry promoter is a specific feature of the Bari transposon family, we have extended this study to promoters isolated from three additional DNA transposon and from two additional LTR retrotransposons. Results Here we show that the blurry promoter is also a feature of two vertebrate transposable elements, Sleeping Beauty and Hsmar1, belonging to the Tc1/mariner superfamily. In contrast, this feature is not shared by the promoter of the hobo transposon, which belongs to the hAT superfamily, nor by LTR retrotransposon-derived promoters, which, in general, do not activate transcription when introduced into non-related genomes. Conclusions Our results suggest that the blurry promoter could be a shared feature of the members of the Tc1/mariner superfamily with possible evolutionary and biotechnological implications. Electronic supplementary material The online version of this article (10.1186/s13100-019-0155-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonio Palazzo
- 1Department of Biology, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy.,Present address: Laboratory of Translational Nanotechnology, "Istituto Tumori Giovanni Paolo II" I.R.C.C.S, Viale Orazio Flacco 65, 70125 Bari, Italy
| | - Patrizio Lorusso
- 1Department of Biology, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy
| | - Csaba Miskey
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Oliver Walisko
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Andrea Gerbino
- 3Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | | | - Zoltán Ivics
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
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19
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Scheuermann B, Diem T, Ivics Z, Andrade-Navarro MA. Evolution-guided evaluation of the inverted terminal repeats of the synthetic transposon Sleeping Beauty. Sci Rep 2019; 9:1171. [PMID: 30718656 PMCID: PMC6362248 DOI: 10.1038/s41598-018-38061-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/18/2018] [Indexed: 11/09/2022] Open
Abstract
Sleeping Beauty (SB) is a synthetic Tc1/mariner transposon that is widely used for genetic engineering in vertebrates, including humans. Its sequence was derived from a consensus of sequences found in fish species including the Atlantic salmon (Salmo salar). One of the functional components of SB, the transposase enzyme, has been subject to extensive mutagenesis yielding hyperactive protein variants for advanced applications. The second functional component, the transposon inverted terminal repeats (ITRs), has so far not been extensively modified, mainly due to a lack of natural sequence information. Importantly, as genome sequences become available, they can provide a rich source of information for a refined molecular definition of the functional components of these transposons. Here we have mined the Salmo salar genome for a comprehensive set of transposon sequences that were used to build a refined consensus sequence. We synthetically produced the new consensus ITR sequences and used them to build a new transposon, the performance of which has been tested in cell-based transposition assays. The consensus sequence did not support enhanced transposition, suggesting alternative mechanisms responsible for the preferential amplification of these sequence variants in the salmon genome.
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Affiliation(s)
- Barbara Scheuermann
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128, Mainz, Germany
| | - Tanja Diem
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany.
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20
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Innovative Disease Model: Zebrafish as an In Vivo Platform for Intestinal Disorder and Tumors. Biomedicines 2017; 5:biomedicines5040058. [PMID: 28961226 PMCID: PMC5744082 DOI: 10.3390/biomedicines5040058] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is one of the world’s most common cancers and is the second leading cause of cancer deaths, causing more than 50,000 estimated deaths each year. Several risk factors are highly associated with CRC, including being overweight, eating a diet high in red meat and over-processed meat, having a history of inflammatory bowel disease, and smoking. Previous zebrafish studies have demonstrated that multiple oncogenes and tumor suppressor genes can be regulated through genetic or epigenetic alterations. Zebrafish research has also revealed that the activation of carcinogenesis-associated signal pathways plays an important role in CRC. The biology of cancer, intestinal disorders caused by carcinogens, and the morphological patterns of tumors have been found to be highly similar between zebrafish and humans. Therefore, the zebrafish has become an important animal model for translational medical research. Several zebrafish models have been developed to elucidate the characteristics of gastrointestinal diseases. This review article focuses on zebrafish models that have been used to study human intestinal disorders and tumors, including models involving mutant and transgenic fish. We also report on xenograft models and chemically-induced enterocolitis. This review demonstrates that excellent zebrafish models can provide novel insights into the pathogenesis of gastrointestinal diseases and help facilitate the evaluation of novel anti-tumor drugs.
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21
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Biondi A, Magnani CF, Tettamanti S, Gaipa G, Biagi E. Redirecting T cells with Chimeric Antigen Receptor (CAR) for the treatment of childhood acute lymphoblastic leukemia. J Autoimmun 2017; 85:141-152. [PMID: 28843422 DOI: 10.1016/j.jaut.2017.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 12/27/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children. Nowadays the survival rate is around 85%. Nevertheless, an urgent clinical need is still represented by primary refractory and relapsed patients who do not significantly benefit from standard approaches, including chemo-radiotherapy and hematopoietic stem cell transplantation (HSCT). For this reason, immunotherapy has so far represented a challenging novel treatment opportunity, including, as the most validated therapeutic options, cancer vaccines, donor-lymphocyte infusions and tumor-specific immune effector cells. More recently, unexpected positive clinical results in ALL have been achieved by application of gene-engineered chimeric antigen expressing (CAR) T cells. Several CAR designs across different trials have generated similar response rates, with Complete Response (CR) of 60-90% at 1 month and an Event-Free Survival (EFS) of 70% at 6 months. Relevant challenges anyway remain to be addressed, such as amelioration of technical, cost and feasibility aspects of cell and gene manipulation and the necessity to face the occurrence of relapse mechanisms. This review describes the state of the art of ALL immunotherapies, the novelties in terms of gene manipulation approaches and the problems emerged from early clinical studies. We describe and discuss the process of clinical translation, including the design of a cell manufacturing protocol, vector production and regulatory issues. Multiple antigen targeting and combination of CAR T cells with molecular targeted drugs have also been evaluated as latest strategies to prevail over immune-evasion.
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Affiliation(s)
- Andrea Biondi
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Fondazione MBBM, Osp. San Gerardo, Monza, Italy.
| | - Chiara F Magnani
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Fondazione MBBM, Osp. San Gerardo, Monza, Italy
| | - Sarah Tettamanti
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Fondazione MBBM, Osp. San Gerardo, Monza, Italy
| | - Giuseppe Gaipa
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Fondazione MBBM, Osp. San Gerardo, Monza, Italy
| | - Ettore Biagi
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Fondazione MBBM, Osp. San Gerardo, Monza, Italy
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22
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Oldham RAA, Medin JA. Practical considerations for chimeric antigen receptor design and delivery. Expert Opin Biol Ther 2017; 17:961-978. [DOI: 10.1080/14712598.2017.1339687] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Robyn A. A. Oldham
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jeffrey A. Medin
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, USA
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Biochemistry, The Medical College of Wisconsin, Milwaukee, USA
- The Institute of Medical Sciences, University of Toronto, Toronto, Canada
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23
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Hudecek M, Izsvák Z, Johnen S, Renner M, Thumann G, Ivics Z. Going non-viral: the Sleeping Beauty transposon system breaks on through to the clinical side. Crit Rev Biochem Mol Biol 2017; 52:355-380. [PMID: 28402189 DOI: 10.1080/10409238.2017.1304354] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular medicine has entered a high-tech age that provides curative treatments of complex genetic diseases through genetically engineered cellular medicinal products. Their clinical implementation requires the ability to stably integrate genetic information through gene transfer vectors in a safe, effective and economically viable manner. The latest generation of Sleeping Beauty (SB) transposon vectors fulfills these requirements, and may overcome limitations associated with viral gene transfer vectors and transient non-viral gene delivery approaches that are prevalent in ongoing pre-clinical and translational research. The SB system enables high-level stable gene transfer and sustained transgene expression in multiple primary human somatic cell types, thereby representing a highly attractive gene transfer strategy for clinical use. Here we review several recent refinements of the system, including the development of optimized transposons and hyperactive SB variants, the vectorization of transposase and transposon as mRNA and DNA minicircles (MCs) to enhance performance and facilitate vector production, as well as a detailed understanding of SB's genomic integration and biosafety features. This review also provides a perspective on the regulatory framework for clinical trials of gene delivery with SB, and illustrates the path to successful clinical implementation by using, as examples, gene therapy for age-related macular degeneration (AMD) and the engineering of chimeric antigen receptor (CAR)-modified T cells in cancer immunotherapy.
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Affiliation(s)
- Michael Hudecek
- a Medizinische Klinik und Poliklinik II , Universitätsklinikum Würzburg , Würzburg , Germany
| | - Zsuzsanna Izsvák
- b Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Sandra Johnen
- c Department of Ophthalmology , University Hospital RWTH Aachen , Aachen , Germany
| | - Matthias Renner
- d Division of Medical Biotechnology , Paul Ehrlich Institute , Langen, Germany
| | - Gabriele Thumann
- e Département des Neurosciences Cliniques Service d'Ophthalmologie , Hôpitaux Universitaires de Genève , Genève , Switzerland
| | - Zoltán Ivics
- d Division of Medical Biotechnology , Paul Ehrlich Institute , Langen, Germany
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24
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Konnova TA, Singer CM, Nesmelova IV. NMR solution structure of the RED subdomain of the Sleeping Beauty transposase. Protein Sci 2017; 26:1171-1181. [PMID: 28345263 DOI: 10.1002/pro.3167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/22/2017] [Indexed: 12/22/2022]
Abstract
DNA transposons can be employed for stable gene transfer in vertebrates. The Sleeping Beauty (SB) DNA transposon has been recently adapted for human application and is being evaluated in clinical trials, however its molecular mechanism is not clear. SB transposition is catalyzed by the transposase enzyme, which is a multi-domain protein containing the catalytic and the DNA-binding domains. The DNA-binding domain of the SB transposase contains two structurally independent subdomains, PAI and RED. Recently, the structures of the catalytic domain and the PAI subdomain have been determined, however no structural information on the RED subdomain and its interactions with DNA has been available. Here, we used NMR spectroscopy to determine the solution structure of the RED subdomain and characterize its interactions with the transposon DNA.
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Affiliation(s)
- Tatiana A Konnova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223
| | - Christopher M Singer
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223
| | - Irina V Nesmelova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223.,Center for Biomedical Engineering and Science, University of North Carolina, Charlotte, North Carolina, 28223
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25
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da Silva KR, Mariotto S, Centofante L, Parise-Maltempi PP. Chromosome mapping of a Tc1-like transposon in species of the catfish Ancistrus. COMPARATIVE CYTOGENETICS 2017; 11:65-79. [PMID: 28919950 PMCID: PMC5599695 DOI: 10.3897/compcytogen.v11i1.10519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/28/2016] [Indexed: 06/07/2023]
Abstract
The Tc1 mariner element is widely distributed among organisms and have been already described in different species of fish. The genus Ancistrus (Kner, 1854) has 68 nominal species and is part of an interesting taxonomic and cytogenetic group, as well as presenting a variation of chromosome number, ranging from 2n=34 to 54 chromosomes, and the existence of simple and multiple sex chromosome system and the occurrence of chromosomal polymorphisms involving chromosomes that carry the nucleolus organizer region. In this study, a repetitive element by restriction enzyme, from Ancistrus sp.1 "Flecha" was isolated, which showed similarity with a transposable element Tc1-mariner. Its chromosomal location is distributed in heterochromatic regions and along the chromosomal arms of all specimens covered in this study, confirming the pattern dispersed of this element found in other studies carried out with other species. Thus, this result reinforces the hypothesis that the sequence AnDraI is really a dispersed element isolated. As this isolated sequence showed the same pattern in all species which have different sex chromosomes systems, including in all sex chromosomes, we could know that it is not involved in sex chromosome differentiation.
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Affiliation(s)
- Keteryne Rodrigues da Silva
- Laboratório de Citogenética Animal – Universidade Estadual Paulista “Júlio de Mesquita Filho” Campus de Rio Claro – Av 24A, 1515 Jardim Bela Vista- 13600-000- Rio Claro/SP, Brasil
| | - Sandra Mariotto
- Instituto Federal de Ciências e Tecnologia do Mato Grosso, campus de Cuiabá – Bela Vista, MT, Brasil
| | - Liano Centofante
- Instituto de Biociências, UFMT Universidade Federal de Mato Grosso, Cuiabá, MT, Brasil
| | - Patricia Pasquali Parise-Maltempi
- Laboratório de Citogenética Animal – Universidade Estadual Paulista “Júlio de Mesquita Filho” Campus de Rio Claro – Av 24A, 1515 Jardim Bela Vista- 13600-000- Rio Claro/SP, Brasil
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26
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Narayanavari SA, Chilkunda SS, Ivics Z, Izsvák Z. Sleeping Beauty transposition: from biology to applications. Crit Rev Biochem Mol Biol 2016; 52:18-44. [PMID: 27696897 DOI: 10.1080/10409238.2016.1237935] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sleeping Beauty (SB) is the first synthetic DNA transposon that was shown to be active in a wide variety of species. Here, we review studies from the last two decades addressing both basic biology and applications of this transposon. We discuss how host-transposon interaction modulates transposition at different steps of the transposition reaction. We also discuss how the transposon was translated for gene delivery and gene discovery purposes. We critically review the system in clinical, pre-clinical and non-clinical settings as a non-viral gene delivery tool in comparison with viral technologies. We also discuss emerging SB-based hybrid vectors aimed at combining the attractive safety features of the transposon with effective viral delivery. The success of the SB-based technology can be fundamentally attributed to being able to insert fairly randomly into genomic regions that allow stable long-term expression of the delivered transgene cassette. SB has emerged as an efficient and economical toolkit for safe and efficient gene delivery for medical applications.
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Affiliation(s)
- Suneel A Narayanavari
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Shreevathsa S Chilkunda
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Zoltán Ivics
- b Division of Medical Biotechnology , Paul Ehrlich Institute , Langen , Germany
| | - Zsuzsanna Izsvák
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
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27
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Abstract
Sleeping Beauty (SB) is a synthetic transposon that was constructed based on sequences of transpositionally inactive elements isolated from fish genomes. SB is a Tc1/mariner superfamily transposon following a cut-and-paste transpositional reaction, during which the element-encoded transposase interacts with its binding sites in the terminal inverted repeats of the transposon, promotes the assembly of a synaptic complex, catalyzes excision of the element out of its donor site, and integrates the excised transposon into a new location in target DNA. SB transposition is dependent on cellular host factors. Transcriptional control of transposase expression is regulated by the HMG2L1 transcription factor. Synaptic complex assembly is promoted by the HMGB1 protein and regulated by chromatin structure. SB transposition is highly dependent on the nonhomologous end joining (NHEJ) pathway of double-strand DNA break repair that generates a transposon footprint at the excision site. Through its association with the Miz-1 transcription factor, the SB transposase downregulates cyclin D1 expression that results in a slowdown of the cell-cycle in the G1 phase, where NHEJ is preferentially active. Transposon integration occurs at TA dinucleotides in the target DNA, which are duplicated at the flanks of the integrated transposon. SB shows a random genome-wide insertion profile in mammalian cells when launched from episomal vectors and "local hopping" when launched from chromosomal donor sites. Some of the excised transposons undergo a self-destructive autointegration reaction, which can partially explain why longer elements transpose less efficiently. SB became an important molecular tool for transgenesis, insertional mutagenesis, and gene therapy.
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28
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Bürglin TR, Affolter M. Homeodomain proteins: an update. Chromosoma 2015; 125:497-521. [PMID: 26464018 PMCID: PMC4901127 DOI: 10.1007/s00412-015-0543-8] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/20/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
Abstract
Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MATα2.
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Affiliation(s)
- Thomas R. Bürglin
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
- />Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Markus Affolter
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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Terencio ML, Schneider CH, Gross MC, do Carmo EJ, Nogaroto V, de Almeida MC, Artoni RF, Vicari MR, Feldberg E. Repetitive sequences: the hidden diversity of heterochromatin in prochilodontid fish. COMPARATIVE CYTOGENETICS 2015; 9:465-481. [PMID: 26752156 PMCID: PMC4698564 DOI: 10.3897/compcytogen.v9i4.5299] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/17/2015] [Indexed: 06/05/2023]
Abstract
The structure and organization of repetitive elements in fish genomes are still relatively poorly understood, although most of these elements are believed to be located in heterochromatic regions. Repetitive elements are considered essential in evolutionary processes as hotspots for mutations and chromosomal rearrangements, among other functions - thus providing new genomic alternatives and regulatory sites for gene expression. The present study sought to characterize repetitive DNA sequences in the genomes of Semaprochilodus insignis (Jardine & Schomburgk, 1841) and Semaprochilodus taeniurus (Valenciennes, 1817) and identify regions of conserved syntenic blocks in this genome fraction of three species of Prochilodontidae (Semaprochilodus insignis, Semaprochilodus taeniurus, and Prochilodus lineatus (Valenciennes, 1836) by cross-FISH using Cot-1 DNA (renaturation kinetics) probes. We found that the repetitive fractions of the genomes of Semaprochilodus insignis and Semaprochilodus taeniurus have significant amounts of conserved syntenic blocks in hybridization sites, but with low degrees of similarity between them and the genome of Prochilodus lineatus, especially in relation to B chromosomes. The cloning and sequencing of the repetitive genomic elements of Semaprochilodus insignis and Semaprochilodus taeniurus using Cot-1 DNA identified 48 fragments that displayed high similarity with repetitive sequences deposited in public DNA databases and classified as microsatellites, transposons, and retrotransposons. The repetitive fractions of the Semaprochilodus insignis and Semaprochilodus taeniurus genomes exhibited high degrees of conserved syntenic blocks in terms of both the structures and locations of hybridization sites, but a low degree of similarity with the syntenic blocks of the Prochilodus lineatus genome. Future comparative analyses of other prochilodontidae species will be needed to advance our understanding of the organization and evolution of the genomes in this group of fish.
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Affiliation(s)
- Maria L Terencio
- Federal University of Integration American-Latin (Universidade Federal da Integração Latino-Americana), Laboratory of Genetics, Av. Tarquínio Joslin dos Santos, 1000, Jardim Universitário, Foz do Iguaçu, PR, Brazil 85857-190
| | - Carlos H Schneider
- Federal University of Amazonas (Universidade Federal do Amazonas), Institute of Biological Sciences, Department of Genetics, Laboratory of Animal Cytogenomics, Manaus, AM, Brazil
| | - Maria C Gross
- Federal University of Amazonas (Universidade Federal do Amazonas), Institute of Biological Sciences, Department of Genetics, Laboratory of Animal Cytogenomics, Manaus, AM, Brazil
| | - Edson Junior do Carmo
- Federal University of Amazonas, Institute of Biological Sciences, Laboratory of DNA Technologies, Manaus, AM, Brazil
| | - Viviane Nogaroto
- State University of Ponta Grossa, Department of Structural and Molecular Biology and Genetics, Laboratory of Cytogenetics and Evolution, Ponta Grossa, PR, Brazil
| | - Mara Cristina de Almeida
- State University of Ponta Grossa, Department of Structural and Molecular Biology and Genetics, Laboratory of Cytogenetics and Evolution, Ponta Grossa, PR, Brazil
| | - Roberto Ferreira Artoni
- State University of Ponta Grossa, Department of Structural and Molecular Biology and Genetics, Laboratory of Cytogenetics and Evolution, Ponta Grossa, PR, Brazil
| | - Marcelo R Vicari
- State University of Ponta Grossa, Department of Structural and Molecular Biology and Genetics, Laboratory of Cytogenetics and Evolution, Ponta Grossa, PR, Brazil
| | - Eliana Feldberg
- National Institute of Amazonian Research, Laboratory of Animal Genetics, Av. André Araújo, 2936, Petrópolis, Manaus, AM, Brazil 69011-970
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30
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Origins and evolvability of the PAX family. Semin Cell Dev Biol 2015; 44:64-74. [DOI: 10.1016/j.semcdb.2015.08.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 08/07/2015] [Accepted: 08/22/2015] [Indexed: 01/18/2023]
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Kranz LM, Birtel M, Krienke C, Grunwitz C, Petschenka J, Reuter KC, van de Roemer N, Vascotto F, Vormehr M, Kreiter S, Diken M. CIMT 2015: The right patient for the right therapy - Report on the 13th annual meeting of the Association for Cancer Immunotherapy. Hum Vaccin Immunother 2015; 12:213-21. [PMID: 26186022 PMCID: PMC4962731 DOI: 10.1080/21645515.2015.1068485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 06/29/2015] [Indexed: 12/22/2022] Open
Affiliation(s)
- Lena M Kranz
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
- Research Center for Immunotherapy (FZI); University Medical Center; Johannes Gutenberg University; Mainz, Germany
| | - Matthias Birtel
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
| | - Christina Krienke
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
- Research Center for Immunotherapy (FZI); University Medical Center; Johannes Gutenberg University; Mainz, Germany
| | - Christian Grunwitz
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
- BioNTech RNA Pharmaceuticals GmbH; Mainz, Germany
| | - Jutta Petschenka
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
| | | | - Niels van de Roemer
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
- Research Center for Immunotherapy (FZI); University Medical Center; Johannes Gutenberg University; Mainz, Germany
| | - Fulvia Vascotto
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
| | - Mathias Vormehr
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
- BioNTech RNA Pharmaceuticals GmbH; Mainz, Germany
| | - Sebastian Kreiter
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH; Mainz, Germany
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Calinescu AA, Núñez FJ, Koschmann C, Kolb BL, Lowenstein PR, Castro MG. Transposon mediated integration of plasmid DNA into the subventricular zone of neonatal mice to generate novel models of glioblastoma. J Vis Exp 2015. [PMID: 25741859 DOI: 10.3791/52443] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
An urgent need exists to test the contribution of new genes to the pathogenesis and progression of human glioblastomas (GBM), the most common primary brain tumor in adults with dismal prognosis. New potential therapies are rapidly emerging from the bench and require systematic testing in experimental models which closely reproduce the salient features of the human disease. Herein we describe in detail a method to induce new models of GBM with transposon-mediated integration of plasmid DNA into cells of the subventricular zone of neonatal mice. We present a simple way to clone new transposons amenable for genomic integration using the Sleeping Beauty transposon system and illustrate how to monitor plasmid uptake and disease progression using bioluminescence, histology and immuno-histochemistry. We also describe a method to create new primary GBM cell lines. Ideally, this report will allow further dissemination of the Sleeping Beauty transposon system among brain tumor researchers, leading to an in depth understanding of GBM pathogenesis and progression and to the timely design and testing of effective therapies for patients.
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Affiliation(s)
| | | | - Carl Koschmann
- Department of Pediatrics, Division of Hematology-Oncology, University of Michigan School of Medicine
| | - Bradley L Kolb
- Department of Neurosurgery, University of Michigan School of Medicine
| | - Pedro R Lowenstein
- Department of Neurosurgery, University of Michigan School of Medicine; Department of Cell and Developmental Biology, University of Michigan
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan School of Medicine; Department of Cell and Developmental Biology, University of Michigan;
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Manufacture of T cells using the Sleeping Beauty system to enforce expression of a CD19-specific chimeric antigen receptor. Cancer Gene Ther 2015; 22:95-100. [PMID: 25591810 DOI: 10.1038/cgt.2014.69] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 01/10/2023]
Abstract
T cells can be reprogrammed to redirect specificity to tumor-associated antigens (TAAs) through the enforced expression of chimeric antigen receptors (CARs). The prototypical CAR is a single-chain molecule that docks with TAA expressed on the cell surface and, in contrast to the T-cell receptor complex, recognizes target cells independent of human leukocyte antigen. The bioprocessing to generate CAR(+) T cells has been reduced to clinical practice based on two common steps that are accomplished in compliance with current good manufacturing practice. These are (1) gene transfer to stably integrate the CAR using viral and nonviral approaches and (2) activating the T cells for proliferation by crosslinking CD3 or antigen-driven numeric expansion using activating and propagating cells (AaPCs). Here, we outline our approach to nonviral gene transfer using the Sleeping Beauty system and the selective propagation of CD19-specific CAR(+) T cells on AaPCs.
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Wolf DA, Banerjee S, Hackett PB, Whitley CB, McIvor RS, Low WC. Gene therapy for neurologic manifestations of mucopolysaccharidoses. Expert Opin Drug Deliv 2014; 12:283-96. [PMID: 25510418 DOI: 10.1517/17425247.2015.966682] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Mucopolysaccharidoses (MPS) are a family of lysosomal disorders caused by mutations in genes that encode enzymes involved in the catabolism of glycoaminoglycans. These mutations affect multiple organ systems and can be particularly deleterious to the nervous system. At the present time, enzyme replacement therapy and hematopoietic stem-cell therapy are used to treat patients with different forms of these disorders. However, to a great extent, the nervous system is not adequately responsive to current therapeutic approaches. AREAS COVERED Recent advances in gene therapy show great promise for treating MPS. This article reviews the current state of the art for routes of delivery in developing genetic therapies for treating the neurologic manifestations of MPS. EXPERT OPINION Gene therapy for treating neurological manifestations of MPS can be achieved by intraventricular, intrathecal, intranasal and systemic administrations. The intraventricular route of administration appears to provide the most widespread distribution of gene therapy vectors to the brain. The intrathecal route of delivery results in predominant distribution to the caudal areas of the brain. The systemic route of delivery via intravenous infusion can also achieve widespread delivery to the CNS; however, the distribution to the brain is greatly dependent on the vector system. Intravenous delivery using lentiviral vectors appear to be less effective than adeno-associated viral (AAV) vectors. Moreover, some subtypes of AAV vectors are more effective than others in crossing the blood-brain barrier. In summary, the recent advances in gene vector technology and routes of delivery to the CNS will facilitate the clinical translation of gene therapy for the treatment of the neurological manifestations of MPS.
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Affiliation(s)
- Daniel A Wolf
- University of Minnesota, Department of Genetics, Cell Biology, and Development , Minneapolis, MN 55455 , USA
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35
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Turchiano G, Latella MC, Gogol-Döring A, Cattoglio C, Mavilio F, Izsvák Z, Ivics Z, Recchia A. Genomic analysis of Sleeping Beauty transposon integration in human somatic cells. PLoS One 2014; 9:e112712. [PMID: 25390293 PMCID: PMC4229213 DOI: 10.1371/journal.pone.0112712] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/14/2014] [Indexed: 12/21/2022] Open
Abstract
The Sleeping Beauty (SB) transposon is a non-viral integrating vector system with proven efficacy for gene transfer and functional genomics. However, integration efficiency is negatively affected by the length of the transposon. To optimize the SB transposon machinery, the inverted repeats and the transposase gene underwent several modifications, resulting in the generation of the hyperactive SB100X transposase and of the high-capacity “sandwich” (SA) transposon. In this study, we report a side-by-side comparison of the SA and the widely used T2 arrangement of transposon vectors carrying increasing DNA cargoes, up to 18 kb. Clonal analysis of SA integrants in human epithelial cells and in immortalized keratinocytes demonstrates stability and integrity of the transposon independently from the cargo size and copy number-dependent expression of the cargo cassette. A genome-wide analysis of unambiguously mapped SA integrations in keratinocytes showed an almost random distribution, with an overrepresentation in repetitive elements (satellite, LINE and small RNAs) compared to a library representing insertions of the first-generation transposon vector and to gammaretroviral and lentiviral libraries. The SA transposon/SB100X integrating system therefore shows important features as a system for delivering large gene constructs for gene therapy applications.
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Affiliation(s)
- Giandomenico Turchiano
- Center for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Maria Carmela Latella
- Center for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Andreas Gogol-Döring
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Claudia Cattoglio
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Fulvio Mavilio
- Center for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Genethon, Evry, France
| | | | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Alessandra Recchia
- Center for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- * E-mail:
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Singh H, Huls H, Kebriaei P, Cooper LJN. A new approach to gene therapy using Sleeping Beauty to genetically modify clinical-grade T cells to target CD19. Immunol Rev 2014; 257:181-90. [PMID: 24329797 DOI: 10.1111/imr.12137] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The advent of efficient approaches to the genetic modification of T cells has provided investigators with clinically appealing methods to improve the potency of tumor-specific clinical grade T cells. For example, gene therapy has been successfully used to enforce expression of chimeric antigen receptors (CARs) that provide T cells with ability to directly recognize tumor-associated antigens without the need for presentation by human leukocyte antigen. Gene transfer of CARs can be undertaken using viral-based and non-viral approaches. We have advanced DNA vectors derived from the Sleeping Beauty (SB) system to avoid the expense and manufacturing difficulty associated with transducing T cells with recombinant viral vectors. After electroporation, the transposon/transposase improves the efficiency of integration of plasmids used to express CAR and other transgenes in T cells. The SB system combined with artificial antigen-presenting cells (aAPC) can selectively propagate and thus retrieve CAR(+) T cells suitable for human application. This review describes the translation of the SB system and aAPC for use in clinical trials and highlights how a nimble and cost-effective approach to developing genetically modified T cells can be used to implement clinical trials infusing next-generation T cells with improved therapeutic potential.
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Affiliation(s)
- Harjeet Singh
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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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: 1.2] [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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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: 53] [Impact Index Per Article: 4.4] [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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Cheng LD, Jiang XY, Tian YM, Chen J, Zou SM. The goldfish hAT-family transposon Tgf2 is capable of autonomous excision in zebrafish embryos. Gene 2013; 536:74-8. [PMID: 24321692 DOI: 10.1016/j.gene.2013.11.084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 09/24/2013] [Accepted: 11/30/2013] [Indexed: 12/17/2022]
Abstract
The goldfish (Carassius auratus) Tgf2 transposon is a vertebrate DNA transposon that belongs to the hAT transposon family. In this study, we constructed plasmids containing either the full-length Tgf2 transposon (pTgf2 plasmid) or a partially-deleted Tgf2 transposon (ΔpTgf2 plasmid), and microinjected these plasmids into fertilized zebrafish (Danio rerio) eggs at the one- to two-cell stage. DNA extracted from the embryos was analyzed by PCR to assess transient excision, if any, of the exogenous plasmid and to verify whether Tgf2 is an autonomous transposon. The results showed that excision-specific bands were not detected in embryos injected with the ΔpTgf2 plasmid, while bands of 300-500bp were detected in embryos injected with pTgf2, which indicated that the full-length Tgf2-containing plasmid could undergo autonomous excision in zebrafish embryos. DNA cloned from 24 embryos injected with pTgf2 was sequenced, and the results suggested that Tgf2 underwent self-excision in zebrafish embryos. Cloning and PCR analysis of DNA extracted from embryos co-injected with ΔpTgf2 and in vitro-transcribed transposase mRNA indicated that partially-deleted-Tgf2-containing ΔpTgf2 plasmid also underwent excision, in the presence of functional transposase mRNA. DNA cloned from 25 embryos co-injected with ΔpTgf2 and transposase mRNA was sequenced, and the results suggested that partially-deleted Tgf2 transposons plasmids were excised. These results demonstrated that excisions of Tgf2 transposons were mediated by the Tgf2 transposase, which in turn confirmed that Tgf2 is an autonomous transposon.
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Affiliation(s)
- Luo-Dan Cheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China
| | - Xia-Yun Jiang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China
| | - Yu-Mei Tian
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China
| | - Jie Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China
| | - Shu-Ming Zou
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai 201306, China.
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Palazzo A, Marconi S, Specchia V, Bozzetti MP, Ivics Z, Caizzi R, Marsano RM. Functional characterization of the Bari1 transposition system. PLoS One 2013; 8:e79385. [PMID: 24244492 PMCID: PMC3828361 DOI: 10.1371/journal.pone.0079385] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/20/2013] [Indexed: 01/12/2023] Open
Abstract
The transposons of the Bari family are mobile genetic elements widespread in the Drosophila genus. However, despite a broad diffusion, virtually no information is available on the mechanisms underlying their mobility. In this paper we report the functional characterization of the Bari elements transposition system. Using the Bari1 element as a model, we investigated the subcellular localization of the transposase, its physical interaction with the transposon, and its catalytic activity. The Bari1 transposase localized in the nucleus and interacted with the terminal sequences of the transposon both in vitro and in vivo, however, no transposition activity was detected in transposition assays. Profiling of mRNAs expressed by the transposase gene revealed the expression of abnormal, internally processed transposase transcripts encoding truncated, catalytically inactive transposase polypeptides. We hypothesize that a post-transcriptional control mechanism produces transposase-derived polypeptides that effectively repress transposition. Our findings suggest further clues towards understanding the mechanisms that control transposition of an important class of mobile elements, which are both an endogenous source of genomic variability and widely used as transformation vectors/biotechnological tools.
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Affiliation(s)
| | - Simona Marconi
- Dipartimento di Biologia, Università di Bari, Bari, Italy
| | - Valeria Specchia
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA), Università del Salento, Lecce, Italy
| | - Maria Pia Bozzetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA), Università del Salento, Lecce, Italy
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
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Mos1 transposon-based transformation of fish cell lines using baculoviral vectors. Biochem Biophys Res Commun 2013; 439:18-22. [PMID: 23958306 DOI: 10.1016/j.bbrc.2013.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 08/10/2013] [Indexed: 11/24/2022]
Abstract
Drosophila Mos1 belongs to the mariner family of transposons, which are one of the most ubiquitous transposons among eukaryotes. We first determined nuclear transportation of the Drosophila Mos1-EGFP fusion protein in fish cell lines because it is required for a function of transposons. We next constructed recombinant baculoviral vectors harboring the Drosophila Mos1 transposon or marker genes located between Mos1 inverted repeats. The infectivity of the recombinant virus to fish cells was assessed by monitoring the expression of a fluorescent protein encoded in the viral genome. We detected transgene expression in CHSE-214, HINAE, and EPC cells, but not in GF or RTG-2 cells. In the co-infection assay of the Mos1-expressing virus and reporter gene-expressing virus, we successfully transformed CHSE-214 and HINAE cells. These results suggest that the combination of a baculovirus and Mos1 transposable element may be a tool for transgenesis in fish cells.
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42
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Levesque MP, Krauss J, Koehler C, Boden C, Harris MP. New tools for the identification of developmentally regulated enhancer regions in embryonic and adult zebrafish. Zebrafish 2013; 10:21-9. [PMID: 23461416 DOI: 10.1089/zeb.2012.0775] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We have conducted a screen to identify developmentally regulated enhancers that drive tissue-specific Gal4 expression in zebrafish. We obtained 63 stable transgenic lines with expression patterns in embryonic or adult zebrafish. The use of a newly identified minimal promoter from the medaka edar locus resulted in a relatively unbiased set of expression patterns representing many tissue types derived from all germ layers. Subsequent detailed characterization of selected lines showed strong and reproducible Gal4-driven GFP expression in diverse tissues, including neurons from the central and peripheral nervous systems, pigment cells, erythrocytes, and peridermal cells. By screening adults for GFP expression, we also isolated lines expressed in tissues of the adult zebrafish, including scales, fin rays, and joints. The new and efficient minimal promoter and large number of transactivating driver-lines we identified will provide the zebrafish community with a useful resource for further enhancer trap screening, as well as precise investigation of tissue-specific processes in vivo.
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Affiliation(s)
- Mitchell P Levesque
- Department of Genetics, Max-Planck-Institut für Entwicklungsbiologie, Tübingen, Germany .
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43
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Ahn SJ, Kim JY, Kim MS, Lee HH. Cloning and characterization of Tc1 family-derived PPTN related transposons from ridged-eye flounder (Pleuronichthys cornutus) and inshore hagfish (Eptatretus burgeri). Genes Genomics 2013. [DOI: 10.1007/s13258-013-0068-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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44
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Abrusán G, Szilágyi A, Zhang Y, Papp B. Turning gold into 'junk': transposable elements utilize central proteins of cellular networks. Nucleic Acids Res 2013; 41:3190-200. [PMID: 23341038 PMCID: PMC3597677 DOI: 10.1093/nar/gkt011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The numerous discovered cases of domesticated transposable element (TE) proteins led to the recognition that TEs are a significant source of evolutionary innovation. However, much less is known about the reverse process, whether and to what degree the evolution of TEs is influenced by the genome of their hosts. We addressed this issue by searching for cases of incorporation of host genes into the sequence of TEs and examined the systems-level properties of these genes using the Saccharomyces cerevisiae and Drosophila melanogaster genomes. We identified 51 cases where the evolutionary scenario was the incorporation of a host gene fragment into a TE consensus sequence, and we show that both the yeast and fly homologues of the incorporated protein sequences have central positions in the cellular networks. An analysis of selective pressure (Ka/Ks ratio) detected significant selection in 37% of the cases. Recent research on retrovirus-host interactions shows that virus proteins preferentially target hubs of the host interaction networks enabling them to take over the host cell using only a few proteins. We propose that TEs face a similar evolutionary pressure to evolve proteins with high interacting capacities and take some of the necessary protein domains directly from their hosts.
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Affiliation(s)
- György Abrusán
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesváry krt. 62. Szeged H-6701, Hungary.
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Di Matteo M, Belay E, Chuah MK, Vandendriessche T. Recent developments in transposon-mediated gene therapy. Expert Opin Biol Ther 2012; 12:841-58. [PMID: 22679910 DOI: 10.1517/14712598.2012.684875] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION The continuous improvement of gene transfer technologies has broad implications for stem cell biology, gene discovery, and gene therapy. Although viral vectors are efficient gene delivery vehicles, their safety, immunogenicity and manufacturing challenges hamper clinical progress. In contrast, non-viral gene delivery systems are less immunogenic and easier to manufacture. AREAS COVERED In this review, we explore the emerging potential of transposons in gene and cell therapy. The safety, efficiency, and biology of novel hyperactive Sleeping Beauty (SB) and piggyBac (PB) transposon systems will be highlighted for ex vivo gene therapy in clinically relevant adult stem/progenitor cells, particularly hematopoietic stem cells (HSCs), mesenchymal stem cells (MSCs), myoblasts, and induced pluripotent stem (iPS) cells. Moreover, efforts toward in vivo transposon-based gene therapy will be discussed. EXPERT OPINION The latest generation SB and PB transposons currently represent some of the most attractive systems for stable non-viral genetic modification of primary cells, particularly adult stem cells. This paves the way toward the use of transposons as a non-viral gene therapy approach to correct hereditary disorders including those that affect the hematopoietic system. The development of targeted integration into "safe harbor" genetic loci may further improve their safety profile.
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Affiliation(s)
- Mario Di Matteo
- Free University of Brussels, Division of Gene Therapy & Regenerative Medicine, Laarbeeklaan 103, B-1090 Brussels, Belgium
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Pujolar JM, Astolfi L, Boscari E, Vidotto M, Barbisan F, Bruson A, Congiu L. Tana1, a new putatively active Tc1-like transposable element in the genome of sturgeons. Mol Phylogenet Evol 2012; 66:223-32. [PMID: 23032571 DOI: 10.1016/j.ympev.2012.09.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/21/2012] [Accepted: 09/23/2012] [Indexed: 01/05/2023]
Abstract
We report the discovery of a new putatively active Tc1-like transposable element (Tana1) in the genome of sturgeons, an ancient group of fish considered as living fossils. The complete sequence of Tana1 was first characterized in the 454-sequenced transcriptome of the Adriatic sturgeon (Acipenser naccarii) and then isolated from the genome of the same species and from 12 additional sturgeons including three genera of the Acipenseridae (Acipenser, Huso, Scaphirhynchus). The element has a total length of 1588bp and presents inverted repeats of 210bp, one of which partially overlapping the 3' region of the transposase gene. The spacing of the DDE motif within the catalytic domain in Tana1 is unique (DD38E) and indicates that Tana1 can be considered as the first representative of a new Tc1 subfamily. The integrity of the native form (with no premature termination codons within the transposase), the presence of all expected functional domains and its occurrence in the sturgeon transcriptome suggest a current or recent activity of Tana1. The presence of Tana1 in the genome of the 13 sturgeon species in our study points to an ancient origin of the element that existed before the split of the group 170 million years ago. The dissemination of Tana1 across sturgeon genomes could be interpreted by postulating vertical transmission from an ancestral Tana1 with a particularly slow evolutionary rate Horizontal transmission might have also played a role in the dissemination of Tana1 as evidenced by the presence of a complete copy in the genome of Atlantic salmon. Vertical and horizontal transmission are not mutually exclusive and may have concurred in shaping the evolution of Tana1.
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Jiang XY, Du XD, Tian YM, Shen RJ, Sun CF, Zou SM. Goldfish transposase Tgf2 presumably from recent horizontal transfer is active. FASEB J 2012; 26:2743-52. [PMID: 22441985 DOI: 10.1096/fj.11-199273] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Hobo/Activator/Tam3 (hAT) superfamily transposons occur in plants and animals and play a role in genomic evolution. Certain hAT transposons are active and have been developed as incisive genetic tools. Active vertebrate elements are rarely discovered; however, Tgf2 transposon was recently discovered in goldfish (Carassius auratus). Here, we found that the endogenous Tgf2 element can transpose in goldfish genome. Seven different goldfish mRNA transcripts, encoding three lengths of Tgf2 transposase, were identified. Tgf2 transposase mRNA was detected in goldfish embryos, mainly in epithelial cells; levels were high in ovaries and mature eggs and in all adult tissues tested. Endogenous Tgf2 transposase mRNA is active in mature eggs and can mediate high rates of transposition (>30%) when injected with donor plasmids harboring a Tgf2 cis-element. When donor plasmid was coinjected with capped Tgf2 transposase mRNA, the insertion rate reached >90% at 1 yr. Nonautonomous copies of the Tgf2 transposon with large-fragment deletions and low levels of point mutations were also detected in common goldfish. Phylogenetic analysis indicates the taxonomic distribution of Tgf2 in goldfish is not due to vertical inheritance. We propose that the goldfish Tgf2 transposon originated by recent horizontal transfer and maintains a highly native activity.
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Affiliation(s)
- Xia-Yun Jiang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
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Demattei MV, Hedhili S, Sinzelle L, Bressac C, Casteret S, Moiré N, Cambefort J, Thomas X, Pollet N, Gantet P, Bigot Y. Nuclear importation of Mariner transposases among eukaryotes: motif requirements and homo-protein interactions. PLoS One 2011; 6:e23693. [PMID: 21876763 PMCID: PMC3158080 DOI: 10.1371/journal.pone.0023693] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 07/22/2011] [Indexed: 12/13/2022] Open
Abstract
Mariner-like elements (MLEs) are widespread transposable elements in animal genomes. They have been divided into at least five sub-families with differing host ranges. We investigated whether the ability of transposases encoded by Mos1, Himar1 and Mcmar1 to be actively imported into nuclei varies between host belonging to different eukaryotic taxa. Our findings demonstrate that nuclear importation could restrict the host range of some MLEs in certain eukaryotic lineages, depending on their expression level. We then focused on the nuclear localization signal (NLS) in these proteins, and showed that the first 175 N-terminal residues in the three transposases were required for nuclear importation. We found that two components are involved in the nuclear importation of the Mos1 transposase: an SV40 NLS-like motif (position: aa 168 to 174), and a dimerization sub-domain located within the first 80 residues. Sequence analyses revealed that the dimerization moiety is conserved among MLE transposases, but the Himar1 and Mcmar1 transposases do not contain any conserved NLS motif. This suggests that other NLS-like motifs must intervene in these proteins. Finally, we showed that the over-expression of the Mos1 transposase prevents its nuclear importation in HeLa cells, due to the assembly of transposase aggregates in the cytoplasm.
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Affiliation(s)
| | - Sabah Hedhili
- CIRAD, UMR 1098 Développement et Amélioration des Plantes, Montpellier, France
| | - Ludivine Sinzelle
- Metamorphosys, CNRS UPS3201-Université d'Evry Val d'Essonne, Genavenir 3 - Genopole Campus 1, Evry, France
| | | | - Sophie Casteret
- PRC, UMR INRA-CNRS 6175, Nouzilly, France
- GICC, UMR CNRS 6239, UFR des Sciences et Techniques, Tours, France
| | | | - Jeanne Cambefort
- GICC, UMR CNRS 6239, UFR des Sciences et Techniques, Tours, France
| | - Xavier Thomas
- GICC, UMR CNRS 6239, UFR des Sciences et Techniques, Tours, France
| | - Nicolas Pollet
- Metamorphosys, CNRS UPS3201-Université d'Evry Val d'Essonne, Genavenir 3 - Genopole Campus 1, Evry, France
| | - Pascal Gantet
- CIRAD, UMR 1098 Développement et Amélioration des Plantes, Montpellier, France
| | - Yves Bigot
- PRC, UMR INRA-CNRS 6175, Nouzilly, France
- * E-mail:
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Bak RO, Mikkelsen JG. Mobilization of DNA transposable elements from lentiviral vectors. Mob Genet Elements 2011; 1:139-144. [PMID: 22016863 DOI: 10.4161/mge.1.2.17062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 06/17/2011] [Accepted: 06/18/2011] [Indexed: 01/08/2023] Open
Abstract
With the Sleeping Beauty (SB) DNA transposon, a reconstructed Tc1/mariner element, as the driving force, DNA transposable elements have emerged as new gene delivery vectors with therapeutic potential. The bipartite transposon vector system consists of a transposon vector carrying the transgene and a source of the transposase that catalyzes transposon mobilization. The components of the system are typically residing on separate plasmids that are transfected into cells or tissues of interest. We have recently shown that SB vector technology can be successfully combined with lentiviral delivery. Hence, SB transposons are efficiently mobilized from HIV-based integrase-defective lentiviral vectors by the hyperactive SB100X transposase, leading to the genomic insertion of lentivirally delivered DNA in a reaction controlled by a nonviral integration machinery. This new technology combines the better of two vector worlds and leads to integration profiles that are significantly altered and potentially safer relative to conventional lentiviral vectors. In this short commentary, we discuss our recent findings and the road ahead for hybrid lentivirus-transposon vectors.
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Affiliation(s)
- Rasmus O Bak
- Department of Biomedicine; University of Aarhus; Aarhus C, Denmark
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Raincrow JD, Dewar K, Stocsits C, Prohaska SJ, Amemiya CT, Stadler PF, Chiu CH. Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 316:451-64. [PMID: 21688387 DOI: 10.1002/jez.b.21420] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/27/2011] [Accepted: 04/24/2011] [Indexed: 12/12/2022]
Abstract
Teleost fishes have extra Hox gene clusters owing to shared or lineage-specific genome duplication events in rayfinned fish (actinopterygian) phylogeny. Hence, extrapolating between genome function of teleosts and human or even between different fish species is difficult. We have sequenced and analyzed Hox gene clusters of the Senegal bichir (Polypterus senegalus), an extant representative of the most basal actinopterygian lineage. Bichir possesses four Hox gene clusters (A, B, C, D); phylogenetic analysis supports their orthology to the four Hox gene clusters of the gnathostome ancestor. We have generated a comprehensive database of conserved Hox noncoding sequences that include cartilaginous, lobe-finned, and ray-finned fishes (bichir and teleosts). Our analysis identified putative and known Hox cis-regulatory sequences with differing depths of conservation in Gnathostoma. We found that although bichir possesses four Hox gene clusters, its pattern of conservation of noncoding sequences is mosaic between outgroups, such as human, coelacanth, and shark, with four Hox gene clusters and teleosts, such as zebrafish and pufferfish, with seven or eight Hox gene clusters. Notably, bichir Hox gene clusters have been invaded by DNA transposons and this trend is further exemplified in teleosts, suggesting an as yet unrecognized mechanism of genome evolution that may explain Hox cluster plasticity in actinopterygians. Taken together, our results suggest that actinopterygian Hox gene clusters experienced a reduction in selective constraints that surprisingly predates the teleost-specific genome duplication.
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Affiliation(s)
- Jeremy D Raincrow
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
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