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Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401797. [PMID: 38728624 DOI: 10.1002/advs.202401797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
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Affiliation(s)
- Yongfeng Liu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
- Mudi Meng Honors College, China Pharmaceutical University, Nanjing, 210009, China
| | - Jianping Kong
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Gongyu Liu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhaoxing Li
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China
| | - Yibei Xiao
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China
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2
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Stucchi A, Maspes F, Montee-Rodrigues E, Fousteri G. Engineered Treg cells: The heir to the throne of immunotherapy. J Autoimmun 2024; 144:102986. [PMID: 36639301 DOI: 10.1016/j.jaut.2022.102986] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/15/2022] [Indexed: 01/13/2023]
Abstract
Recently, increased interest in the use of Tregs as adoptive cell therapy for the treatment of autoimmune diseases and transplant rejection had led to several advances in the field. However, Treg cell therapies, while constantly advancing, indiscriminately suppress the immune system without the permanent stabilization of certain diseases. Genetically modified Tregs hold great promise towards solving these problems, but, challenges in identifying the most potent Treg subtype, accompanied by the ambiguity involved in identifying the optimal Treg source, along with its expansion and engineering in a clinical-grade setting remain paramount. This review highlights the recent advances in methodologies for the development of genetically engineered Treg cell-based treatments for autoimmune, inflammatory diseases, and organ rejection. Additionally, it provides a systematized guide to all the recent progress in the field and informs the readers of the feasibility and safety of engineered adoptive Treg cell therapy, with the aim to provide a framework for researchers involved in the development of engineered Tregs.
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Affiliation(s)
- Adriana Stucchi
- Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Federica Maspes
- Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ely Montee-Rodrigues
- Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy; Cambridge Epigenetix, Cambridge, Cambridgeshire, United Kingdom
| | - Georgia Fousteri
- Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy.
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3
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Magnani CF, Myburgh R, Brunn S, Chambovey M, Ponzo M, Volta L, Manfredi F, Pellegrino C, Pascolo S, Miskey C, Ivics Z, Shizuru JA, Neri D, Manz MG. Anti-CD117 CAR T cells incorporating a safety switch eradicate human acute myeloid leukemia and hematopoietic stem cells. Mol Ther Oncolytics 2023; 30:56-71. [PMID: 37583386 PMCID: PMC10424000 DOI: 10.1016/j.omto.2023.07.003] [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] [Received: 01/13/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
Discrimination between hematopoietic stem cells and leukemic stem cells remains a major challenge for acute myeloid leukemia immunotherapy. CAR T cells specific for the CD117 antigen can deplete malignant and healthy hematopoietic stem cells before consolidation with allogeneic hematopoietic stem cell transplantation in absence of cytotoxic conditioning. Here we exploit non-viral technology to achieve early termination of CAR T cell activity to prevent incoming graft rejection. Transient expression of an anti-CD117 CAR by mRNA conferred T cells the ability to eliminate CD117+ targets in vitro and in vivo. As an alternative approach, we used a Sleeping Beauty transposon vector for the generation of CAR T cells incorporating an inducible Caspase 9 safety switch. Stable CAR expression was associated with high proportion of T memory stem cells, low levels of exhaustion markers, and potent cellular cytotoxicity. Anti-CD117 CAR T cells mediated depletion of leukemic cells and healthy hematopoietic stem cells in NSG mice reconstituted with human leukemia or CD34+ cord blood cells, respectively, and could be terminated in vivo. The use of a non-viral technology to control CAR T cell pharmacokinetic properties is attractive for a first-in-human study in patients with acute myeloid leukemia prior to hematopoietic stem cell transplantation.
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Affiliation(s)
- Chiara F. Magnani
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Renier Myburgh
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Silvan Brunn
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Morgane Chambovey
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Marianna Ponzo
- Tettamanti Center, Fondazione IRCCS San Gerardo Dei Tintori, 20900 Monza, Italy
| | - Laura Volta
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Francesco Manfredi
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Christian Pellegrino
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Judith A. Shizuru
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, 8093 ETH Zurich, Switzerland
| | - Markus G. Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
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4
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Zhang C, Yang Y, Qi T, Zhang Y, Hou L, Wei J, Yang J, Shi L, Ong SG, Wang H, Wang H, Yu B, Wang Y. Prediction of base editor off-targets by deep learning. Nat Commun 2023; 14:5358. [PMID: 37660097 PMCID: PMC10475126 DOI: 10.1038/s41467-023-41004-3] [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: 09/15/2022] [Accepted: 08/21/2023] [Indexed: 09/04/2023] Open
Abstract
Due to the tolerance of mismatches between gRNA and targeting sequence, base editors frequently induce unwanted Cas9-dependent off-target mutations. Here, to develop models to predict such off-targets, we design gRNA-off- target pairs for adenine base editors (ABEs) and cytosine base editors (CBEs) and stably integrate them into the human cells. After five days of editing, we obtain valid efficiency datasets of 54,663 and 55,727 off-targets for ABEs and CBEs, respectively. We use the datasets to train deep learning models, resulting in ABEdeepoff and CBEdeepoff, which can predict off-target sites. We use these tools to predict off-targets for a panel of endogenous loci and achieve Spearman correlation values varying from 0.710 to 0.859. Finally, we develop an integrated tool that is freely accessible via an online web server http://www.deephf.com/#/bedeep/bedeepoff . These tools could facilitate minimizing the off-target effects of base editing.
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Affiliation(s)
- Chengdong Zhang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yuan Yang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Tao Qi
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Yuening Zhang
- SJTU-Yale Joint Center for Biostatistics and Data Science, (Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology) Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linghui Hou
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Jingjing Wei
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Jingcheng Yang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Leming Shi
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Sang-Ging Ong
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Illinois, USA
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Illinois, USA
| | - Hongyan Wang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
| | - Bo Yu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
| | - Yongming Wang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China.
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5
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Liu S, Hur YH, Cai X, Cong Q, Yang Y, Xu C, Bilate AM, Gonzales KAU, Parigi SM, Cowley CJ, Hurwitz B, Luo JD, Tseng T, Gur-Cohen S, Sribour M, Omelchenko T, Levorse J, Pasolli HA, Thompson CB, Mucida D, Fuchs E. A tissue injury sensing and repair pathway distinct from host pathogen defense. Cell 2023; 186:2127-2143.e22. [PMID: 37098344 PMCID: PMC10321318 DOI: 10.1016/j.cell.2023.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/27/2023]
Abstract
Pathogen infection and tissue injury are universal insults that disrupt homeostasis. Innate immunity senses microbial infections and induces cytokines/chemokines to activate resistance mechanisms. Here, we show that, in contrast to most pathogen-induced cytokines, interleukin-24 (IL-24) is predominately induced by barrier epithelial progenitors after tissue injury and is independent of microbiome or adaptive immunity. Moreover, Il24 ablation in mice impedes not only epidermal proliferation and re-epithelialization but also capillary and fibroblast regeneration within the dermal wound bed. Conversely, ectopic IL-24 induction in the homeostatic epidermis triggers global epithelial-mesenchymal tissue repair responses. Mechanistically, Il24 expression depends upon both epithelial IL24-receptor/STAT3 signaling and hypoxia-stabilized HIF1α, which converge following injury to trigger autocrine and paracrine signaling involving IL-24-mediated receptor signaling and metabolic regulation. Thus, parallel to innate immune sensing of pathogens to resolve infections, epithelial stem cells sense injury signals to orchestrate IL-24-mediated tissue repair.
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Affiliation(s)
- Siqi Liu
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Yun Ha Hur
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Xin Cai
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qian Cong
- McDermott Center for Human Growth and Development, Department of Biophysics, and Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yihao Yang
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Chiwei Xu
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Angelina M Bilate
- Laboratory of Mucosal Immunology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Kevin Andrew Uy Gonzales
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - S Martina Parigi
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Christopher J Cowley
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Brian Hurwitz
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Tiffany Tseng
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Shiri Gur-Cohen
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Megan Sribour
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Tatiana Omelchenko
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - John Levorse
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Hilda Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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6
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Ochoa MC, Sanchez-Gregorio S, de Andrea CE, Garasa S, Alvarez M, Olivera I, Glez-Vaz J, Luri-Rey C, Etxeberria I, Cirella A, Azpilikueta A, Berraondo P, Argemi J, Sangro B, Teijeira A, Melero I. Synergistic effects of combined immunotherapy strategies in a model of multifocal hepatocellular carcinoma. Cell Rep Med 2023; 4:101009. [PMID: 37040772 PMCID: PMC10140615 DOI: 10.1016/j.xcrm.2023.101009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/20/2022] [Accepted: 03/20/2023] [Indexed: 04/13/2023]
Abstract
Immune checkpoint-inhibitor combinations are the best therapeutic option for advanced hepatocellular carcinoma (HCC) patients, but improvements in efficacy are needed to improve response rates. We develop a multifocal HCC model to test immunotherapies by introducing c-myc using hydrodynamic gene transfer along with CRISPR-Cas9-mediated disruption of p53 in mouse hepatocytes. Additionally, induced co-expression of luciferase, EGFP, and the melanosomal antigen gp100 facilitates studies on the underlying immunological mechanisms. We show that treatment of the mice with a combination of anti-CTLA-4 + anti-PD1 mAbs results in partial clearance of the tumor with an improvement in survival. However, the addition of either recombinant IL-2 or an anti-CD137 mAb markedly improves both outcomes in these mice. Combining tumor-specific adoptive T cell therapy to the aCTLA-4/aPD1/rIL2 or aCTLA-4/aPD1/aCD137 regimens enhances efficacy in a synergistic manner. As shown by multiplex tissue immunofluorescence and intravital microscopy, combined immunotherapy treatments enhance T cell infiltration and the intratumoral performance of T lymphocytes.
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Affiliation(s)
- Maria Carmen Ochoa
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain; Department of Immunology and Immunotherapy, Clínica Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Sandra Sanchez-Gregorio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain; Department of Immunology and Immunotherapy, Clínica Universidad de Navarra, Pamplona, Spain
| | - Carlos E de Andrea
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain; Department of Anatomy, Physiology and Pathology, University of Navarra, Pamplona, Spain
| | - Saray Garasa
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - Maite Alvarez
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - Irene Olivera
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - Javier Glez-Vaz
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - Carlos Luri-Rey
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - Iñaki Etxeberria
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain
| | - Assunta Cirella
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain
| | - Arantza Azpilikueta
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain
| | - Pedro Berraondo
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Josepmaria Argemi
- Liver Unit and HPB Oncology Area, Clínica Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBEREHD), Madrid, Spain
| | - Bruno Sangro
- Liver Unit and HPB Oncology Area, Clínica Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBEREHD), Madrid, Spain
| | - Alvaro Teijeira
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain; Department of Immunology and Immunotherapy, Clínica Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ignacio Melero
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain; Navarra Institute for Health Research (IDISNA), Pamplona, Spain; Department of Immunology and Immunotherapy, Clínica Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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7
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Tsai HC, Pietrobon V, Peng M, Wang S, Zhao L, Marincola FM, Cai Q. Current strategies employed in the manipulation of gene expression for clinical purposes. J Transl Med 2022; 20:535. [PMID: 36401279 PMCID: PMC9673226 DOI: 10.1186/s12967-022-03747-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
Abnormal gene expression level or expression of genes containing deleterious mutations are two of the main determinants which lead to genetic disease. To obtain a therapeutic effect and thus to cure genetic diseases, it is crucial to regulate the host's gene expression and restore it to physiological conditions. With this purpose, several molecular tools have been developed and are currently tested in clinical trials. Genome editing nucleases are a class of molecular tools routinely used in laboratories to rewire host's gene expression. Genome editing nucleases include different categories of enzymes: meganucleses (MNs), zinc finger nucleases (ZFNs), clustered regularly interspaced short palindromic repeats (CRISPR)- CRISPR associated protein (Cas) and transcription activator-like effector nuclease (TALENs). Transposable elements are also a category of molecular tools which includes different members, for example Sleeping Beauty (SB), PiggyBac (PB), Tol2 and TcBuster. Transposons have been used for genetic studies and can serve as gene delivery tools. Molecular tools to rewire host's gene expression also include episomes, which are divided into different categories depending on their molecular structure. Finally, RNA interference is commonly used to regulate gene expression through the administration of small interfering RNA (siRNA), short hairpin RNA (shRNA) and bi-functional shRNA molecules. In this review, we will describe the different molecular tools that can be used to regulate gene expression and discuss their potential for clinical applications. These molecular tools are delivered into the host's cells in the form of DNA, RNA or protein using vectors that can be grouped into physical or biochemical categories. In this review we will also illustrate the different types of payloads that can be used, and we will discuss recent developments in viral and non-viral vector technology.
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Affiliation(s)
| | | | - Maoyu Peng
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | - Suning Wang
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | - Lihong Zhao
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | | | - Qi Cai
- Kite Pharma Inc, Santa Monica, CA, 90404, USA.
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8
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Lalli M, Yen A, Thopte U, Dong F, Moudgil A, Chen X, Milbrandt J, Dougherty JD, Mitra RD. Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes. NAR Genom Bioinform 2022; 4:lqac061. [PMID: 36062164 PMCID: PMC9428926 DOI: 10.1093/nargab/lqac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/04/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Calling cards technology using self-reporting transposons enables the identification of DNA-protein interactions through RNA sequencing. Although immensely powerful, current implementations of calling cards in bulk experiments on populations of cells are technically cumbersome and require many replicates to identify independent insertions into the same genomic locus. Here, we have drastically reduced the cost and labor requirements of calling card experiments in bulk populations of cells by introducing a DNA barcode into the calling card itself. An additional barcode incorporated during reverse transcription enables simultaneous transcriptome measurement in a facile and affordable protocol. We demonstrate that barcoded self-reporting transposons recover in vitro binding sites for four basic helix-loop-helix transcription factors with important roles in cell fate specification: ASCL1, MYOD1, NEUROD2 and NGN1. Further, simultaneous calling cards and transcriptional profiling during transcription factor overexpression identified both binding sites and gene expression changes for two of these factors. Lastly, we demonstrated barcoded calling cards can record binding in vivo in the mouse brain. In sum, RNA-based identification of transcription factor binding sites and gene expression through barcoded self-reporting transposon calling cards and transcriptomes is an efficient and powerful method to infer gene regulatory networks in a population of cells.
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Affiliation(s)
- Matthew Lalli
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allen Yen
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Urvashi Thopte
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fengping Dong
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Arnav Moudgil
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Xuhua Chen
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Jeffrey Milbrandt
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robi D Mitra
- Department of Genetics, School of Medicine, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.,Edison Family Center for Genome Sciences and Systems Biology Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
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9
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Wang PY, Yang X, Guo L, Wang YW, Zhang WL, Sun YX, Li J, Gan CY, Long SY, Liu JJ, Fan SY, Huang AL, Hu JL. Establishment of a human cell line with a surface display system for screening and optimizing Na+-taurocholate cotransporting polypeptide-binding peptides. Front Microbiol 2022; 13:920280. [PMID: 36060770 PMCID: PMC9428559 DOI: 10.3389/fmicb.2022.920280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/05/2022] [Indexed: 11/26/2022] Open
Abstract
One of the most desirable targets for HBV medications is the sodium taurocholate cotransporting polypeptide (NTCP), an entry receptor for the hepatitis B virus (HBV). N-myristoylated preS1 2–48 (Myrcludex B or Hepcludex), an NTCP-binding peptide from the large surface protein of HBV, has been developed as the first-in-class entry inhibitor. However, its relatively large molecular weight contributes to increased immunogenicity and antibody production. As a result, it is preferable to look for an NTCP-binding peptide with a smaller size. To do this, we developed a human cell surface display strategy and screened peptides based on preS1-21. PreS1-21 (genotype D) was extended by 7 random amino acids and fused with mCherry and FasL transmembrane domain. The pooled constructs were transfected into HEK293 cells by using the transposon/transposase system to create a library displaying various peptides on the cell surface with red fluorescence. On the other hand, we expressed NTCP protein fused with EGFP on HEK293 and used the membrane lysate containing NTCP-GFP as the bait protein to select peptides with increased NTCP affinity. After 7 cycles of selection, the deep sequencing results revealed that some polypeptides were more than 1,000 times enriched. Further screening of the mostly enriched 10 peptides yields the peptide preS1-21-pep3. Replacing the preS1-21 sequence of preS1-21-pep3 with those from different genotypes demonstrated that the consensus sequence of genotype A–F had the best performance. The peptide (Myr-preS1-21-pep3) was synthesized and tested on the HepG2-NTCP cell model. The results showed that Myr-preS1-21-pep3 is approximately 10 times more potent than the initial peptide Myr-preS1-21 in preventing HBV infection. In conclusion, we developed a new strategy for screening peptides binding to membrane proteins and identified a new NTCP-binding peptide with a much smaller size than Hepcludex.
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Affiliation(s)
- Pei-yun Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xue Yang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Lin Guo
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yu-wei Wang
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
- Laboratory for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Wen-lu Zhang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yu-xue Sun
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jie Li
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Chun-yang Gan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shao-yuan Long
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jia-jun Liu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shu-ying Fan
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ai-long Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- *Correspondence: Ai-long Huang,
| | - Jie-Li Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- Jie-Li Hu,
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10
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Prommersberger S, Monjezi R, Botezatu L, Miskey C, Amberger M, Mestermann K, Hudecek M, Ivics Z. Generation of CAR-T Cells with Sleeping Beauty Transposon Gene Transfer. Methods Mol Biol 2022; 2521:41-66. [PMID: 35732992 DOI: 10.1007/978-1-0716-2441-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Human T lymphocytes that transgenically express a chimeric antigen receptor (CAR) have proven efficacy and safety in gene- and cell-based immunotherapy of certain hematological cancers. Appropriate gene vectors and methods of genetic engineering are required for therapeutic cell products to be biologically potent and their manufacturing to be economically viable. Transposon-based gene transfer satisfies these needs, and is currently being evaluated in clinical trials. In this protocol we describe the basic Sleeping Beauty (SB) transposon vector components required for stable gene integration in human cells, with special emphasis on minicircle DNA vectors and the use of synthetic mRNA. We provide a protocol for functional validation of the vector components in cultured human cell lines on the basis of fluorescent reporter gene expression. Finally, we provide a protocol for CAR-T cell engineering and describe assays that address transgene expression, biological potency and genomic vector copy numbers in polyclonal cell populations. Because transposons allow virus-free gene transfer with naked nucleic acids, the protocol can be adopted by any laboratory equipped with biological safety level S1 facilities.
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Affiliation(s)
| | - Razieh Monjezi
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | | | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | | | - Katrin Mestermann
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Michael Hudecek
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany.
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11
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Miskey C, Kesselring L, Querques I, Abrusán G, Barabas O, Ivics Z. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2807-2825. [PMID: 35188569 PMCID: PMC8934666 DOI: 10.1093/nar/gkac092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/14/2022] Open
Abstract
The Sleeping Beauty (SB) transposon system is a popular tool for genome engineering, but random integration into the genome carries a certain genotoxic risk in therapeutic applications. Here we investigate the role of amino acids H187, P247 and K248 in target site selection of the SB transposase. Structural modeling implicates these three amino acids located in positions analogous to amino acids with established functions in target site selection in retroviral integrases and transposases. Saturation mutagenesis of these residues in the SB transposase yielded variants with altered target site selection properties. Transposon integration profiling of several mutants reveals increased specificity of integrations into palindromic AT repeat target sequences in genomic regions characterized by high DNA bendability. The H187V and K248R mutants redirect integrations away from exons, transcriptional regulatory elements and nucleosomal DNA in the human genome, suggesting enhanced safety and thus utility of these SB variants in gene therapy applications.
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Affiliation(s)
| | | | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - György Abrusán
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Zoltán Ivics
- To whom correspondence should be addressed. Tel: +49 6103 77 6000; Fax: +49 6103 77 1280;
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12
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Sandoval-Villegas N, Nurieva W, Amberger M, Ivics Z. Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications of Sleeping Beauty, piggyBac and Tol2 for Genome Engineering. Int J Mol Sci 2021; 22:ijms22105084. [PMID: 34064900 PMCID: PMC8151067 DOI: 10.3390/ijms22105084] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/19/2023] Open
Abstract
Transposons are mobile genetic elements evolved to execute highly efficient integration of their genes into the genomes of their host cells. These natural DNA transfer vehicles have been harnessed as experimental tools for stably introducing a wide variety of foreign DNA sequences, including selectable marker genes, reporters, shRNA expression cassettes, mutagenic gene trap cassettes, and therapeutic gene constructs into the genomes of target cells in a regulated and highly efficient manner. Given that transposon components are typically supplied as naked nucleic acids (DNA and RNA) or recombinant protein, their use is simple, safe, and economically competitive. Thus, transposons enable several avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture comprising the generation of pluripotent stem cells, the production of germline-transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species and therapy of genetic disorders in humans. This review describes the molecular mechanisms involved in transposition reactions of the three most widely used transposon systems currently available (Sleeping Beauty, piggyBac, and Tol2), and discusses the various parameters and considerations pertinent to their experimental use, highlighting the state-of-the-art in transposon technology in diverse genetic applications.
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Affiliation(s)
| | | | | | - Zoltán Ivics
- Correspondence: ; Tel.: +49-6103-77-6000; Fax: +49-6103-77-1280
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13
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Ochmann MT, Ivics Z. Jumping Ahead with Sleeping Beauty: Mechanistic Insights into Cut-and-Paste Transposition. Viruses 2021; 13:v13010076. [PMID: 33429848 PMCID: PMC7827188 DOI: 10.3390/v13010076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/16/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Sleeping Beauty (SB) is a transposon system that has been widely used as a genetic engineering tool. Central to the development of any transposon as a research tool is the ability to integrate a foreign piece of DNA into the cellular genome. Driven by the need for efficient transposon-based gene vector systems, extensive studies have largely elucidated the molecular actors and actions taking place during SB transposition. Close transposon relatives and other recombination enzymes, including retroviral integrases, have served as useful models to infer functional information relevant to SB. Recently obtained structural data on the SB transposase enable a direct insight into the workings of this enzyme. These efforts cumulatively allowed the development of novel variants of SB that offer advanced possibilities for genetic engineering due to their hyperactivity, integration deficiency, or targeting capacity. However, many aspects of the process of transposition remain poorly understood and require further investigation. We anticipate that continued investigations into the structure-function relationships of SB transposition will enable the development of new generations of transposition-based vector systems, thereby facilitating the use of SB in preclinical studies and clinical trials.
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14
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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: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/29/2020] [Indexed: 12/13/2022]
Abstract
The Sleeping Beauty transposon system is a nonviral DNA transfer tool capable of efficiently mediating transposition-based, stable integration of DNA sequences of choice into eukaryotic genomes. Continuous refinements of the system, including the emergence of hyperactive transposase mutants and novel approaches in vectorology, greatly improve upon transposition efficiency rivaling viral-vector-based methods for stable gene insertion. Current developments, such as reversible transgenesis and proof-of-concept RNA-guided transposition, further expand on possible applications in the future. In addition, innate advantages such as lack of preferential integration into genes reduce insertional mutagenesis-related safety concerns while comparably low manufacturing costs enable widespread implementation. Accordingly, the system is recognized as a powerful and versatile tool for genetic engineering and is playing a central role in an ever-expanding number of gene and cell therapy clinical trials with the potential to become a key technology to meet the growing demand for advanced therapy medicinal products.
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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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15
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Rotiroti MC, Buracchi C, Arcangeli S, Galimberti S, Valsecchi MG, Perriello VM, Rasko T, Alberti G, Magnani CF, Cappuzzello C, Lundberg F, Pande A, Dastoli G, Introna M, Serafini M, Biagi E, Izsvák Z, Biondi A, Tettamanti S. Targeting CD33 in Chemoresistant AML Patient-Derived Xenografts by CAR-CIK Cells Modified with an Improved SB Transposon System. Mol Ther 2020; 28:1974-1986. [PMID: 32526203 DOI: 10.1016/j.ymthe.2020.05.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/31/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022] Open
Abstract
The successful implementation of chimeric antigen receptor (CAR)-T cell therapy in the clinical context of B cell malignancies has paved the way for further development in the more critical setting of acute myeloid leukemia (AML). Among the potentially targetable AML antigens, CD33 is insofar one of the main validated molecules. Here, we describe the feasibility of engineering cytokine-induced killer (CIK) cells with a CD33.CAR by using the latest optimized version of the non-viral Sleeping Beauty (SB) transposon system "SB100X-pT4." This offers the advantage of improving CAR expression on CIK cells, while reducing the amount of DNA transposase as compared to the previously employed "SB11-pT" version. SB-modified CD33.CAR-CIK cells exhibited significant antileukemic activity in vitro and in vivo in patient-derived AML xenograft models, reducing AML development when administered as an "early treatment" and delaying AML progression in mice with established disease. Notably, by exploiting an already optimized xenograft chemotherapy model that mimics human induction therapy in mice, we demonstrated for the first time that CD33.CAR-CIK cells are also effective toward chemotherapy resistant/residual AML cells, further supporting its future clinical development and implementation within the current standard regimens.
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Affiliation(s)
- Maria Caterina Rotiroti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Chiara Buracchi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Silvia Arcangeli
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Stefania Galimberti
- Center of Biostatistics for Clinical Epidemiology, School of Medicine and Surgery, University of Milano - Bicocca, 20900 Monza, Italy
| | - Maria Grazia Valsecchi
- Center of Biostatistics for Clinical Epidemiology, School of Medicine and Surgery, University of Milano - Bicocca, 20900 Monza, Italy
| | - Vincenzo Maria Perriello
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy; Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Tamas Rasko
- Max-Delbrück-Centrum für Molekulare Medizin in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Gaia Alberti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Chiara Francesca Magnani
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Claudia Cappuzzello
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Felix Lundberg
- Max-Delbrück-Centrum für Molekulare Medizin in the Helmholtz Association (MDC), 13125 Berlin, Germany; The Milner Centre for Evolution, University of Bath, BA2 7AY Bath, UK
| | - Amit Pande
- Max-Delbrück-Centrum für Molekulare Medizin in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Giuseppe Dastoli
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Martino Introna
- Center of Cellular Therapy "G. Lanzani," USC Ematologia ASST Papa Giovanni XXIII, 24124 Bergamo, Italy
| | - Marta Serafini
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Ettore Biagi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Zsuzsanna Izsvák
- Max-Delbrück-Centrum für Molekulare Medizin in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Andrea Biondi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy.
| | - Sarah Tettamanti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
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16
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Magnani CF, Tettamanti S, Alberti G, Pisani I, Biondi A, Serafini M, Gaipa G. Transposon-Based CAR T Cells in Acute Leukemias: Where are We Going? Cells 2020; 9:cells9061337. [PMID: 32471151 PMCID: PMC7349235 DOI: 10.3390/cells9061337] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 02/07/2023] Open
Abstract
Chimeric Antigen Receptor (CAR) T-cell therapy has become a new therapeutic reality for refractory and relapsed leukemia patients and is also emerging as a potential therapeutic option in solid tumors. Viral vector-based CAR T-cells initially drove these successful efforts; however, high costs and cumbersome manufacturing processes have limited the widespread clinical implementation of CAR T-cell therapy. Here we will discuss the state of the art of the transposon-based gene transfer and its application in CAR T immunotherapy, specifically focusing on the Sleeping Beauty (SB) transposon system, as a valid cost-effective and safe option as compared to the viral vector-based systems. A general overview of SB transposon system applications will be provided, with an update of major developments, current clinical trials achievements and future perspectives exploiting SB for CAR T-cell engineering. After the first clinical successes achieved in the context of B-cell neoplasms, we are now facing a new era and it is paramount to advance gene transfer technology to fully exploit the potential of CAR T-cells towards next-generation immunotherapy.
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17
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Kesselring L, Miskey C, Zuliani C, Querques I, Kapitonov V, Laukó A, Fehér A, Palazzo A, Diem T, Lustig J, Sebe A, Wang Y, Dinnyés A, Izsvák Z, Barabas O, Ivics Z. A single amino acid switch converts the Sleeping Beauty transposase into an efficient unidirectional excisionase with utility in stem cell reprogramming. Nucleic Acids Res 2020; 48:316-331. [PMID: 31777924 PMCID: PMC6943129 DOI: 10.1093/nar/gkz1119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022] Open
Abstract
The Sleeping Beauty (SB) transposon is an advanced tool for genetic engineering and a useful model to investigate cut-and-paste DNA transposition in vertebrate cells. Here, we identify novel SB transposase mutants that display efficient and canonical excision but practically unmeasurable genomic re-integration. Based on phylogenetic analyses, we establish compensating amino acid replacements that fully rescue the integration defect of these mutants, suggesting epistasis between these amino acid residues. We further show that the transposons excised by the exc+/int− transposase mutants form extrachromosomal circles that cannot undergo a further round of transposition, thereby representing dead-end products of the excision reaction. Finally, we demonstrate the utility of the exc+/int− transposase in cassette removal for the generation of reprogramming factor-free induced pluripotent stem cells. Lack of genomic integration and formation of transposon circles following excision is reminiscent of signal sequence removal during V(D)J recombination, and implies that cut-and-paste DNA transposition can be converted to a unidirectional process by a single amino acid change.
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Affiliation(s)
- Lisa Kesselring
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Vladimir Kapitonov
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | | | - Anita Fehér
- BioTalentum Ltd, Gödöllő, 2100 Gödöllő, Hungary
| | - Antonio Palazzo
- Department of Biology, University of Bari 'Aldo Moro', Italy
| | - Tanja Diem
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Janna Lustig
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Attila Sebe
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Yongming Wang
- Mobile DNA, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Zsuzsanna Izsvák
- Mobile DNA, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
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18
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Kovač A, Miskey C, Menzel M, Grueso E, Gogol-Döring A, Ivics Z. RNA-guided retargeting of S leeping Beauty transposition in human cells. eLife 2020; 9:e53868. [PMID: 32142408 PMCID: PMC7077980 DOI: 10.7554/elife.53868] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
An ideal tool for gene therapy would enable efficient gene integration at predetermined sites in the human genome. Here we demonstrate biased genome-wide integration of the Sleeping Beauty (SB) transposon by combining it with components of the CRISPR/Cas9 system. We provide proof-of-concept that it is possible to influence the target site selection of SB by fusing it to a catalytically inactive Cas9 (dCas9) and by providing a single guide RNA (sgRNA) against the human Alu retrotransposon. Enrichment of transposon integrations was dependent on the sgRNA, and occurred in an asymmetric pattern with a bias towards sites in a relatively narrow, 300 bp window downstream of the sgRNA targets. Our data indicate that the targeting mechanism specified by CRISPR/Cas9 forces integration into genomic regions that are otherwise poor targets for SB transposition. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.
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Affiliation(s)
- Adrian Kovač
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Esther Grueso
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
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19
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Guimaraes-Young A, Feddersen CR, Dupuy AJ. Sleeping Beauty Mouse Models of Cancer: Microenvironmental Influences on Cancer Genetics. Front Oncol 2019; 9:611. [PMID: 31338332 PMCID: PMC6629774 DOI: 10.3389/fonc.2019.00611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
The Sleeping Beauty (SB) transposon insertional mutagenesis system offers a streamlined approach to identify genetic drivers of cancer. With a relatively random insertion profile, SB is uniquely positioned for conducting unbiased forward genetic screens. Indeed, SB mouse models of cancer have revealed insights into the genetics of tumorigenesis. In this review, we highlight experiments that have exploited the SB system to interrogate the genetics of cancer in distinct biological contexts. We also propose experimental designs that could further our understanding of the relationship between tumor microenvironment and tumor progression.
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Affiliation(s)
- Amy Guimaraes-Young
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Charlotte R Feddersen
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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Hodge R, Narayanavari SA, Izsvák Z, Ivics Z. Wide Awake and Ready to Move: 20 Years of Non-Viral Therapeutic Genome Engineering with the Sleeping Beauty Transposon System. Hum Gene Ther 2018; 28:842-855. [PMID: 28870121 DOI: 10.1089/hum.2017.130] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene therapies will only become a widespread tool in the clinical treatment of human diseases with the advent of gene transfer vectors that integrate genetic information stably, safely, effectively, and economically. Two decades after the discovery of the Sleeping Beauty (SB) transposon, it has been transformed into a vector system that is fulfilling these requirements. SB may well overcome some of the limitations associated with viral gene transfer vectors and transient non-viral gene delivery approaches that are being used in the majority of ongoing clinical trials. The SB system has achieved a high level of stable gene transfer and sustained transgene expression in multiple primary human somatic cell types, representing crucial steps that may permit its clinical use in the near future. This article reviews the most important aspects of SB as a tool for gene therapy, including aspects of its vectorization and genomic integration. As an illustration, the clinical development of the SB system toward gene therapy of age-related macular degeneration and cancer immunotherapy is highlighted.
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Affiliation(s)
- Russ Hodge
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin, Germany
| | - Suneel A Narayanavari
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin, Germany
| | - Zsuzsanna Izsvák
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin, Germany
| | - Zoltán Ivics
- 2 Division of Medical Biotechnology, Paul Ehrlich Institute , Langen, Germany
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21
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Guo Y, Zhang Y, Hu K. Sleeping Beauty transposon integrates into non-TA dinucleotides. Mob DNA 2018; 9:8. [PMID: 29445422 PMCID: PMC5801840 DOI: 10.1186/s13100-018-0113-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/30/2018] [Indexed: 12/16/2022] Open
Abstract
Background Sleeping Beauty transposon (SB) has become an increasingly important genetic tool for generating mutations in vertebrate cells. It is widely thought that SB exclusively integrates into TA dinucleotides. However, this strict TA-preference has not been rigorously tested in large numbers of insertion sites that now can be detected with next generation sequencing. Li et al. found 71 SB insertions in non-TA dinucleotides in 2013, suggesting that TA dinucleotides are not the only sites of SB integration, yet further studies on this topic have not been carried out. Results In this study, we re-analyzed 600 million pairs of Illumina sequence reads from a high-throughput SB mutagenesis screen and identified 28 thousand SB insertions in non-TA sites. We recovered some of these non-TA sites using PCR and confirmed that at least a subset of the insertions at non-TA sites are real integrations. The consensus sequence of these non-TA sites shows an asymmetric pattern distinct from the symmetric pattern of the canonical TA sites. Perfect similarity between the downstream flanking sequence and SB transposon ends indicates there may be interaction between the transposon DNA binding domain of transposase and the target DNA. Conclusion The TA-preference of SB transposon is not as strict as what people had thought. And the SB integrations at non-TA sites might be guided by the interaction between the transposon DNA binding domain of SB transposase and the target DNA. Electronic supplementary material The online version of this article (10.1186/s13100-018-0113-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yabin Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120 China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120 China
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120 China
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22
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Kebriaei P, Izsvák Z, Narayanavari SA, Singh H, Ivics Z. Gene Therapy with the Sleeping Beauty Transposon System. Trends Genet 2017; 33:852-870. [PMID: 28964527 DOI: 10.1016/j.tig.2017.08.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/24/2017] [Accepted: 08/31/2017] [Indexed: 11/16/2022]
Abstract
The widespread clinical implementation of gene therapy requires the ability to stably integrate genetic information through gene transfer vectors in a safe, effective, and economical 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 nonviral gene delivery approaches that are prevalent in ongoing clinical trials. 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 the most important aspects of using SB for gene therapy, including vectorization as well as genomic integration features. We also illustrate the path to successful clinical implementation by highlighting the application of chimeric antigen receptor (CAR)-modified T cells in cancer immunotherapy.
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Affiliation(s)
- Partow Kebriaei
- Department of Stem Cell Transplant and Cellular Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Zsuzsanna Izsvák
- Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Suneel A Narayanavari
- Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Harjeet Singh
- Department of Pediatrics, MD Anderson Cancer Center, Houston, TX, USA
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany.
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23
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Römer C, Singh M, Hurst LD, Izsvák Z. How to tame an endogenous retrovirus: HERVH and the evolution of human pluripotency. Curr Opin Virol 2017; 25:49-58. [PMID: 28750248 DOI: 10.1016/j.coviro.2017.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/13/2017] [Accepted: 07/03/2017] [Indexed: 12/18/2022]
Abstract
HERVH is one of the most successful endogenous retrovirus in the human genome. Relative to other endogenous retroviruses, slower degradation of HERVH internal sequences indicates their potential relevance for the host. HERVH is transcriptionally active during human preimplantation embryogenesis. In this review, we focus on the role of HERVH in regulating human pluripotency. The HERVH-mediated pluripotency network has been evolved recently in primates. Nevertheless, it became an essential feature of human pluripotency. We discuss how HERVH modulates the human pluripotency network by providing alternative transcription factor binding sites, functioning as a long-range enhancer, and as being a major source for pluripotency specific long non-coding RNAs and chimeric transcripts.
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Affiliation(s)
- Christine Römer
- Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Manvendra Singh
- Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Laurence D Hurst
- Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Zsuzsanna Izsvák
- Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
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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: 60] [Impact Index Per Article: 8.6] [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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25
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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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