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Diaby M, Wu H, Gao B, Shi S, Wang B, Wang S, Wang Y, Wu Z, Chen C, Wang X, Song C. A Naturally Active Spy Transposon Discovered from the Insect Genome of Colletes gigas as a Promising Novel Gene Transfer Tool. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400969. [PMID: 38774947 PMCID: PMC11304231 DOI: 10.1002/advs.202400969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/09/2024] [Indexed: 08/09/2024]
Abstract
Novel active DNA transposons, such as Spy transposons from the PHIS superfamily, are identified through bioinformatics in this study. The native transposases cgSpy and cvSpy displayed transposition activities of approximately 85% and 35% compared to the hyperactive piggyBac transposase (hyPB). The cgSpy transposon showed unique characteristics, including a lack of overproduction inhibition and reduced efficiency for insertion sizes between 3.1 to 8.5 kb. Integration preferences of cgSpy are found in genes and regulatory regions, making it suitable for genetic manipulation. Evaluation in T-cell engineering demonstrated that cgSpy-mediated chimeric antigen receptor (CAR) modification is comparable to the PB system, indicating its potential utility in cell therapy. This study unveils the promising application of the active native transposase, Spy, from Colletes gigas, as a valuable tool for genetic engineering, particularly in T-cell manipulation.
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Affiliation(s)
- Mohamed Diaby
- College of Animal Science & TechnologyYangzhou UniversityYangzhouJiangsu225009China
| | - Han Wu
- School of Basic Medical SciencesShenzhen University Medical SchoolShenzhen UniversityShenzhenGuangdong518055China
| | - Bo Gao
- College of Animal Science & TechnologyYangzhou UniversityYangzhouJiangsu225009China
| | - Shasha Shi
- College of Animal Science & TechnologyYangzhou UniversityYangzhouJiangsu225009China
| | - Bingqing Wang
- College of Animal Science & TechnologyYangzhou UniversityYangzhouJiangsu225009China
| | - Saisai Wang
- College of Animal Science & TechnologyYangzhou UniversityYangzhouJiangsu225009China
| | - Yali Wang
- College of Animal Science & TechnologyYangzhou UniversityYangzhouJiangsu225009China
| | - Zherui Wu
- School of Basic Medical SciencesShenzhen University Medical SchoolShenzhen UniversityShenzhenGuangdong518055China
| | - Cai Chen
- College of Animal Science & TechnologyYangzhou UniversityYangzhouJiangsu225009China
| | - Xiaoyan Wang
- College of Animal Science & TechnologyYangzhou UniversityYangzhouJiangsu225009China
| | - Chengyi Song
- College of Animal Science & TechnologyYangzhou UniversityYangzhouJiangsu225009China
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2
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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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Metanat Y, Viktor P, Amajd A, Kaur I, Hamed AM, Abed Al-Abadi NK, Alwan NH, Chaitanya MVNL, Lakshmaiya N, Ghildiyal P, Khalaf OM, Ciongradi CI, Sârbu I. The paths toward non-viral CAR-T cell manufacturing: A comprehensive review of state-of-the-art methods. Life Sci 2024; 348:122683. [PMID: 38702027 DOI: 10.1016/j.lfs.2024.122683] [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: 01/24/2024] [Revised: 04/11/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Although CAR-T cell therapy has emerged as a game-changer in cancer immunotherapy several bottlenecks limit its widespread use as a front-line therapy. Current protocols for the production of CAR-T cells rely mainly on the use of lentiviral/retroviral vectors. Nevertheless, according to the safety concerns around the use of viral vectors, there are several regulatory hurdles to their clinical use. Large-scale production of viral vectors under "Current Good Manufacturing Practice" (cGMP) involves rigorous quality control assessments and regulatory requirements that impose exorbitant costs on suppliers and as a result, lead to a significant increase in the cost of treatment. Pursuing an efficient non-viral method for genetic modification of immune cells is a hot topic in cell-based gene therapy. This study aims to investigate the current state-of-the-art in non-viral methods of CAR-T cell manufacturing. In the first part of this study, after reviewing the advantages and disadvantages of the clinical use of viral vectors, different non-viral vectors and the path of their clinical translation are discussed. These vectors include transposons (sleeping beauty, piggyBac, Tol2, and Tc Buster), programmable nucleases (ZFNs, TALENs, and CRISPR/Cas9), mRNA, plasmids, minicircles, and nanoplasmids. Afterward, various methods for efficient delivery of non-viral vectors into the cells are reviewed.
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Affiliation(s)
- Yekta Metanat
- Faculty of Medicine, Zahedan University of Medical Sciences, Sistan and Baluchestan Province, Iran
| | - Patrik Viktor
- Óbuda University, Karoly Keleti faculty, Tavaszmező u. 15-17, H-1084 Budapest, Hungary
| | - Ayesha Amajd
- Faculty of Transport and Aviation Engineering, Silesian University of Technology, Krasińskiego 8 Street, 40-019 Katowice, Poland
| | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bangalore, Karnataka, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan-303012, India
| | | | | | | | - M V N L Chaitanya
- School of pharmaceutical sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab - 144411, India
| | | | - Pallavi Ghildiyal
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | | | - Carmen Iulia Ciongradi
- 2nd Department of Surgery-Pediatric Surgery and Orthopedics, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iași, Romania.
| | - Ioan Sârbu
- 2nd Department of Surgery-Pediatric Surgery and Orthopedics, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iași, Romania.
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4
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Skeate JG, Pomeroy EJ, Slipek NJ, Jones BJ, Wick BJ, Chang JW, Lahr WS, Stelljes EM, Patrinostro X, Barnes B, Zarecki T, Krueger JB, Bridge JE, Robbins GM, McCormick MD, Leerar JR, Wenzel KT, Hornberger KM, Walker K, Smedley D, Largaespada DA, Otto N, Webber BR, Moriarity BS. Evolution of the clinical-stage hyperactive TcBuster transposase as a platform for robust non-viral production of adoptive cellular therapies. Mol Ther 2024; 32:1817-1834. [PMID: 38627969 PMCID: PMC11184336 DOI: 10.1016/j.ymthe.2024.04.024] [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: 08/31/2023] [Revised: 03/06/2024] [Accepted: 04/12/2024] [Indexed: 06/09/2024] Open
Abstract
Cellular therapies for the treatment of human diseases, such as chimeric antigen receptor (CAR) T and natural killer (NK) cells have shown remarkable clinical efficacy in treating hematological malignancies; however, current methods mainly utilize viral vectors that are limited by their cargo size capacities, high cost, and long timelines for production of clinical reagent. Delivery of genetic cargo via DNA transposon engineering is a more timely and cost-effective approach, yet has been held back by less efficient integration rates. Here, we report the development of a novel hyperactive TcBuster (TcB-M) transposase engineered through structure-guided and in vitro evolution approaches that achieves high-efficiency integration of large, multicistronic CAR-expression cassettes in primary human cells. Our proof-of-principle TcB-M engineering of CAR-NK and CAR-T cells shows low integrated vector copy number, a safe insertion site profile, robust in vitro function, and improves survival in a Burkitt lymphoma xenograft model in vivo. Overall, TcB-M is a versatile, safe, efficient and open-source option for the rapid manufacture and preclinical testing of primary human immune cell therapies through delivery of multicistronic large cargo via transposition.
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Affiliation(s)
- Joseph G Skeate
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Bryce J Wick
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jae-Woong Chang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Erin M Stelljes
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | - Joshua B Krueger
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jacob E Bridge
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gabrielle M Robbins
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Madeline D McCormick
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | | | | | - David A Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Neil Otto
- Bio-Techne, Minneapolis, MN 55413, USA
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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5
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Marie C, Scherman D. Antibiotic-Free Gene Vectors: A 25-Year Journey to Clinical Trials. Genes (Basel) 2024; 15:261. [PMID: 38540320 PMCID: PMC10970329 DOI: 10.3390/genes15030261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 06/15/2024] Open
Abstract
Until very recently, the major use, for gene therapy, specifically of linear or circular DNA, such as plasmids, was as ancillary products for viral vectors' production or as a genetic template for mRNA production. Thanks to targeted and more efficient physical or chemical delivery techniques and to the refinement of their structure, non-viral plasmid DNA are now under intensive consideration as pharmaceutical drugs. Plasmids traditionally carry an antibiotic resistance gene for providing the selection pressure necessary for maintenance in a bacterial host. Nearly a dozen different antibiotic-free gene vectors have now been developed and are currently assessed in preclinical assays and phase I/II clinical trials. Their reduced size leads to increased transfection efficiency and prolonged transgene expression. In addition, associating non-viral gene vectors and DNA transposons, which mediate transgene integration into the host genome, circumvents plasmid dilution in dividing eukaryotic cells which generate a loss of the therapeutic gene. Combining these novel molecular tools allowed a significantly higher yield of genetically engineered T and Natural Killer cells for adoptive immunotherapies due to a reduced cytotoxicity and increased transposition rate. This review describes the main progresses accomplished for safer, more efficient and cost-effective gene and cell therapies using non-viral approaches and antibiotic-free gene vectors.
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Affiliation(s)
- Corinne Marie
- Université Paris Cité, CNRS, Inserm, UTCBS, 75006 Paris, France;
- Chimie ParisTech, Université PSL, 75005 Paris, France
| | - Daniel Scherman
- Université Paris Cité, CNRS, Inserm, UTCBS, 75006 Paris, France;
- Fondation Maladies Rares, 75014 Paris, France
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Bexte T, Reindl LM, Ullrich E. Nonviral technologies can pave the way for CAR-NK cell therapy. J Leukoc Biol 2023; 114:475-486. [PMID: 37403203 DOI: 10.1093/jleuko/qiad074] [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: 12/03/2022] [Revised: 05/25/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
Natural killer cells are a promising platform for cancer immunotherapy. Natural killer cells have high intrinsic killing capability, and the insertion of a chimeric antigen receptor can further enhance their antitumor potential. In first-in-human trials, chimeric antigen receptor-natural killer cells demonstrated strong clinical activity without therapy-induced side effects. The applicability of natural killer cells as an "off-the-shelf" product makes them highly attractive for gene-engineered cell therapies. Traditionally, viral transduction has been used for gene editing; however, the use of viral vectors remains a safety concern and is associated with high costs and regulatory requirements. Here, we review the current landscape of nonviral approaches for chimeric antigen receptor-natural killer cell generation. This includes transfection of vector particles and electroporation of mRNA and DNA vectors, resulting in transient modification and chimeric antigen receptor expression. In addition, using nonviral transposon technologies, natural killer cells can be stably modified ensuring long-lasting chimeric antigen receptor expression. Finally, we discuss CRISPR/Cas9 tools to edit key genes for natural killer cell functionality.
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Affiliation(s)
- Tobias Bexte
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
- University Cancer Center (UCT), Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Lisa Marie Reindl
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
| | - Evelyn Ullrich
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
- University Cancer Center (UCT), Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Frankfurt/Mainz; Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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7
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Zhu EY, Schillo JL, Murray SD, Riordan JD, Dupuy AJ. Understanding cancer drug resistance with Sleeping Beauty functional genomic screens: Application to MAPK inhibition in cutaneous melanoma. iScience 2023; 26:107805. [PMID: 37860756 PMCID: PMC10582486 DOI: 10.1016/j.isci.2023.107805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/10/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023] Open
Abstract
Combined BRAF and MEK inhibition is an effective treatment for BRAF-mutant cutaneous melanoma. However, most patients progress on this treatment due to drug resistance. Here, we applied the Sleeping Beauty transposon system to understand how melanoma evades MAPK inhibition. We found that the specific drug resistance mechanisms differed across melanomas in our genetic screens of five cutaneous melanoma cell lines. While drivers that reactivated MAPK were highly conserved, many others were cell-line specific. One such driver, VAV1, activated a de-differentiated transcriptional program like that of hyperactive RAC1, RAC1P29S. To target this mechanism, we showed that an inhibitor of SRC, saracatinib, blunts the VAV1-induced transcriptional reprogramming. Overall, we highlighted the importance of accounting for melanoma heterogeneity in treating cutaneous melanoma with MAPK inhibitors. Moreover, we demonstrated the utility of the Sleeping Beauty transposon system in understanding cancer drug resistance.
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Affiliation(s)
- Eliot Y. Zhu
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jacob L. Schillo
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Sarina D. Murray
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jesse D. Riordan
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
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8
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Zapater LJ, Rodriguez-Fos E, Planas-Felix M, Lewis S, Cameron D, Demarest P, Nabila A, Zhao J, Bergin P, Reed C, Yamada M, Pagnozzi A, Nava C, Bourel-Ponchel E, Neilson DE, Dursun A, Özgül RK, Akar HT, Socci ND, Hayes M, Rabadan R, Torrents D, Kruer MC, Toth M, Kentsis A. A transposase-derived gene required for human brain development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538770. [PMID: 37163102 PMCID: PMC10168387 DOI: 10.1101/2023.04.28.538770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA transposable elements and transposase-derived genes are present in most living organisms, including vertebrates, but their function is largely unknown. PiggyBac Transposable Element Derived 5 (PGBD5) is an evolutionarily conserved vertebrate DNA transposase-derived gene with retained nuclease activity in cells. Vertebrate brain development is known to be associated with prominent neuronal cell death and DNA breaks, but their causes and functions are not well understood. Here, we show that PGBD5 contributes to normal brain development in mice and humans, where its deficiency causes disorder of intellectual disability, movement and seizures. In mice, Pgbd5 is required for the developmental induction of post-mitotic DNA breaks and recurrent somatic genome rearrangements in neurons. Together, these studies nominate PGBD5 as the long-hypothesized neuronal DNA nuclease required for brain function in mammals.
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Affiliation(s)
- Luz Jubierre Zapater
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center; New York, United States, 10021
| | | | | | - Sara Lewis
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children’s Hospital and Departments of Child Health, Neurology, Genetics and Cellular & Molecular Medicine, Phoenix, AZ
| | - Daniel Cameron
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center; New York, United States, 10021
| | - Phillip Demarest
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
| | - Anika Nabila
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10021
| | - Junfei Zhao
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY
| | - Paul Bergin
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10021
| | - Casie Reed
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
| | - Makiko Yamada
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center; New York, United States, 10021
| | - Alex Pagnozzi
- CSIRO Health and Biosecurity, The Australian e-Health Research Centre, Brisbane, Australia
| | - Caroline Nava
- Assistance Publique-Hôpitaux de Paris, Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Emilie Bourel-Ponchel
- Research Group on Multimodal Analysis of Brain Function, University of Picardie Jules Verne, France
- Pediatric Neurophysiology Unit, Amiens Picardie University Hospital, France
| | | | - Ali Dursun
- Hacettepe University, Faculty of Medicine & Institute of Child Health, Department of Pediatric Metabolism, Ankara, Turkey
| | - R. Köksal Özgül
- Hacettepe University, Faculty of Medicine & Institute of Child Health, Department of Pediatric Metabolism, Ankara, Turkey
| | - Halil Tuna Akar
- Hacettepe University, Faculty of Medicine & Institute of Child Health, Department of Pediatric Metabolism, Ankara, Turkey
| | - Nicholas D. Socci
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
| | - Matthew Hayes
- Department of Physics and Computer Science, Xavier University of Louisiana, New Orleans, LA
| | - Raul Rabadan
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain, 08034
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Miklos Toth
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10021
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center; New York, United States, 10021
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10021
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University; New York, United States
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9
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Wang S, Gao B, Miskey C, Guan Z, Sang Y, Chen C, Wang X, Ivics Z, Song C. Passer, a highly active transposon from a fish genome, as a potential new robust genetic manipulation tool. Nucleic Acids Res 2023; 51:1843-1858. [PMID: 36688327 PMCID: PMC9976928 DOI: 10.1093/nar/gkad005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
The discovery of new, active DNA transposons can expand the range of genetic tools and provide more options for genomic manipulation. In this study, a bioinformatics analysis suggested that Passer (PS) transposons, which are members of the pogo superfamily, show signs of recent and current activity in animals and may be active in some species. Cell-based transposition assays revealed that the native PS transposases from Gasterosteus aculeatus and Danio rerio displayed very high activity in human cells relative to the Sleeping Beauty transposon. A typical overproduction inhibition phenomenon was observed for PS, and transposition capacity was decreased by ∼12% with each kilobase increase in the insertion size. Furthermore, PS exhibited a pronounced integration preference for genes and their transcriptional regulatory regions. We further show that two domesticated human proteins derived from PS transposases have lost their transposition activity. Overall, PS may represent an alternative with a potentially efficient genetic manipulation tool for transgenesis and mutagenesis applications.
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Affiliation(s)
- Saisai Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, D-63225 Langen, Germany
| | - Zhongxia Guan
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, D-63225 Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
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10
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Genomic Structure, Protein Character, Phylogenic Implication, and Embryonic Expression Pattern of a Zebrafish New Member of Zinc Finger BED-Type Gene Family. Genes (Basel) 2023; 14:genes14010179. [PMID: 36672921 PMCID: PMC9859435 DOI: 10.3390/genes14010179] [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: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
We reported a new member of the C2H2-zinc-finger BED-type (ZBED) protein family found in zebrafish (Danio rerio). It was previously assigned as an uncharacterized protein LOC569044 encoded by the Zgc:161969 gene, the transcripts of which were highly expressed in the CNS after the spinal cord injury of zebrafish. As such, this novel gene deserves a more detailed investigation. The 2.79-kb Zgc:161969 gene contains one intron located on Chromosome 6 at 16,468,776-16,475,879 in the zebrafish genome encoding a 630-aa protein LOC569044. This protein is composed of a DNA-binding BED domain, which is highly conserved among the ZBED protein family, and a catalytic domain consisting of an α-helix structure and an hAT dimerization region. Phylogenetic analysis revealed the LOC569044 protein to be clustered into the monophyletic clade of the ZBED protein family of golden fish. Specifically, the LOC569044 protein was classified as closely related to the monophyletic clades of zebrafish ZBED4-like isoforms and ZBED isoform 2. Furthermore, Zgc:161969 transcripts represented maternal inheritance, expressed in the brain and eyes at early developmental stages and in the telencephalon ventricular zone at late developmental stages. After characterizing the LOC569044 protein encoded by the Zgc:161969 gene, it was identified as a new member of the zebrafish ZBED protein family, named the ZBEDX protein.
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11
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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: 10] [Impact Index Per Article: 5.0] [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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12
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Concurrent transposon engineering and CRISPR/Cas9 genome editing of primary CLL-1 chimeric antigen receptor–natural killer cells. Cytotherapy 2022; 24:1087-1094. [DOI: 10.1016/j.jcyt.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/06/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022]
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13
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Beckermann TM, Luo W, Wilson CM, Veach RA, Wilson MH. Cognate restriction of transposition by piggyBac-like proteins. Nucleic Acids Res 2021; 49:8135-8144. [PMID: 34232995 DOI: 10.1093/nar/gkab578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/16/2021] [Accepted: 06/26/2021] [Indexed: 11/14/2022] Open
Abstract
Mobile genetic elements have been harnessed for gene transfer for a wide variety of applications including generation of stable cell lines, recombinant protein production, creation of transgenic animals, and engineering cell and gene therapy products. The piggyBac transposon family includes transposase or transposase-like proteins from a variety of species including insect, bat and human. Recently, human piggyBac transposable element derived 5 (PGBD5) protein was reported to be able to transpose piggyBac transposons in human cells raising possible safety concerns for piggyBac-mediated gene transfer applications. We evaluated three piggyBac-like proteins across species including piggyBac (insect), piggyBat (bat) and PGBD5 (human) for their ability to mobilize piggyBac transposons in human cells. We observed a lack of cross-species transposition activity. piggyBac and piggyBat activity was restricted to their cognate transposons. PGBD5 was unable to mobilize piggyBac transposons based on excision, colony count and plasmid rescue analysis, and it was unable to bind piggyBac terminal repeats. Within the piggyBac family, we observed a lack of cross-species activity and found that PGBD5 was unable to bind, excise or integrate piggyBac transposons in human cells. Transposition activity appears restricted within species within the piggyBac family of mobile genetic elements.
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Affiliation(s)
- Thomas M Beckermann
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA
| | - Wentian Luo
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA
| | - Catherine M Wilson
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ruth Ann Veach
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA
| | - Matthew H Wilson
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Veterans Affairs, Tennessee Valley Health Services, Nashville, TN 37212, USA.,Departments of Pharmacology and Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
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14
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Robbins GM, Wang M, Pomeroy EJ, Moriarity BS. Nonviral genome engineering of natural killer cells. Stem Cell Res Ther 2021; 12:350. [PMID: 34134774 PMCID: PMC8207670 DOI: 10.1186/s13287-021-02406-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/21/2021] [Indexed: 12/02/2022] Open
Abstract
Natural killer (NK) cells are cytotoxic lymphocytes of the innate immune system capable of immune surveillance. Given their ability to rapidly and effectively recognize and kill aberrant cells, especially transformed cells, NK cells represent a unique cell type to genetically engineer to improve its potential as a cell-based therapy. NK cells do not express a T cell receptor and thus do not contribute to graft-versus-host disease, nor do they induce T cell-driven cytokine storms, making them highly suited as an off-the-shelf cellular therapy. The clinical efficacy of NK cell-based therapies has been hindered by limited in vivo persistence and the immunosuppressive tumor microenvironment characteristic of many cancers. Enhancing NK cell resistance to tumor inhibitory signaling through genome engineering has the potential to improve NK cell persistence in the tumor microenvironment and restore cytotoxic functions. Alongside silencing NK cell inhibitory receptors, NK cell killing can be redirected by the integration of chimeric antigen receptors (CARs). However, NK cells are associated with technical and biological challenges not observed in T cells, typically resulting in low genome editing efficiencies. Viral vectors have achieved the greatest gene transfer efficiencies but carry concerns of random, insertional mutagenesis given the high viral titers necessary. As such, this review focuses on nonviral methods of gene transfer within the context of improving cancer immunotherapy using engineered NK cells.
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Affiliation(s)
- Gabrielle M Robbins
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.,College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, 55455, USA
| | - Minjing Wang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA. .,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA. .,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
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15
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Schrevens S, Sanglard D. Hijacking Transposable Elements for Saturation Mutagenesis in Fungi. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:633876. [PMID: 37744130 PMCID: PMC10512250 DOI: 10.3389/ffunb.2021.633876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 09/26/2023]
Abstract
Transposable elements are present in almost all known genomes, these endogenous transposons have recently been referred to as the mobilome. They are now increasingly used in research in order to make extensive mutant libraries in different organisms. Fungi are an essential part of our lives on earth, they influence the availability of our food and they live inside our own bodies both as commensals and pathogenic organisms. Only few fungal species have been studied extensively, mainly due to the lack of appropriate molecular genetic tools. The use of transposon insertion libraries can however help to rapidly advance our knowledge of (conditional) essential genes, compensatory mutations and drug target identification in fungi. Here we give an overview of some recent developments in the use of different transposons for saturation mutagenesis in different fungi.
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Affiliation(s)
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
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16
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Functional analysis of the catalytic triad of the hAT-family transposase TcBuster. Plasmid 2021; 114:102554. [PMID: 33476638 DOI: 10.1016/j.plasmid.2021.102554] [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: 09/29/2020] [Revised: 11/16/2020] [Accepted: 11/25/2020] [Indexed: 11/23/2022]
Abstract
TcBuster is a hAT-family DNA transposon from the red flour beetle, Tribolium castaneum. The TcBuster transposase is of interest for genome engineering as it is highly active in insect and mammalian cells. To test the predicted catalytic triad of TcBuster, each residue of the catalytic triad of a haemagglutinin-tagged TcBuster transposase was individually mutated to a structurally conserved amino acid. Using a drug-resistant colony assay for transposon integration, we found that the D223N, D289N, and E589Q mutants of TcBuster transposase were inactive in human cells. We used a modified chromatin immunoprecipitation assay to determine that each mutant maintained binding to TcBuster transposon inverted repeat elements. Although the catalytic mutants retained their transposon binding properties, mutants displayed altered expression and localization in human cells. None of the catalytic mutants formed characteristic TcBuster transposase rodlet structures, and the D223N and D289N mutants were not able to be detected by immunofluorescence microscopy. Immunoblot analysis demonstrated that the E589Q mutant is less abundant than wild-type TcBuster transposase. Cells transfected with either TcBuster or TcBuster-E589Q transposase were imaged by structured illumination microscopy to quantify differences in the length of the transposase rodlets. The average length of the TcBuster transposase rodlets (N = 39) was 3.284 μm while the E589Q rodlets (N = 33) averaged 1.157 μm (p < 0.0001; t-test). The catalytic triad mutations decreased overall protein levels and disrupted transposase rodlet formation while nuclear localization and DNA binding to the inverted repeat elements were maintained. Our results may have broader implications for the overproduction inhibition phenomenon observed for DNA transposons.
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17
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Helou L, Beauclair L, Dardente H, Arensburger P, Buisine N, Jaszczyszyn Y, Guillou F, Lecomte T, Kentsis A, Bigot Y. The C-terminal Domain of piggyBac Transposase Is Not Required for DNA Transposition. J Mol Biol 2021; 433:166805. [PMID: 33450253 DOI: 10.1016/j.jmb.2020.166805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/29/2020] [Indexed: 12/21/2022]
Abstract
PiggyBac(PB)-like elements (pble) are members of a eukaryotic DNA transposon family. This family is of interest to evolutionary genomics because pble transposases have been domesticated at least 9 times in vertebrates. The amino acid sequence of pble transposases can be split into three regions: an acidic N-terminal domain (~100 aa), a central domain (~400 aa) containing a DD[D/E] catalytic triad, and a cysteine-rich domain (CRD; ~90 aa). Two recent reports suggested that a functional CRD is required for pble transposase activity. Here we found that two CRD-deficient pble transposases, a PB variant and an isoform encoded by the domesticated PB-derived vertebrate transposase gene 5 (pgbd5) trigger transposition of the Ifp2 pble. When overexpressed in HeLa cells, these CRD-deficient transposases can insert Ifp2 elements with proper and improper transposon ends, associated with deleterious effects on cells. Finally, we found that mouse CRD-deficient transposase Pgbd5, as well as PB, do not insert pbles at random into chromosomes. Transposition events occurred more often in genic regions, in the neighbourhood of the transcription start sites and were often found in genes predominantly expressed in the human central nervous system.
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Affiliation(s)
- Laura Helou
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Linda Beauclair
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Hugues Dardente
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | - Peter Arensburger
- Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, USA
| | - Nicolas Buisine
- UMR CNRS 7221, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Florian Guillou
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France
| | | | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, Cornell University, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yves Bigot
- PRC, UMR INRAE 0085, CNRS 7247, Centre INRAE Val de Loire, 37380 Nouzilly, France.
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18
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Blommaert J. Genome size evolution: towards new model systems for old questions. Proc Biol Sci 2020; 287:20201441. [PMID: 32842932 PMCID: PMC7482279 DOI: 10.1098/rspb.2020.1441] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
Genome size (GS) variation is a fundamental biological characteristic; however, its evolutionary causes and consequences are the topic of ongoing debate. Whether GS is a neutral trait or one subject to selective pressures, and how strong these selective pressures are, may remain open questions. Fundamentally, the genomic sequences responsible for this variation directly impact the potential evolutionary outcomes and, equally, are the targets of different evolutionary pressures. For example, duplications and deletions of genic regions (large or small) can have immediate and drastic phenotypic effects, while an expansion or contraction of non-coding DNA is less likely to cause catastrophic phenotypic effects. However, in the long term, the accumulation or deletion of ncDNA is likely to have larger effects. Modern sequencing technologies are allowing for the dissection of these proximate causes, but a combination of these new technologies with more traditional evolutionary experiments and approaches could revolutionize this debate and potentially resolve many of these arguments. Here, I discuss an ambitious way forward for GS research, putting it in context of historical debates, theories and sometimes contradictory evidence, and highlighting the promise of combining new sequencing technologies and analytical developments with more traditional experimental evolution approaches.
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Affiliation(s)
- Julie Blommaert
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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19
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Feddersen CR, Wadsworth LS, Zhu EY, Vaughn HR, Voigt AP, Riordan JD, Dupuy AJ. A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells. BMC Genomics 2019; 20:497. [PMID: 31208320 PMCID: PMC6580595 DOI: 10.1186/s12864-019-5888-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/06/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gain-of-function screens are less common, although some reports have utilized arrayed viral expression libraries or the CRISPR activation system. However, a variety of technical and logistical challenges make these approaches difficult for many labs to execute. In addition, genome-wide shRNA or CRISPR libraries typically contain of hundreds of thousands of individual engineered elements, and the associated complexity creates issues with replication and reproducibility for these methods. RESULTS Here we describe a simple, reproducible approach using the SB transposon system to perform phenotypic cell-based genetic screens. This approach employs only three plasmids to perform unbiased, whole-genome transposon mutagenesis. We also describe a ligation-mediated PCR method that can be used in conjunction with the included software tools to map raw sequence data, identify candidate genes associated with phenotypes of interest, and predict the impact of recurrent transposon insertions on candidate gene function. Finally, we demonstrate the high reproducibility of our approach by having three individuals perform independent replicates of a mutagenesis screen to identify drivers of vemurafenib resistance in cultured melanoma cells. CONCLUSIONS Collectively, our work establishes a facile, adaptable method that can be performed by labs of any size to perform robust, genome-wide screens to identify genes that influence phenotypes of interest.
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Affiliation(s)
- Charlotte R. Feddersen
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Lexy S. Wadsworth
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Eliot Y. Zhu
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Hayley R. Vaughn
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Andrew P. Voigt
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Jesse D. Riordan
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
| | - Adam J. Dupuy
- Department of Anatomy & Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246 USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52246 USA
- Department of Anatomy & Cell Biology, Cancer Biology Graduate Program, University of Iowa, MERF, 375 Newton Road, Iowa City, IA 3202 USA
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20
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Woodard LE, Galvan DL, Wilson MH. Site-Directed Genome Modification with Engineered Zinc Finger Proteins. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Lauren E. Woodard
- Department of Veterans Affairs; Nashville TN 37212 USA
- Vanderbilt University Medical Center; Department of Medicine, Department of Pharmacology; Nashville TN 37232 USA
| | - Daniel L. Galvan
- University of Texas at MD Anderson Cancer Center; Section of Nephrology; Houston TX 77030 USA
| | - Matthew H. Wilson
- Department of Veterans Affairs; Nashville TN 37212 USA
- Vanderbilt University Medical Center; Department of Medicine, Department of Pharmacology; Nashville TN 37232 USA
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21
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Woodard LE, Downes LM, Lee YC, Kaja A, Terefe ES, Wilson MH. Temporal self-regulation of transposition through host-independent transposase rodlet formation. Nucleic Acids Res 2016; 45:353-366. [PMID: 27899587 PMCID: PMC5224482 DOI: 10.1093/nar/gkw1115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 11/12/2022] Open
Abstract
Transposons are highly abundant in eukaryotic genomes, but their mobilization must be finely tuned to maintain host organism fitness and allow for transposon propagation. Forty percent of the human genome is comprised of transposable element sequences, and the most abundant cut-and-paste transposons are from the hAT superfamily. We found that the hAT transposase TcBuster from Tribolium castaneum formed filamentous structures, or rodlets, in human tissue culture cells, after gene transfer to adult mice, and ex vivo in cell-free conditions, indicating that host co-factors or cellular structures were not required for rodlet formation. Time-lapsed imaging of GFP-laced rodlets in human cells revealed that they formed quickly in a dynamic process involving fusion and fission. We delayed the availability of the transposon DNA and found that transposition declined after transposase concentrations became high enough for visible transposase rodlets to appear. In combination with earlier findings for maize Ac elements, these results give insight into transposase overproduction inhibition by demonstrating that the appearance of transposase protein structures and the end of active transposition are simultaneous, an effect with implications for genetic engineering and horizontal gene transfer.
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Affiliation(s)
- Lauren E Woodard
- Department of Veterans Affairs, Nashville, TN 37212, USA and Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA.,Department of Veterans Affairs, Houston, TX 77030, USA and Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Laura M Downes
- Department of Veterans Affairs, Nashville, TN 37212, USA and Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Yi-Chien Lee
- Department of Veterans Affairs, Houston, TX 77030, USA and Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aparna Kaja
- Department of Veterans Affairs, Houston, TX 77030, USA and Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eyuel S Terefe
- Department of Veterans Affairs, Houston, TX 77030, USA and Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew H Wilson
- Department of Veterans Affairs, Nashville, TN 37212, USA and Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA .,Department of Veterans Affairs, Houston, TX 77030, USA and Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Abstract
DNA transposons are defined segments of DNA that are able to move from one genomic location to another. Movement is facilitated by one or more proteins, called the transposase, typically encoded by the mobile element itself. Here, we first provide an overview of the classification of such mobile elements in a variety of organisms. From a mechanistic perspective, we have focused on one particular group of DNA transposons that encode a transposase with a DD(E/D) catalytic domain that is topologically similar to RNase H. For these, a number of three-dimensional structures of transpososomes (transposase-nucleic acid complexes) are available, and we use these to describe the basics of their mechanisms. The DD(E/D) group, in addition to being the largest and most common among all DNA transposases, is the one whose members have been used for a wide variety of genomic applications. Therefore, a second focus of the article is to provide a nonexhaustive overview of transposon applications. Although several non-transposon-based approaches to site-directed genome modifications have emerged in the past decade, transposon-based applications are highly relevant when integration specificity is not sought. In fact, for many applications, the almost-perfect randomness and high frequency of integration make transposon-based approaches indispensable.
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Affiliation(s)
- Alison B. Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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23
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Abstract
hAT transposons are ancient in their origin and they are widespread across eukaryote kingdoms. They can be present in large numbers in many genomes. However, only a few active forms of these elements have so far been discovered indicating that, like all transposable elements, there is selective pressure to inactivate them. Nonetheless, there have been sufficient numbers of active hAT elements and their transposases characterized that permit an analysis of their structure and function. This review analyzes these and provides a comparison with the several domesticated hAT genes discovered in eukaryote genomes. Active hAT transposons have also been developed as genetic tools and understanding how these may be optimally utilized in new hosts will depend, in part, on understanding the basis of their function in genomes.
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24
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Dhivya S, Premkumar K. Nomadic genetic elements contribute to oncogenic translocations: Implications in carcinogenesis. Crit Rev Oncol Hematol 2015; 98:81-93. [PMID: 26548742 DOI: 10.1016/j.critrevonc.2015.10.012] [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: 03/04/2015] [Revised: 10/05/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022] Open
Abstract
Chromosomal translocations as molecular signatures have been reported in various malignancies but, the mechanism behind which is largely unknown. Swapping of chromosomal fragments occurs by induction of double strand breaks (DSBs), most of which were initially assumed de novo. However, decoding of human genome proved that transposable elements (TE) might have profound influence on genome integrity. TEs are highly conserved mobile genetic elements that generate DSBs, subsequently resulting in large chromosomal rearrangements. Previously TE insertions were thought to be harmless, but recently gains attention due to the origin of spectrum of post-insertional genomic alterations and subsequent transcriptional alterations leading to development of deleterious effects mainly carcinogenesis. Though the existing knowledge on the cancer-associated TE dynamics is very primitive, exploration of underlying mechanism promises better therapeutic strategies for cancer. Thus, this review focuses on the prevalence of TE in the genome, associated genomic instability upon transposition activation and impact on tumorigenesis.
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Affiliation(s)
- Sridaran Dhivya
- Cancer Genetics and Nanomedicine Laboratory, Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Kumpati Premkumar
- Cancer Genetics and Nanomedicine Laboratory, Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India.
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25
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Low-cost generation of Good Manufacturing Practice–grade CD19-specific chimeric antigen receptor–expressing T cells using piggyBac gene transfer and patient-derived materials. Cytotherapy 2015. [DOI: 10.1016/j.jcyt.2015.05.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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Abstract
DNA transposons offer an efficient nonviral method of permanently modifying the genomes of mammalian cells. The piggyBac transposon system has proven effective in genomic engineering of mammalian cells for preclinical applications, including gene discovery, simultaneous multiplexed genome modification, animal transgenesis, gene transfer in vivo achieving long-term gene expression in animals, and the genetic modification of clinically relevant cell types, such as induced pluripotent stem cells and human T lymphocytes. piggyBac has many desirable features, including seamless excision of transposons from the genomic DNA and the potential to target integration events to desired DNA sequences. In this review, we explore these recent applications and also highlight the unique advantages of using piggyBac for developing new molecular therapeutic strategies.
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Affiliation(s)
- Lauren E Woodard
- Department of Veterans Affairs, Tennessee Valley Health System, Nashville, TN, USA; Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew H Wilson
- Department of Veterans Affairs, Tennessee Valley Health System, Nashville, TN, USA; Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.
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27
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Abstract
DNA transposases use a limited repertoire of structurally and mechanistically distinct nuclease domains to catalyze the DNA strand breaking and rejoining reactions that comprise DNA transposition. Here, we review the mechanisms of the four known types of transposition reactions catalyzed by (1) RNase H-like transposases (also known as DD(E/D) enzymes); (2) HUH single-stranded DNA transposases; (3) serine transposases; and (4) tyrosine transposases. The large body of accumulated biochemical and structural data, particularly for the RNase H-like transposases, has revealed not only the distinguishing features of each transposon family, but also some emerging themes that appear conserved across all families. The more-recently characterized single-stranded DNA transposases provide insight into how an ancient HUH domain fold has been adapted for transposition to accomplish excision and then site-specific integration. The serine and tyrosine transposases are structurally and mechanistically related to their cousins, the serine and tyrosine site-specific recombinases, but have to date been less intensively studied. These types of enzymes are particularly intriguing as in the context of site-specific recombination they require strict homology between recombining sites, yet for transposition can catalyze the joining of transposon ends to form an excised circle and then integration into a genomic site with much relaxed sequence specificity.
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Affiliation(s)
- Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Center Dr., Bethesda, MD 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Center Dr., Bethesda, MD 20892, USA
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28
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Saha S, Woodard LE, Charron EM, Welch RC, Rooney CM, Wilson MH. Evaluating the potential for undesired genomic effects of the piggyBac transposon system in human cells. Nucleic Acids Res 2015; 43:1770-82. [PMID: 25605795 PMCID: PMC4330379 DOI: 10.1093/nar/gkv017] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Non-viral transposons have been used successfully for genetic modification of clinically relevant cells including embryonic stem, induced pluripotent stem, hematopoietic stem and primary human T cell types. However, there has been limited evaluation of undesired genomic effects when using transposons for human genome modification. The prevalence of piggyBac(PB)-like terminal repeat (TR) elements in the human genome raises concerns. We evaluated if there were undesired genomic effects of the PB transposon system to modify human cells. Expression of the transposase alone revealed no mobilization of endogenous PB-like sequences in the human genome and no increase in DNA double-strand breaks. The use of PB in a plasmid containing both transposase and transposon greatly increased the probability of transposase integration; however, using transposon and transposase from separate vectors circumvented this. Placing a eGFP transgene within transposon vector backbone allowed isolation of cells free from vector backbone DNA. We confirmed observable directional promoter activity within the 5'TR element of PB but found no significant enhancer effects from the transposon DNA sequence. Long-term culture of primary human cells modified with eGFP-transposons revealed no selective growth advantage of transposon-harboring cells. PB represents a promising vector system for genetic modification of human cells with limited undesired genomic effects.
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Affiliation(s)
- Sunandan Saha
- Department of Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lauren E Woodard
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elizabeth M Charron
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard C Welch
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cliona M Rooney
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA Department of Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew H Wilson
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA Department of Immunology, Baylor College of Medicine, Houston, TX 77030, USA
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29
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Riordan JD, Drury LJ, Smith RP, Brett BT, Rogers LM, Scheetz TE, Dupuy AJ. Sequencing methods and datasets to improve functional interpretation of sleeping beauty mutagenesis screens. BMC Genomics 2014; 15:1150. [PMID: 25526783 PMCID: PMC4378557 DOI: 10.1186/1471-2164-15-1150] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Animal models of cancer are useful to generate complementary datasets for comparison to human tumor data. Insertional mutagenesis screens, such as those utilizing the Sleeping Beauty (SB) transposon system, provide a model that recapitulates the spontaneous development and progression of human disease. This approach has been widely used to model a variety of cancers in mice. Comprehensive mutation profiles are generated for individual tumors through amplification of transposon insertion sites followed by high-throughput sequencing. Subsequent statistical analyses identify common insertion sites (CISs), which are predicted to be functionally involved in tumorigenesis. Current methods utilized for SB insertion site analysis have some significant limitations. For one, they do not account for transposon footprints - a class of mutation generated following transposon remobilization. Existing methods also discard quantitative sequence data due to uncertainty regarding the extent to which it accurately reflects mutation abundance within a heterogeneous tumor. Additionally, computational analyses generally assume that all potential insertion sites have an equal probability of being detected under non-selective conditions, an assumption without sufficient relevant data. The goal of our study was to address these potential confounding factors in order to enhance functional interpretation of insertion site data from tumors. RESULTS We describe here a novel method to detect footprints generated by transposon remobilization, which revealed minimal evidence of positive selection in tumors. We also present extensive characterization data demonstrating an ability to reproducibly assign semi-quantitative information to individual insertion sites within a tumor sample. Finally, we identify apparent biases for detection of inserted transposons in several genomic regions that may lead to the identification of false positive CISs. CONCLUSION The information we provide can be used to refine analyses of data from insertional mutagenesis screens, improving functional interpretation of results and facilitating the identification of genes important in cancer development and progression.
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Affiliation(s)
| | | | | | | | | | | | - Adam J Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City IA 52242, USA.
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30
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Skipper KA, Andersen PR, Sharma N, Mikkelsen JG. DNA transposon-based gene vehicles - scenes from an evolutionary drive. J Biomed Sci 2013; 20:92. [PMID: 24320156 PMCID: PMC3878927 DOI: 10.1186/1423-0127-20-92] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/27/2013] [Indexed: 12/12/2022] Open
Abstract
DNA transposons are primitive genetic elements which have colonized living organisms from plants to bacteria and mammals. Through evolution such parasitic elements have shaped their host genomes by replicating and relocating between chromosomal loci in processes catalyzed by the transposase proteins encoded by the elements themselves. DNA transposable elements are constantly adapting to life in the genome, and self-suppressive regulation as well as defensive host mechanisms may assist in buffering ‘cut-and-paste’ DNA mobilization until accumulating mutations will eventually restrict events of transposition. With the reconstructed Sleeping Beauty DNA transposon as a powerful engine, a growing list of transposable elements with activity in human cells have moved into biomedical experimentation and preclinical therapy as versatile vehicles for delivery and genomic insertion of transgenes. In this review, we aim to link the mechanisms that drive transposon evolution with the realities and potential challenges we are facing when adapting DNA transposons for gene transfer. We argue that DNA transposon-derived vectors may carry inherent, and potentially limiting, traits of their mother elements. By understanding in detail the evolutionary journey of transposons, from host colonization to element multiplication and inactivation, we may better exploit the potential of distinct transposable elements. Hence, parallel efforts to investigate and develop distinct, but potent, transposon-based vector systems will benefit the broad applications of gene transfer. Insight and clever optimization have shaped new DNA transposon vectors, which recently debuted in the first DNA transposon-based clinical trial. Learning from an evolutionary drive may help us create gene vehicles that are safer, more efficient, and less prone for suppression and inactivation.
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Affiliation(s)
| | | | | | - Jacob Giehm Mikkelsen
- Department of Biomedicine, Aarhus University, Wilh, Meyers Allé 4, DK-8000, Aarhus C, Denmark.
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31
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Cai Y, Bak RO, Krogh LB, Staunstrup NH, Moldt B, Corydon TJ, Schrøder LD, Mikkelsen JG. DNA transposition by protein transduction of the piggyBac transposase from lentiviral Gag precursors. Nucleic Acids Res 2013; 42:e28. [PMID: 24270790 PMCID: PMC3936723 DOI: 10.1093/nar/gkt1163] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
DNA transposon-based vectors have emerged as gene vehicles with a wide biomedical and therapeutic potential. So far, genomic insertion of such vectors has relied on the co-delivery of genetic material encoding the gene-inserting transposase protein, raising concerns related to persistent expression, insertional mutagenesis and cytotoxicity. This report describes potent DNA transposition achieved by direct delivery of transposase protein. By adapting integrase-deficient lentiviral particles (LPs) as carriers of the hyperactive piggyBac transposase protein (hyPBase), we demonstrate rates of DNA transposition that are comparable with the efficiency of a conventional plasmid-based strategy. Embedded in the Gag polypeptide, hyPBase is robustly incorporated into LPs and liberated from the viral proteins by the viral protease during particle maturation. We demonstrate lentiviral co-delivery of the transposase protein and vector RNA carrying the transposon sequence, allowing robust DNA transposition in a variety of cell types. Importantly, this novel delivery method facilitates a balanced cellular uptake of hyPBase, as shown by confocal microscopy, and allows high-efficiency production of clones harboring a single transposon insertion. Our findings establish engineered LPs as a new tool for transposase delivery. We believe that protein transduction methods will increase applicability and safety of DNA transposon-based vector technologies.
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Affiliation(s)
- Yujia Cai
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark and Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
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32
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Bire S, Casteret S, Arnaoty A, Piégu B, Lecomte T, Bigot Y. Transposase concentration controls transposition activity: myth or reality? Gene 2013; 530:165-71. [PMID: 23994686 DOI: 10.1016/j.gene.2013.08.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 12/11/2022]
Abstract
Deciphering the mechanisms underlying the regulation of DNA transposons might be central to understanding their function and dynamics in genomes. From results obtained under artificial experimental conditions, it has been proposed that some DNA transposons self-regulate their activity via overproduction inhibition (OPI), a mechanism by which transposition activity is down-regulated when the transposase is overconcentrated in cells. However, numerous studies have given contradictory results depending on the experimental conditions. Moreover, we do not know in which cellular compartment this phenomenon takes place, or whether transposases assemble to form dense foci when they are highly expressed in cells. In the present review, we focus on investigating the data available about eukaryotic transposons to explain the mechanisms underlying OPI. Data in the literature indicate that members of the IS630-Tc1-mariner, Hobo-Ac-Tam, and piggyBac superfamilies are able to use OPI to self-regulate their transposition activity in vivo in most eukaryotic cells, and that some of them are able to assemble so as to form higher order soluble oligomers. We also investigated the localization and behavior of GFP-fused transposases belonging to the mariner, Tc1-like, and piggyBac families, investigating their ability to aggregate in cells when they are overexpressed. Transposases are able to form dense foci when they are highly expressed. Moreover, the cellular compartments in which these foci are concentrated depend on the transposase, and on its expression. The data presented here suggest that sequestration in cytoplasmic or nucleoplasmic foci, or within the nucleoli, might protect the genome against the potentially genotoxic effects of the non-specific nuclease activities of eukaryotic transposases.
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Affiliation(s)
- Solenne Bire
- PRC, UMR INRA-CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly Cedex, France
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33
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Doherty JE, Woodard LE, Bear AS, Foster AE, Wilson MH. An adaptable system for improving transposon-based gene expression in vivo via transient transgene repression. FASEB J 2013; 27:3753-62. [PMID: 23752206 DOI: 10.1096/fj.13-232090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transposons permit permanent cellular genome engineering in vivo. However, transgene expression falls rapidly postdelivery due to a variety of mechanisms, including immune responses. We hypothesized that delaying initial transgene expression would improve long-term transgene expression by using an engineered piggyBac transposon system that can regulate expression. We found that a 2-part nonviral Tet-KRAB inducible expression system repressed expression of a luciferase reporter in vitro. However, we also observed nonspecific promoter-independent repression. Thus, to achieve temporary transgene repression after gene delivery in vivo, we utilized a nonintegrating version of the repressor plasmid while the gene of interest was delivered in an integrating piggyBac transposon vector. When we delivered the luciferase transposon and repressor to immunocompetent mice by hydrodynamic injection, initial luciferase expression was repressed by 2 orders of magnitude. When luciferase expression was followed long term in vivo, we found that expression was increased >200-fold compared to mice that received only the luciferase transposon and piggyBac transposase. We found that repression of early transgene expression could prevent the priming of luciferase-specific T cells in vivo. Therefore, transient transgene repression postgene delivery is an effective strategy for inhibiting the antitransgene immune response and improving long-term expression in vivo without using immunosuppression.
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Affiliation(s)
- Joseph E Doherty
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
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34
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Identification of rtl1, a retrotransposon-derived imprinted gene, as a novel driver of hepatocarcinogenesis. PLoS Genet 2013; 9:e1003441. [PMID: 23593033 PMCID: PMC3616914 DOI: 10.1371/journal.pgen.1003441] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 02/22/2013] [Indexed: 12/23/2022] Open
Abstract
We previously utilized a Sleeping Beauty (SB) transposon mutagenesis screen to discover novel drivers of HCC. This approach identified recurrent mutations within the Dlk1-Dio3 imprinted domain, indicating that alteration of one or more elements within the domain provides a selective advantage to cells during the process of hepatocarcinogenesis. For the current study, we performed transcriptome and small RNA sequencing to profile gene expression in SB–induced HCCs in an attempt to clarify the genetic element(s) contributing to tumorigenesis. We identified strong induction of Retrotransposon-like 1 (Rtl1) expression as the only consistent alteration detected in all SB–induced tumors with Dlk1-Dio3 integrations, suggesting that Rtl1 activation serves as a driver of HCC. While previous studies have identified correlations between disrupted expression of multiple Dlk1-Dio3 domain members and HCC, we show here that direct modulation of a single domain member, Rtl1, can promote hepatocarcinogenesis in vivo. Overexpression of Rtl1 in the livers of adult mice using a hydrodynamic gene delivery technique resulted in highly penetrant (86%) tumor formation. Additionally, we detected overexpression of RTL1 in 30% of analyzed human HCC samples, indicating the potential relevance of this locus as a therapeutic target for patients. The Rtl1 locus is evolutionarily derived from the domestication of a retrotransposon. In addition to identifying Rtl1 as a novel driver of HCC, our study represents one of the first direct in vivo demonstrations of a role for such a co-opted genetic element in promoting carcinogenesis. HCC is the third deadliest cancer worldwide, largely due to a lack of effective treatment options. Therapeutic approaches targeted at the molecular mechanisms underlying tumor formation and progression have shown great efficacy for treating other tumor types. Unfortunately, however, much remains to be learned about the molecular pathogenesis of HCC. There is an urgent need to identify and characterize genetic alterations that drive HCC in order to facilitate the development of more effective targeted therapeutics for patients. Here, we present data showing that recurrent mutations identified in a mouse model of HCC result in overexpression of the Rtl1 gene. We have validated Rtl1 as a driver of HCC by demonstrating that its overexpression in mouse liver causes tumor formation. We also detected overexpression of this gene in a significant proportion of human HCC samples, suggesting that it may be a relevant therapeutic target for patients with this disease.
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