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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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2
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Durrant MG, Perry NT, Pai JJ, Jangid AR, Athukoralage JS, Hiraizumi M, McSpedon JP, Pawluk A, Nishimasu H, Konermann S, Hsu PD. Bridge RNAs direct programmable recombination of target and donor DNA. Nature 2024; 630:984-993. [PMID: 38926615 PMCID: PMC11208160 DOI: 10.1038/s41586-024-07552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/09/2024] [Indexed: 06/28/2024]
Abstract
Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes that are involved in fundamental DNA repair processes, such as homologous recombination, or in the transposition of foreign genetic material by viruses and mobile genetic elements1,2. Here we report that IS110 insertion sequences, a family of minimal and autonomous mobile genetic elements, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and the donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables the insertion of DNA into genomic target sites, as well as programmable DNA excision and inversion. The IS110 bridge recombination system expands the diversity of nucleic-acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements-insertion, excision and inversion-that are required for genome design.
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Affiliation(s)
- Matthew G Durrant
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T Perry
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Aditya R Jangid
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Masahiro Hiraizumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | | | | | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
- Structural Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Inamori Research Institute for Science, Kyoto, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Saitama, Japan
| | - Silvana Konermann
- Arc Institute, Palo Alto, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
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3
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Tian J, Tong D, Li Z, Wang E, Yu Y, Lv H, Hu Z, Sun F, Wang G, He M, Xia T. Mage transposon: a novel gene delivery system for mammalian cells. Nucleic Acids Res 2024; 52:2724-2739. [PMID: 38300794 PMCID: PMC10954464 DOI: 10.1093/nar/gkae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Transposons, as non-viral integration vectors, provide a secure and efficient method for stable gene delivery. In this study, we have discovered Mage (MG), a novel member of the piggyBac(PB) family, which exhibits strong transposability in a variety of mammalian cells and primary T cells. The wild-type MG showed a weaker insertion preference for near genes, transcription start sites (TSS), CpG islands, and DNaseI hypersensitive sites in comparison to PB, approaching the random insertion pattern. Utilizing in silico virtual screening and feasible combinatorial mutagenesis in vitro, we effectively produced the hyperactive MG transposase (hyMagease). This variant boasts a transposition rate 60% greater than its native counterpart without significantly altering its insertion pattern. Furthermore, we applied the hyMagease to efficiently deliver chimeric antigen receptor (CAR) into T cells, leading to stable high-level expression and inducing significant anti-tumor effects both in vitro and in xenograft mice models. These findings provide a compelling tool for gene transfer research, emphasizing its potential and prospects in the domains of genetic engineering and gene therapy.
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Affiliation(s)
- Jinghan Tian
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Doudou Tong
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | | | - Erqiang Wang
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yifei Yu
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Hangya Lv
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Zhendan Hu
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Fang Sun
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Guoping Wang
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Min He
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Tian Xia
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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4
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Durrant MG, Perry NT, Pai JJ, Jangid AR, Athukoralage JS, Hiraizumi M, McSpedon JP, Pawluk A, Nishimasu H, Konermann S, Hsu PD. Bridge RNAs direct modular and programmable recombination of target and donor DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577089. [PMID: 38328150 PMCID: PMC10849738 DOI: 10.1101/2024.01.24.577089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions, or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes involved in fundamental DNA repair processes such as homologous recombination or in the transposition of foreign genetic material by viruses and mobile genetic elements (MGEs). We report that IS110 insertion sequences, a family of minimal and autonomous MGEs, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables DNA insertion into genomic target sites as well as programmable DNA excision and inversion. The IS110 bridge system expands the diversity of nucleic acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design.
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Affiliation(s)
- Matthew G. Durrant
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T. Perry
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - James J. Pai
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
| | - Aditya R. Jangid
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Masahiro Hiraizumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | - April Pawluk
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto 600-8411, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Silvana Konermann
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick D. Hsu
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
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5
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Zimowska GJ, Xavier N, Qadri M, Handler AM. A transposon-based genetic marker for conspecific identity within the Bactrocera dorsalis species complex. Sci Rep 2024; 14:1924. [PMID: 38253542 PMCID: PMC10803768 DOI: 10.1038/s41598-023-51068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Here we describe a molecular approach to assess conspecific identity that relies on the comparison of an evolved mutated transposable element sequence and its genomic insertion site in individuals from closely related species. This was explored with the IFP2 piggyBac transposon, originally discovered in Trichoplusia ni as a 2472 bp functional element, that was subsequently found as mutated elements in seven species within the Bactrocera dorsalis species complex. In a B. dorsalis [Hendel] strain collected in Kahuku, Hawaii, a degenerate 2420 bp piggyBac sequence (pBacBd-Kah) having ~ 94.5% sequence identity to IFP2 was isolated, and it was reasoned that common species, or strains within species, should share the same evolved element and its precise genomic insertion site. To test this assumption, PCR using primers to pBacBd-Kah and adjacent genomic sequences was used to isolate and compare homologous sequences in strains of four sibling species within the complex. Three of these taxa, B. papayae, B. philippinensis, and B. invadens, were previously synonymized with B. dorsalis, and found to share nearly identical pBacBd-Kah homologous elements (> 99% nucleotide identity) within the identical insertion site consistent with conspecific species. The fourth species tested, B. carambolae, considered to be a closely related yet independent species sympatric with B. dorsalis, also shared the pBacBd-Kah sequence and insertion site in one strain from Suriname, while another divergent pBacBd-Kah derivative, closer in identity to IFP2, was found in individuals from French Guiana, Bangladesh and Malaysia. This data, along with the absence of pBacBd-Kah in distantly related Bactrocera, indicates that mutated descendants of piggyBac, as well as other invasive mobile elements, could be reliable genomic markers for common species identity.
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Affiliation(s)
- Grazyna J Zimowska
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Nirmala Xavier
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Masroor Qadri
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Alfred M Handler
- U.S. Department of Agriculture, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, 1700 SW 23rd Drive, Gainesville, FL, 32608, USA.
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Han M, Perkins MH, Novaes LS, Xu T, Chang H. Advances in transposable elements: from mechanisms to applications in mammalian genomics. Front Genet 2023; 14:1290146. [PMID: 38098473 PMCID: PMC10719622 DOI: 10.3389/fgene.2023.1290146] [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: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
It has been 70 years since Barbara McClintock discovered transposable elements (TE), and the mechanistic studies and functional applications of transposable elements have been at the forefront of life science research. As an essential part of the genome, TEs have been discovered in most species of prokaryotes and eukaryotes, and the relative proportion of the total genetic sequence they comprise gradually increases with the expansion of the genome. In humans, TEs account for about 40% of the genome and are deeply involved in gene regulation, chromosome structure maintenance, inflammatory response, and the etiology of genetic and non-genetic diseases. In-depth functional studies of TEs in mammalian cells and the human body have led to a greater understanding of these fundamental biological processes. At the same time, as a potent mutagen and efficient genome editing tool, TEs have been transformed into biological tools critical for developing new techniques. By controlling the random insertion of TEs into the genome to change the phenotype in cells and model organisms, critical proteins of many diseases have been systematically identified. Exploiting the TE's highly efficient in vitro insertion activity has driven the development of cutting-edge sequencing technologies. Recently, a new technology combining CRISPR with TEs was reported, which provides a novel targeted insertion system to both academia and industry. We suggest that interrogating biological processes that generally depend on the actions of TEs with TEs-derived genetic tools is a very efficient strategy. For example, excessive activation of TEs is an essential factor in the occurrence of cancer in humans. As potent mutagens, TEs have also been used to unravel the key regulatory elements and mechanisms of carcinogenesis. Through this review, we aim to effectively combine the traditional views of TEs with recent research progress, systematically link the mechanistic discoveries of TEs with the technological developments of TE-based tools, and provide a comprehensive approach and understanding for researchers in different fields.
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Affiliation(s)
- Mei Han
- Guangzhou National Laboratory, Guangzhou, China
| | - Matthew H. Perkins
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Leonardo Santana Novaes
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tao Xu
- Guangzhou National Laboratory, Guangzhou, China
| | - Hao Chang
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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Kou Z, Luo X, Jiang Y, Chen B, Song Y, Wang Y, Xu J, Tomberlin JK, Huang Y. Establishment of highly efficient transgenic system for black soldier fly (Hermetia illucens). INSECT SCIENCE 2023; 30:888-900. [PMID: 36624657 DOI: 10.1111/1744-7917.13147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/21/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
The black soldier fly (BSF), Hermetia illucens, is a promising insect for mitigating solid waste problems as its larvae are able to bioconvert organic waste into valuable biomass. We recently reported a high-quality genome assembly of the BSF; analysis of this genome sequence will further the understanding of insect biology and identify genes that can be manipulated to improve efficiency of bioconversion. To enable genetic manipulation of the BSF, we have established the first transgenic methods for this economically important insect. We cloned and identified the ubiquitous actin5C promoter (Hiactin5C-p3k) and 3 endogenous U6 promoters (HiU6:1, HiU6:2, and HiU6:3). The Hiactin5C promoter was used to drive expression of a hyperactive variant of the piggyBac transposase, which exhibited up to 6-fold improvement in transformation rate when compared to the wild-type transposase. Furthermore, we evaluated the 3 HiU6 promoters using this transgenic system. HiU6:1 and HiU6:2 promoters provided the highest knockdown efficiency with RNAi and are thus promising candidates for future Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) development. Overall, our findings provide valuable genetic engineering toolkits for basic research and genetic manipulation of the BSF.
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Affiliation(s)
- Zongqing Kou
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingyu Luo
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuguo Jiang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bihui Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Song
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaohui Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jun Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | | | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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The Role of Genetically Modified Human Feeder Cells in Maintaining the Integrity of Primary Cultured Human Deciduous Dental Pulp Cells. J Clin Med 2022; 11:jcm11206087. [PMID: 36294410 PMCID: PMC9605397 DOI: 10.3390/jcm11206087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/30/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Tissue-specific stem cells exist in tissues and organs, such as skin and bone marrow. However, their pluripotency is limited compared to embryonic stem cells. Culturing primary cells on plastic tissue culture dishes can result in the loss of multipotency, because of the inability of tissue-specific stem cells to survive in feeder-less dishes. Recent findings suggest that culturing primary cells in medium containing feeder cells, particularly genetically modified feeder cells expressing growth factors, may be beneficial for their survival and proliferation. Therefore, the aim of this study was to elucidate the role of genetically modified human feeder cells expressing growth factors in maintaining the integrity of primary cultured human deciduous dental pulp cells. Feeder cells expressing leukemia inhibitory factor, bone morphogenetic protein 4, and basic fibroblast growth factor were successfully engineered, as evidenced by PCR. Co-culturing with mitomycin-C-treated feeder cells enhanced the proliferation of newly isolated human deciduous dental pulp cells, promoted their differentiation into adipocytes and neurons, and maintained their stemness properties. Our findings suggest that genetically modified human feeder cells may be used to maintain the integrity of primary cultured human deciduous dental pulp cells.
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Yamamoto Y, Gerbi SA. Development of Transformation for Genome Editing of an Emerging Model Organism. Genes (Basel) 2022; 13:genes13071108. [PMID: 35885891 PMCID: PMC9323590 DOI: 10.3390/genes13071108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 12/10/2022] Open
Abstract
With the advances in genomic sequencing, many organisms with novel biological properties are ripe for use as emerging model organisms. However, to make full use of them, transformation methods need to be developed to permit genome editing. Here, we present the development of transformation for the fungus fly Bradysia (Sciara) coprophila; this may serve as a paradigm for the development of transformation for other emerging systems, especially insects. Bradysia (Sciara) has a variety of unique biological features, including locus-specific developmentally regulated DNA amplification, chromosome imprinting, a monopolar spindle in male meiosis I, non-disjunction of the X chromosome in male meiosis II, X chromosome elimination in early embryogenesis, germ-line-limited (L) chromosomes and high resistance to radiation. Mining the unique biology of Bradysia (Sciara) requires a transformation system to test mutations of DNA sequences that may play roles for these features. We describe a Bradysia (Sciara) transformation system using a modified piggyBac transformation vector and detailed protocols we have developed to accommodate Bradysia (Sciara) specific requirements. This advance will provide a platform for us and others in the growing Bradysia (Sciara) community to take advantage of this unique biological system. In addition, the versatile piggyBac vectors described here and transformation methods will be useful for other emerging model systems.
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Affiliation(s)
| | - Susan A. Gerbi
- Correspondence: ; Tel.: +1-401-863-2359; Fax: +1-401-863-1201
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10
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Suematsu M, Yagyu S, Nagao N, Kubota S, Shimizu Y, Tanaka M, Nakazawa Y, Imamura T. PiggyBac Transposon-Mediated CD19 Chimeric Antigen Receptor-T Cells Derived From CD45RA-Positive Peripheral Blood Mononuclear Cells Possess Potent and Sustained Antileukemic Function. Front Immunol 2022; 13:770132. [PMID: 35154098 PMCID: PMC8829551 DOI: 10.3389/fimmu.2022.770132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
The quality of chimeric antigen receptor (CAR)-T cell products, namely, memory and exhaustion markers, affects the long-term functionality of CAR-T cells. We previously reported that piggyBac (PB) transposon-mediated CD19 CAR-T cells exhibit a memory-rich phenotype that is characterized by the high proportion of CD45RA+/C-C chemokine receptor type 7 (CCR7)+ T-cell fraction. To further investigate the favorable phenotype of PB-CD19 CAR-T cells, we generated PB-CD19 CAR-T cells from CD45RA+ and CD45RA− peripheral blood mononuclear cells (PBMCs) (RA+ CAR and RA− CAR, respectively), and compared their phenotypes and antitumor activity. RA+ CAR-T cells showed better transient gene transfer efficiency 24 h after transduction and superior expansion capacity after 14 days of culture than those shown by RA− CAR-T cells. RA+ CAR-T cells exhibited dominant CD8 expression, decreased expression of the exhaustion marker programmed cell death protein-1 (PD-1) and T-cell senescence marker CD57, and enriched naïve/stem cell memory fraction, which are associated with the longevity of CAR-T cells. Transcriptome analysis showed that canonical exhaustion markers were downregulated in RA+ CAR-T, even after antigen stimulation. Although antigen stimulation could increase CAR expression, leading to tonic CAR signaling and exhaustion, the expression of CAR molecules on cell surface after antigen stimulation in RA+ CAR-T cells was controlled at a relatively lower level than that in RA− CAR-T cells. In the in vivo stress test, RA+ CAR-T cells achieved prolonged tumor control with expansion of CAR-T cells compared with RA− CAR-T cells. CAR-T cells were not detected in the control or RA− CAR-T cells but RA+ CAR-T cells were expanded even after 50 days of treatment, as confirmed by sequential bone marrow aspiration. Our results suggest that PB-mediated RA+ CAR-T cells exhibit a memory-rich phenotype and superior antitumor function, thus CD45RA+ PBMCs might be considered an efficient starting material for PB-CAR-T cell manufacturing. This novel approach will be beneficial for effective treatment of B cell malignancies.
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Affiliation(s)
- Masaya Suematsu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Shigeki Yagyu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Nobuyoshi Nagao
- AGC Inc. Innovative Technology Laboratories, Yokohama, Japan
| | - Susumu Kubota
- AGC Inc. Materials Integration Laboratories, Yokohama, Japan
| | - Yuto Shimizu
- AGC Inc. Materials Integration Laboratories, Yokohama, Japan
| | - Miyuki Tanaka
- Department of Pediatrics, Shinshu University School of Medicine, Nagano, Japan
| | - Yozo Nakazawa
- Department of Pediatrics, Shinshu University School of Medicine, Nagano, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
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11
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Lin Z, Liu X, Liu T, Gao H, Wang S, Zhu X, Rong L, Cheng J, Cai Z, Xu F, Tan X, Lv L, Li Z, Sun Y, Qian Q. Evaluation of Nonviral piggyBac and lentiviral Vector in Functions of CD19chimeric Antigen Receptor T Cells and Their Antitumor Activity for CD19 + Tumor Cells. Front Immunol 2022; 12:802705. [PMID: 35082789 PMCID: PMC8784881 DOI: 10.3389/fimmu.2021.802705] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
Nonviral transposon piggyBac (PB) and lentiviral (LV) vectors have been used to deliver chimeric antigen receptor (CAR) to T cells. To understand the differences in the effects of PB and LV on CAR T-cell functions, a CAR targeting CD19 was cloned into PB and LV vectors, and the resulting pbCAR and lvCAR were delivered to T cells to generate CD19pbCAR and CD19lvCAR T cells. Both CD19CAR T-cell types were strongly cytotoxic and secreted high IFN-γ levels when incubated with Raji cells. TNF-α increased in CD19pbCAR T cells, whereas IL-10 increased in CD19lvCAR T cells. CD19pbCAR and CD19lvCAR T cells showed similar strong anti-tumor activity in Raji cell-induced mouse models, slightly reducing mouse weight while enhancing mouse survival. High, but not low or moderate, concentrations of CD19pbCAR T cells significantly inhibited Raji cell-induced tumor growth in vivo. These CD19pbCAR T cells were distributed mostly in mesenteric lymph nodes, bone marrow of the femur, spleen, kidneys, and lungs, specifically accumulating at CD19-rich sites and CD19-positive tumors, with CAR copy number being increased on day 7. These results indicate that pbCAR has its specific activities and functions in pbCAR T cells, making it a valuable tool for CAR T-cell immunotherapy.
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MESH Headings
- Animals
- Antigens, CD19/genetics
- Antigens, CD19/immunology
- Antigens, CD19/metabolism
- Cell Line, Tumor
- Cells, Cultured
- Cytotoxicity, Immunologic/immunology
- DNA Transposable Elements/genetics
- DNA Transposable Elements/immunology
- Female
- Genetic Vectors/genetics
- Genetic Vectors/immunology
- Humans
- Immunotherapy, Adoptive/methods
- Lentivirus/genetics
- Lentivirus/immunology
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Neoplasms/immunology
- Neoplasms/pathology
- Neoplasms/therapy
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Tumor Burden/immunology
- Xenograft Model Antitumor Assays/methods
- Mice
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Affiliation(s)
- Zhicai Lin
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Xiangzhen Liu
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Tao Liu
- R&D Department, Nucleotide Center, Shanghai Cell Therapy Group, Shanghai, China
| | - Haixia Gao
- R&D Department, Nucleotide Center, Shanghai Cell Therapy Group, Shanghai, China
| | - Sitong Wang
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Xingli Zhu
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Lijie Rong
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Jingbo Cheng
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Zhigang Cai
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Fu Xu
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Xue Tan
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Linjie Lv
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Zhong Li
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
- Department of Immunotherapy, Shanghai Cell Therapy Research Institute, Shanghai, China
| | - Yan Sun
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
| | - Qijun Qian
- Medical, Cell Product and R&D Department, Center for Cell Pharmaceuticals, Shanghai Cell Therapy Group, Shanghai, China
- Department of Immunotherapy, Shanghai Cell Therapy Research Institute, Shanghai, China
- Shanghai Menchao Cancer Hospital, Shanghai University, Shanghai, China
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12
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Takeuchi C, Murano K, Ishikawa M, Okano H, Iwasaki YW. Generation of Stable Drosophila Ovarian Somatic Cell Lines Using the piggyBac System. Methods Mol Biol 2022; 2509:143-153. [PMID: 35796962 DOI: 10.1007/978-1-0716-2380-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) constitute a large proportion of the genome in multiple organisms. Therefore, anti-transposable element machineries are essential to maintain genomic integrity. PIWI-interacting RNAs (piRNAs) are a major force to repress TEs in Drosophila ovaries. Ovarian somatic cells (OSC), in which nuclear piRNA regulation is functional, have been used for research on piRNA pathway as a cell culture system to elucidate the molecular mechanisms underlying the piRNA pathway. Analysis of piRNA pathway using a reporter system to monitor the gene regulation or overexpression of specific genes would be a powerful approach. Here, we present the technical protocol to establish stable cell lines using the piggyBac system, adopted for OSCs. This easy, consistent, and timesaving protocol may accelerate research on the piRNA pathway.
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Affiliation(s)
- Chikara Takeuchi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Mitsuru Ishikawa
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan.
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, Japan.
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13
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Muller H, Loiseau V, Guillier S, Cordaux R, Gilbert C. Assessing the Impact of a Viral Infection on the Expression of Transposable Elements in the Cabbage Looper Moth (Trichoplusia ni). Genome Biol Evol 2021; 13:evab231. [PMID: 34613390 PMCID: PMC8634313 DOI: 10.1093/gbe/evab231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Most studies of stress-induced transposable element (TE) expression have so far focused on abiotic sources of stress. Here, we analyzed the impact of an infection by the AcMNPV baculovirus on TE expression in a cell line (Tnms42) and midgut tissues of the cabbage looper moth (Trichoplusia ni). We find that a large fraction of TE families (576/636 in Tnms42 cells and 503/612 in midgut) is lowly expressed or not expressed at all [≤ 4 transcripts per million (TPM)] in the uninfected condition (median TPM of 0.37 in Tnms42 and 0.46 in midgut cells). In the infected condition, a total of 62 and 187 TE families were differentially expressed (DE) in midgut and Tnms42 cells, respectively, with more up- (46) than downregulated (16) TE families in the former and as many up- (91) as downregulated (96) TE families in the latter. Expression log2 fold changes of DE TE families varied from -4.95 to 9.11 in Tnms42 cells and from -4.28 to 7.66 in midgut. Large variations in expression profiles of DE TEs were observed depending on the type of cells and on time after infection. Overall, the impact of AcMNPV on TE expression in T. ni is moderate but potentially sufficient to affect TE activity and genome architecture. Interestingly, one host-derived TE integrated into AcMNPV genomes is highly expressed in infected Tnms42 cells. This result shows that virus-borne TEs can be expressed, further suggesting that they may be able to transpose and that viruses may act as vectors of horizontal transfer of TEs in insects.
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Affiliation(s)
- Héloïse Muller
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Vincent Loiseau
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Sandra Guillier
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Universite de Poitiers, CNRS, France
| | - Clément Gilbert
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
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14
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Applications of piggyBac Transposons for Genome Manipulation in Stem Cells. Stem Cells Int 2021; 2021:3829286. [PMID: 34567130 PMCID: PMC8460389 DOI: 10.1155/2021/3829286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022] Open
Abstract
Transposons are mobile genetic elements in the genome. The piggyBac (PB) transposon system is increasingly being used for stem cell research due to its high transposition efficiency and seamless excision capacity. Over the past few decades, forward genetic screens based on PB transposons have been successfully established to identify genes associated with drug resistance and stem cell-related characteristics. Moreover, PB transposon is regarded as a promising gene therapy vector and has been used in some clinically relevant stem cells. Here, we review the recent progress on the basic biology of PB, highlight its applications in current stem cell research, and discuss its advantages and challenges.
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15
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Loiseau V, Peccoud J, Bouzar C, Guillier S, Fan J, Alletti GG, Meignin C, Herniou EA, Federici BA, Wennmann JT, Jehle JA, Cordaux R, Gilbert C. Monitoring insect transposable elements in large double-stranded DNA viruses reveals host-to-virus and virus-to-virus transposition. Mol Biol Evol 2021; 38:3512-3530. [PMID: 34191026 PMCID: PMC8383894 DOI: 10.1093/molbev/msab198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The mechanisms by which transposable elements (TEs) can be horizontally transferred between animals are unknown, but viruses are possible candidate vectors. Here, we surveyed the presence of host-derived TEs in viral genomes in 35 deep sequencing data sets produced from 11 host–virus systems, encompassing nine arthropod host species (five lepidopterans, two dipterans, and two crustaceans) and six different double-stranded (ds) DNA viruses (four baculoviruses and two iridoviruses). We found evidence of viral-borne TEs in 14 data sets, with frequencies of viral genomes carrying a TE ranging from 0.01% to 26.33% for baculoviruses and from 0.45% to 7.36% for iridoviruses. The analysis of viral populations separated by a single replication cycle revealed that viral-borne TEs originating from an initial host species can be retrieved after viral replication in another host species, sometimes at higher frequencies. Furthermore, we detected a strong increase in the number of integrations in a viral population for a TE absent from the hosts’ genomes, indicating that this TE has undergone intense transposition within the viral population. Finally, we provide evidence that many TEs found integrated in viral genomes (15/41) have been horizontally transferred in insects. Altogether, our results indicate that multiple large dsDNA viruses have the capacity to shuttle TEs in insects and they underline the potential of viruses to act as vectors of horizontal transfer of TEs. Furthermore, the finding that TEs can transpose between viral genomes of a viral species sets viruses as possible new niches in which TEs can persist and evolve.
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Affiliation(s)
- Vincent Loiseau
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Jean Peccoud
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Clémence Bouzar
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Sandra Guillier
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Jiangbin Fan
- Institute for Biological Control, Julius Kühn-Institut, Darmstadt, Germany
| | | | - Carine Meignin
- Modèles Insectes d'Immunité antivirale (M3i), Université de Strasbourg, IBMC CNRS-UPR9022, F-67000, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR7261 CNRS - Université de Tours, 37200 Tours, France
| | - Brian A Federici
- Department of Entomology, University of California, Riverside, CA 92521, USA
| | - Jörg T Wennmann
- Institute for Biological Control, Julius Kühn-Institut, Darmstadt, Germany
| | - Johannes A Jehle
- Institute for Biological Control, Julius Kühn-Institut, Darmstadt, Germany
| | - Richard Cordaux
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
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16
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Sandoval-Villegas N, Nurieva W, Amberger M, Ivics Z. Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications of Sleeping Beauty, piggyBac and Tol2 for Genome Engineering. Int J Mol Sci 2021; 22:ijms22105084. [PMID: 34064900 PMCID: PMC8151067 DOI: 10.3390/ijms22105084] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/19/2023] Open
Abstract
Transposons are mobile genetic elements evolved to execute highly efficient integration of their genes into the genomes of their host cells. These natural DNA transfer vehicles have been harnessed as experimental tools for stably introducing a wide variety of foreign DNA sequences, including selectable marker genes, reporters, shRNA expression cassettes, mutagenic gene trap cassettes, and therapeutic gene constructs into the genomes of target cells in a regulated and highly efficient manner. Given that transposon components are typically supplied as naked nucleic acids (DNA and RNA) or recombinant protein, their use is simple, safe, and economically competitive. Thus, transposons enable several avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture comprising the generation of pluripotent stem cells, the production of germline-transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species and therapy of genetic disorders in humans. This review describes the molecular mechanisms involved in transposition reactions of the three most widely used transposon systems currently available (Sleeping Beauty, piggyBac, and Tol2), and discusses the various parameters and considerations pertinent to their experimental use, highlighting the state-of-the-art in transposon technology in diverse genetic applications.
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Affiliation(s)
| | | | | | - Zoltán Ivics
- Correspondence: ; Tel.: +49-6103-77-6000; Fax: +49-6103-77-1280
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17
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Jonsdottir TK, Gabriela M, Crabb BS, F de Koning-Ward T, Gilson PR. Defining the Essential Exportome of the Malaria Parasite. Trends Parasitol 2021; 37:664-675. [PMID: 33985912 DOI: 10.1016/j.pt.2021.04.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023]
Abstract
To survive inside red blood cells (RBCs), malaria parasites export many proteins to alter their host cell's physiological properties. Although most proteins of this exportome are involved in immune avoidance or in the trafficking of exported proteins to the host membrane, about 20% are essential for parasite survival in culture but little is known about their biological functions. Here, we have combined information from large-scale genetic screens and targeted gene-disruption studies to tabulate all currently known Plasmodium falciparum exported proteins according to their likelihood of being essential. We also discuss the essential functional pathways that exported proteins might be involved in to help direct research efforts towards a more comprehensive understanding of host-cell remodelling.
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Affiliation(s)
- Thorey K Jonsdottir
- Burnet Institute, Melbourne, Victoria 3004, Australia; Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Mikha Gabriela
- Burnet Institute, Melbourne, Victoria 3004, Australia; School of Medicine, Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Brendan S Crabb
- Burnet Institute, Melbourne, Victoria 3004, Australia; Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | | | - Paul R Gilson
- Burnet Institute, Melbourne, Victoria 3004, Australia.
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18
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Structural basis of seamless excision and specific targeting by piggyBac transposase. Nat Commun 2020; 11:3446. [PMID: 32651359 PMCID: PMC7351741 DOI: 10.1038/s41467-020-17128-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022] Open
Abstract
The piggyBac DNA transposon is used widely in genome engineering applications. Unlike other transposons, its excision site can be precisely repaired without leaving footprints and it integrates specifically at TTAA tetranucleotides. We present cryo-EM structures of piggyBac transpososomes: a synaptic complex with hairpin DNA intermediates and a strand transfer complex capturing the integration step. The results show that the excised TTAA hairpin intermediate and the TTAA target adopt essentially identical conformations, providing a mechanistic link connecting the two unique properties of piggyBac. The transposase forms an asymmetric dimer in which the two central domains synapse the ends while two C-terminal domains form a separate dimer that contacts only one transposon end. In the strand transfer structure, target DNA is severely bent and the TTAA target is unpaired. In-cell data suggest that asymmetry promotes synaptic complex formation, and modifying ends with additional transposase binding sites stimulates activity.
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19
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piggyBac-Based Non-Viral In Vivo Gene Delivery Useful for Production of Genetically Modified Animals and Organs. Pharmaceutics 2020; 12:pharmaceutics12030277. [PMID: 32204422 PMCID: PMC7151002 DOI: 10.3390/pharmaceutics12030277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 11/17/2022] Open
Abstract
In vivo gene delivery involves direct injection of nucleic acids (NAs) into tissues, organs, or tail-veins. It has been recognized as a useful tool for evaluating the function of a gene of interest (GOI), creating models for human disease and basic research targeting gene therapy. Cargo frequently used for gene delivery are largely divided into viral and non-viral vectors. Viral vectors have strong infectious activity and do not require the use of instruments or reagents helpful for gene delivery but bear immunological and tumorigenic problems. In contrast, non-viral vectors strictly require instruments (i.e., electroporator) or reagents (i.e., liposomes) for enhanced uptake of NAs by cells and are often accompanied by weak transfection activity, with less immunological and tumorigenic problems. Chromosomal integration of GOI-bearing transgenes would be ideal for achieving long-term expression of GOI. piggyBac (PB), one of three transposons (PB, Sleeping Beauty (SB), and Tol2) found thus far, has been used for efficient transfection of GOI in various mammalian cells in vitro and in vivo. In this review, we outline recent achievements of PB-based production of genetically modified animals and organs and will provide some experimental concepts using this system.
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20
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Li X, Wang L, Su Q, Ye L, Zhou X, Song D, Huang D. Highly Proliferative Immortalized Human Dental Pulp Cells Retain the Odontogenic Phenotype when Combined with a Beta-Tricalcium Phosphate Scaffold and BMP2. Stem Cells Int 2020; 2020:4534128. [PMID: 32148517 PMCID: PMC7044479 DOI: 10.1155/2020/4534128] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/14/2020] [Accepted: 01/22/2020] [Indexed: 02/05/2023] Open
Abstract
Human dental pulp cells (HDPCs) play a vital role in dentin formation and reparative dentinogenesis, which indicated their potential application in regenerative medicine. However, HDPCs, which can only be obtained from scarce human pulp tissues, also have a limited lifespan in vitro, and stem cells usually lose their original characteristics over a large number of passages. To overcome these challenges, we successfully immortalized human dental pulp cells using the piggyBac system which was employed to efficiently overexpress the SV40 T-Ag, and we then comprehensively described the cell biological behavior. The immortalized human dental pulp cells (iHDPCs) acquired long-term proliferative activity and expressed most HDPC markers. The iHDPCs maintained multiple differentiation potential and could be induced to differentiate into chondrogenic, osteogenic, and adipogenic cells in vitro. We also proved that the iHDPCs gained a stronger ability to migrate than the primary cells, while apoptosis was inhibited. Furthermore, highly proliferative iHDPCs displayed no oncogenicity when subcutaneously implanted into athymic nude mice. Finally, iHDPCs exhibited odontogenic differentiation ability and secreted dentin sialophosphoprotein (DSPP) when combined with a beta-tricalcium phosphate scaffold and bone morphogenetic protein-2 (BMP2) in vivo. Conclusively, the established iHDPCs are a valuable resource for mechanistic study of dental pulp cell differentiation and dental pulp injury repair, as well as for applications in tooth regeneration.
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Affiliation(s)
- Xiangfen Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Liu Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qin Su
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ling Ye
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Dongzhe Song
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Dingming Huang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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21
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Loiseau V, Herniou EA, Moreau Y, Lévêque N, Meignin C, Daeffler L, Federici B, Cordaux R, Gilbert C. Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses. Virus Evol 2020; 6:vez060. [PMID: 32002191 PMCID: PMC6983493 DOI: 10.1093/ve/vez060] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double-stranded (ds) DNA viruses is limited. Here, we sequenced the genome of a baculovirus (Autographa californica multiple nucleopolyhedrovirus [AcMNPV]) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000× using both short- (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications, and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9 per cent of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (<0.01%) and that very few SVs persist after ten replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1,102 SVs carried by 52.4–80.1 per cent of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.
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Affiliation(s)
- Vincent Loiseau
- Laboratoire Evolution, Génomes, Comportement, Écologie, Unité Mixte de Recherche 9191 Centre National de la Recherche Scientifique et Unité Mixte de Recherche 247 Institut de Recherche pour le Développement, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS - Université de Tours, 37200 Tours, France
| | - Yannis Moreau
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS - Université de Tours, 37200 Tours, France
| | - Nicolas Lévêque
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86000 Poitiers, France.,Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, EA 4331, Université de Poitiers, 86000 Poitiers, France
| | - Carine Meignin
- Modèles Insectes d'Immunité Innée (M3i), Université de Strasbourg, IBMC CNRS-UPR9022, Strasbourg F-67000, France
| | - Laurent Daeffler
- Modèles Insectes d'Immunité Innée (M3i), Université de Strasbourg, IBMC CNRS-UPR9022, Strasbourg F-67000, France
| | - Brian Federici
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86000 Poitiers, France
| | - Clément Gilbert
- Laboratoire Evolution, Génomes, Comportement, Écologie, Unité Mixte de Recherche 9191 Centre National de la Recherche Scientifique et Unité Mixte de Recherche 247 Institut de Recherche pour le Développement, Université Paris-Saclay, Gif-sur-Yvette 91198, France
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22
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Intravenous Delivery of piggyBac Transposons as a Useful Tool for Liver-Specific Gene-Switching. Int J Mol Sci 2018; 19:ijms19113452. [PMID: 30400245 PMCID: PMC6274756 DOI: 10.3390/ijms19113452] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/28/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022] Open
Abstract
Hydrodynamics-based gene delivery (HGD) is an efficient method for transfecting plasmid DNA into hepatocytes in vivo. However, the resulting gene expression is transient, and occurs in a non-tissue specific manner. The piggyBac (PB) transposon system allows chromosomal integration of a transgene in vitro. This study aimed to achieve long-term in vivo expression of a transgene by performing hepatocyte-specific chromosomal integration of the transgene using PB and HGD. Using this approach, we generated a novel mouse model for a hepatic disorder. A distinct signal from the reporter plasmid DNA was discernible in the murine liver approximately two months after the administration of PB transposons carrying a reporter gene. Then, to induce the hepatic disorder, we first administered mice with a PB transposon carrying a CETD unit (loxP-flanked stop cassette, diphtheria toxin-A chain gene, and poly(A) sites), and then with a plasmid expressing the Cre recombinase under the control of a liver-specific promoter. We showed that this system can be used for in situ manipulation and analysis of hepatocyte function in vivo in non-transgenic (Tg) animals.
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23
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Chen J, Wu C, Zhang B, Cai Z, Wei L, Li Z, Li G, Guo T, Li Y, Guo W, Wang X. PiggyBac Transposon-Mediated Transgenesis in the Pacific Oyster ( Crassostrea gigas) - First Time in Mollusks. Front Physiol 2018; 9:811. [PMID: 30061837 PMCID: PMC6054966 DOI: 10.3389/fphys.2018.00811] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/08/2018] [Indexed: 11/25/2022] Open
Abstract
As an effective method of transgenesis, the plasmid of PiggyBac transposon containing GFP (PiggyBac) transposon system has been widely used in various organisms but not yet in mollusks. In this work, piggyBac containing green fluorescent protein (GFP) was transferred into the Pacific oyster (Crassostrea gigas) by sperm-mediated gene transfer with or without electroporation. Fluorescent larvae were then observed and isolated under an inverted fluorescence microscope, and insertion of piggyBac was tested by polymerase chain reaction (PCR) using genomic DNA as template. Oyster larvae with green fluorescence were observed after transgenesis with or without electroporation, but electroporation increased the efficiency of sperm-mediated transgenesis. Subsequently, the recombinant piggyBac plasmid containing gGH (piggyBac-gGH) containing GFP and a growth hormone gene from orange-spotted grouper (gGH) was transferred into oysters using sperm mediation with electroporation, and fluorescent larvae were observed and isolated. The insertion of piggyBac-gGH was tested by PCR and genome walking analysis. PCR analysis indicated that piggyBac-gGH was transferred into oyster larvae; genome walking analysis further showed the detailed location where piggyBac-gGH was inserted in the oyster genome. This is the first time that piggyBac transposon-mediated transgenesis has been applied in mollusks.
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Affiliation(s)
- Jun Chen
- School of Agriculture, Ludong University, Yantai, China
| | - Changlu Wu
- School of Agriculture, Ludong University, Yantai, China
| | - Baolu Zhang
- Consultation Center, State Oceanic Administration, Beijing, China
| | - Zhongqiang Cai
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai, China
| | - Lei Wei
- School of Agriculture, Ludong University, Yantai, China
| | - Zhuang Li
- School of Agriculture, Ludong University, Yantai, China
| | - Guangbin Li
- School of Agriculture, Ludong University, Yantai, China
| | - Ting Guo
- School of Agriculture, Ludong University, Yantai, China
| | - Yongchuan Li
- School of Agriculture, Ludong University, Yantai, China
| | - Wen Guo
- Center for Mollusc Study and Development, Marine Biology Institute of Shandong Province, Qingdao, China
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, China
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24
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Eckermann KN, Ahmed HMM, KaramiNejadRanjbar M, Dippel S, Ogaugwu CE, Kitzmann P, Isah MD, Wimmer EA. Hyperactive piggyBac transposase improves transformation efficiency in diverse insect species. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 98:16-24. [PMID: 29653176 DOI: 10.1016/j.ibmb.2018.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 04/06/2018] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Even in times of advanced site-specific genome editing tools, the improvement of DNA transposases is still on high demand in the field of transgenesis: especially in emerging model systems where evaluated integrase landing sites have not yet been created and more importantly in non-model organisms such as agricultural pests and disease vectors, in which reliable sequence information and genome annotations are still pending. In fact, random insertional mutagenesis is essential to identify new genomic locations that are not influenced by position effects and thus can serve as future stable transgene integration sites. In this respect, a hyperactive version of the most widely used piggyBac transposase (PBase) has been engineered. The hyperactive version (hyPBase) is currently available with the original insect codon-based coding sequence (ihyPBase) as well as in a mammalian codon-optimized (mhyPBase) version. Both facilitate significantly higher rates of transposition when expressed in mammalian in vitro and in vivo systems compared to the classical PBase at similar protein levels. Here we demonstrate that the usage of helper plasmids encoding the hyPBase - irrespective of the codon-usage - also strikingly increases the rate of successful germline transformation in the Mediterranean fruit fly (Medfly) Ceratitis capitata, the red flour beetle Tribolium castaneum, and the vinegar fly Drosophila melanogaster. hyPBase-encoding helpers are therefore highly suitable for the generation of transgenic strains of diverse insect orders. Depending on the species, we achieved up to 15-fold higher germline transformation rates compared to PBase and generated hard to obtain transgenic T. castaneum strains that express constructs affecting fitness and viability. Moreover, previously reported high sterility rates supposedly caused by hyPBase (iPB7), encoded by ihyPBase, could not be confirmed by our study. Therefore, we value hyPBase as an effective genetic engineering tool that we highly recommend for insect transgenesis.
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Affiliation(s)
- Kolja N Eckermann
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany; Göttingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, University of Göttingen, 37077 Goettingen, Germany; Molecular Cell Dynamics, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Hassan M M Ahmed
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Mohammad KaramiNejadRanjbar
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Stefan Dippel
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Christian E Ogaugwu
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Peter Kitzmann
- Göttingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, University of Göttingen, 37077 Goettingen, Germany; Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Musa D Isah
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Ernst A Wimmer
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center of Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany; Göttingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, University of Göttingen, 37077 Goettingen, Germany.
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25
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Mutumwinka D, Zhao SB, Liu YS, Mensah EO, Gao XD, Fujita M. PiggyBac-based screening identified BEM4 as a suppressor to rescue growth defects in och1-disrupted yeast cells. Biosci Biotechnol Biochem 2018; 82:1497-1507. [PMID: 29882469 DOI: 10.1080/09168451.2018.1482193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Glycoengineered yeast cells, which express human-compatible glycan structures, are particularly attractive host cells to produce therapeutic glycoproteins. Disruption of OCH1 gene, which encodes an α-1,6-mannosyltransferase required for mannan-type N-glycan formation, is essential for the elimination of yeast-specific N-glycan structures. However, the gene disruption causes cell wall defects leading to growth defects. Here, we tried to identify factors to rescue the growth defects of och1Δ cells by in vivo mutagenesis using piggyBac (PB)-based transposon. We isolated a mutant strain, named 121, which could grow faster than parental och1Δ cells. The PB element was introduced into the promoter region of BEM4 gene and upregulated the BEM4 expression. Overexpression of BEM4 suppressed growth defects in och1Δ cells. The slow grow phenotypes were partially rescued by expression of Rho1p, whose function is regulated by Bem4p. Our results indicate that BEM4 would be useful to produce therapeutic proteins in glycoengineered yeast without the growth defects.
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Affiliation(s)
- Diane Mutumwinka
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Shen-Bao Zhao
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Yi-Shi Liu
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Emmanuel Osei Mensah
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Xiao-Dong Gao
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
| | - Morihisa Fujita
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu , China
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26
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Morellet N, Li X, Wieninger SA, Taylor JL, Bischerour J, Moriau S, Lescop E, Bardiaux B, Mathy N, Assrir N, Bétermier M, Nilges M, Hickman AB, Dyda F, Craig NL, Guittet E. Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase. Nucleic Acids Res 2018; 46:2660-2677. [PMID: 29385532 PMCID: PMC5861402 DOI: 10.1093/nar/gky044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 01/12/2018] [Accepted: 01/17/2018] [Indexed: 12/16/2022] Open
Abstract
The piggyBac transposase (PB) is distinguished by its activity and utility in genome engineering, especially in humans where it has highly promising therapeutic potential. Little is known, however, about the structure-function relationships of the different domains of PB. Here, we demonstrate in vitro and in vivo that its C-terminal Cysteine-Rich Domain (CRD) is essential for DNA breakage, joining and transposition and that it binds to specific DNA sequences in the left and right transposon ends, and to an additional unexpectedly internal site at the left end. Using NMR, we show that the CRD adopts the specific fold of the cross-brace zinc finger protein family. We determine the interaction interfaces between the CRD and its target, the 5'-TGCGT-3'/3'-ACGCA-5' motifs found in the left, left internal and right transposon ends, and use NMR results to propose docking models for the complex, which are consistent with our site-directed mutagenesis data. Our results provide support for a model of the PB/DNA interactions in the context of the transpososome, which will be useful for the rational design of PB mutants with increased activity.
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Affiliation(s)
- Nelly Morellet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Xianghong Li
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Silke A Wieninger
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Jennifer L Taylor
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julien Bischerour
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Séverine Moriau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Benjamin Bardiaux
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Nathalie Mathy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Nadine Assrir
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Mireille Bétermier
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Michael Nilges
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy L Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric Guittet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
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27
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Laptev IA, Raevskaya NM, Filimonova NA, Sineoky SP. The piggyBac Transposon as a Tool in Genetic Engineering. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s000368381709006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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28
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Drezen JM, Josse T, Bézier A, Gauthier J, Huguet E, Herniou EA. Impact of Lateral Transfers on the Genomes of Lepidoptera. Genes (Basel) 2017; 8:E315. [PMID: 29120392 PMCID: PMC5704228 DOI: 10.3390/genes8110315] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 10/31/2017] [Accepted: 11/01/2017] [Indexed: 11/25/2022] Open
Abstract
Transfer of DNA sequences between species regardless of their evolutionary distance is very common in bacteria, but evidence that horizontal gene transfer (HGT) also occurs in multicellular organisms has been accumulating in the past few years. The actual extent of this phenomenon is underestimated due to frequent sequence filtering of "alien" DNA before genome assembly. However, recent studies based on genome sequencing have revealed, and experimentally verified, the presence of foreign DNA sequences in the genetic material of several species of Lepidoptera. Large DNA viruses, such as baculoviruses and the symbiotic viruses of parasitic wasps (bracoviruses), have the potential to mediate these transfers in Lepidoptera. In particular, using ultra-deep sequencing, newly integrated transposons have been identified within baculovirus genomes. Bacterial genes have also been acquired by genomes of Lepidoptera, as in other insects and nematodes. In addition, insertions of bracovirus sequences were present in the genomes of certain moth and butterfly lineages, that were likely corresponding to rearrangements of ancient integrations. The viral genes present in these sequences, sometimes of hymenopteran origin, have been co-opted by lepidopteran species to confer some protection against pathogens.
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Affiliation(s)
- Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Jérémy Gauthier
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Elisabeth Anne Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
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29
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Janune D, Abd El Kader T, Aoyama E, Nishida T, Tabata Y, Kubota S, Takigawa M. Novel role of CCN3 that maintains the differentiated phenotype of articular cartilage. J Bone Miner Metab 2017; 35:582-597. [PMID: 27853940 DOI: 10.1007/s00774-016-0793-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 09/25/2016] [Indexed: 02/07/2023]
Abstract
Knowledge of the microenvironment of articular cartilage in health and disease is the key to accomplishing fundamental disease-modifying treatments for osteoarthritis. The proteins comprising the CCN Family are matricellular proteins with a remarkable relevance within the context of cartilage metabolism. CCN2 displays a great capability for regenerating articular cartilage, and CCN3 has been shown to activate the expression of genes related to articular chondrocytes and to repress genes related to endochondral ossification in epiphyseal chondrocytes. Moreover, mice lacking CCN3 protein have been shown to display ostearthritic changes in their knee articular cartilage. In this study, we employed a monoiodoacetic acid (MIA)-induced osteoarthritic model to investigate whether osteoarthritic changes in the cartilage are reciprocally accompanied by CCN3 down-regulation and an inducible overexpression system to evaluate the effects of CCN3 on articular chondrocytes in vitro. Finally, we also investigated the effects of exogenous CCN3 in vivo during the early stages of MIA-induced osteoarthritis. We discovered that CCN3 is expressed by articular chondrocytes in normal rat knees, whereas it is rapidly down-regulated in osteoarthritic knees. In vitro, we also discovered that CCN3 increases the proteoglycan accumulation, the gene expression of type II collagen, tenascin-C and lubricin, as well as the protein production of tenascin-C and lubricin in articular chondrocytes. In vivo, it was discovered that exogenous CCN3 increased tidemark integrity and produced an increased production of lubricin protein. The potential utility of CCN3 as a future therapeutic agent and possible strategies to improve its therapeutic functions are also discussed.
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Affiliation(s)
- Danilo Janune
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8525, Japan
| | - Tarek Abd El Kader
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
| | - Eriko Aoyama
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
| | - Takashi Nishida
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8525, Japan
| | - Yasuhiko Tabata
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Satoshi Kubota
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan.
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8525, Japan.
| | - Masaharu Takigawa
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan.
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8525, Japan.
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30
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Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum. Nat Commun 2017; 8:455. [PMID: 28878209 PMCID: PMC5587575 DOI: 10.1038/s41467-017-00342-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 06/22/2017] [Indexed: 01/01/2023] Open
Abstract
Polyploid bacteria are common, but the genetic and functional diversity resulting from polyploidy is unknown. Here we use single-cell genomics, metagenomics, single-cell amplicon sequencing, and fluorescence in situ hybridization, to show that individual cells of Achromatium oxaliferum, the world’s biggest known freshwater bacterium, harbor genetic diversity typical of whole bacterial communities. The cells contain tens of transposable elements, which likely cause the unprecedented diversity that we observe in the sequence and synteny of genes. Given the high within-cell diversity of the usually conserved 16S ribosomal RNA gene, we suggest that gene conversion occurs in multiple, separated genomic hotspots. The ribosomal RNA distribution inside the cells hints to spatially differential gene expression. We also suggest that intracellular gene transfer may lead to extensive gene reshuffling and increased diversity. The cells of Achromatium bacteria are remarkably large and contain multiple chromosome copies. Here, Ionescu et al. show that chromosome copies within individual cells display high diversity, similar to that of bacterial communities, and contain tens of transposable elements.
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31
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A reliable and flexible gene manipulation strategy in posthatch zebra finch brain. Sci Rep 2017; 7:43244. [PMID: 28233828 PMCID: PMC5324116 DOI: 10.1038/srep43244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/20/2017] [Indexed: 12/19/2022] Open
Abstract
Songbird models meaningfully contribute to many fields including learned vocal communication, the neurobiology of social interactions, brain development, and ecology. The value of investigating gene-brain-behavior relationships in songbirds is therefore high. Viral infections typically used in other lab animals to deliver gene editing constructs have been less effective in songbirds, likely due to immune system properties. We therefore leveraged the in vivo electroporation strategy used in utero in rodents and in ovo in poultry, and apply it to posthatch zebra finch songbird chicks. We present a series of experiments with a combination of promoters, fluorescent protein genes, and piggyBac transposase vectors to demonstrate that this can be a reliable, efficient, and flexible strategy for genome manipulation. We discuss options for gene delivery experiments to test circuit and behavioral hypotheses using a variety of manipulations, including gene overexpression, CRISPR/Cas9 gene editing, inducible technologies, optogenetic or DREADD cellular control, and cell type-specific expression.
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32
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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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33
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In Vitro Transfection with and Expression of CCN Family of Genes. Methods Mol Biol 2016. [PMID: 27734370 DOI: 10.1007/978-1-4939-6430-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The ability to engineer cells to express a protein of interest in an inducible manner and stably for a long period is a valuable tool in molecular biology and also one that holds promise for regenerative medicine in the future. CCN proteins have been suggested to be involved in tissue regeneration. In this chapter, we describe an in vitro method for stable and inducible expression of CCN protein in a chondroprogenitor cell line and in chondrocytes in primary culture that does not involve the use of any viral vector.
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Yang D, Liao R, Zheng Y, Sun L, Xu T. Analysis of PBase Binding Profile Indicates an Insertion Target Selection Mechanism Dependent on TTAA, But Not Transcriptional Activity. Int J Biol Sci 2016; 12:1074-82. [PMID: 27570481 PMCID: PMC4997051 DOI: 10.7150/ijbs.15589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/15/2016] [Indexed: 12/20/2022] Open
Abstract
Transposons and retroviruses are important pathogenic agents and tools for mutagenesis and transgenesis. Insertion target selection is a key feature for a given transposon or retrovirus. The piggyBac (PB) transposon is highly active in mice and human cells, which has a much better genome-wide distribution compared to the retrovirus and P-element. However, the underlying reason is not clear. Utilizing a tagged functional PB transposase (PBase), we were able to conduct genome-wide profiling for PBase binding sites in the mouse genome. We have shown that PBase binding mainly depends on the distribution of the tetranucleotide TTAA, which is not affected by the presence of PB DNA. Furthermore, PBase binding is negatively influenced by the methylation of CG sites in the genome. Analysis of a large collection of PB insertions in mice has revealed an insertion profile similar to the PBase binding profile. Interestingly, this profile is not correlated with transcriptional active genes in the genome or transcriptionally active regions within a transcriptional unit. This differs from what has been previously shown for P-element and retroviruses insertions. Our study provides an explanation for PB's genome-wide insertion distribution and also suggests that PB target selection relies on a new mechanism independent of active transcription and open chromatin structure.
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Affiliation(s)
- Dong Yang
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433; 2. Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06536
| | - Ruiqi Liao
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433
| | - Yun Zheng
- 3. Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Ling Sun
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433
| | - Tian Xu
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Fudan-Yale Center for Biomedical Research, Innovation Center for International Cooperation of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433; 2. Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06536
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Sato M, Maeda K, Koriyama M, Inada E, Saitoh I, Miura H, Ohtsuka M, Nakamura S, Sakurai T, Watanabe S, Miyoshi K. The piggyBac-Based Gene Delivery System Can Confer Successful Production of Cloned Porcine Blastocysts with Multigene Constructs. Int J Mol Sci 2016; 17:E1424. [PMID: 27589724 PMCID: PMC5037703 DOI: 10.3390/ijms17091424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/06/2016] [Accepted: 08/19/2016] [Indexed: 01/02/2023] Open
Abstract
The introduction of multigene constructs into single cells is important for improving the performance of domestic animals, as well as understanding basic biological processes. In particular, multigene constructs allow the engineering and integration of multiple genes related to xenotransplantation into the porcine genome. The piggyBac (PB) transposon system allows multiple genes to be stably integrated into target genomes through a single transfection event. However, to our knowledge, no attempt to introduce multiple genes into a porcine genome has been made using this system. In this study, we simultaneously introduced seven transposons into a single porcine embryonic fibroblast (PEF). PEFs were transfected with seven transposons containing genes for five drug resistance proteins and two (red and green) fluorescent proteins, together with a PB transposase expression vector, pTrans (experimental group). The above seven transposons (without pTrans) were transfected concomitantly (control group). Selection of these transfected cells in the presence of multiple selection drugs resulted in the survival of several clones derived from the experimental group, but not from the control. PCR analysis demonstrated that approximately 90% (12/13 tested) of the surviving clones possessed all of the introduced transposons. Splinkerette PCR demonstrated that the transposons were inserted through the TTAA target sites of PB. Somatic cell nuclear transfer (SCNT) using a PEF clone with multigene constructs demonstrated successful production of cloned blastocysts expressing both red and green fluorescence. These results indicate the feasibility of this PB-mediated method for simultaneous transfer of multigene constructs into the porcine cell genome, which is useful for production of cloned transgenic pigs expressing multiple transgenes.
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Affiliation(s)
- Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, Kagoshima 890-8544, Japan.
| | - Kosuke Maeda
- Laboratory of Animal Reproduction, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| | - Miyu Koriyama
- Laboratory of Animal Reproduction, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| | - Emi Inada
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan.
| | - Issei Saitoh
- Division of Pediatric Dentistry, Department of Oral Health Sciences, Course for Oral Life Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan.
| | - Hiromi Miura
- Department of Regenerative Medicine, Basic Medical Science, School of Medicine, Tokai University, Kanagawa 259-1193, Japan.
| | - Masato Ohtsuka
- Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa 259-1193, Japan.
- The Institute of Medical Sciences, Tokai University, Kanagawa 259-1193, Japan.
| | - Shingo Nakamura
- Division of Biomedical Engineering, National Defense Medical College Research Institute, Saitama 359-8513, Japan.
| | - Takayuki Sakurai
- Department of Cardiovascular Research, Graduate school of Medicine, Shinshu University, Nagano 390-8621, Japan.
| | - Satoshi Watanabe
- Animal Genome Research Unit, Division of Animal Science, National Institute of Agrobiological Sciences, Ibaraki 305-8602, Japan.
| | - Kazuchika Miyoshi
- Laboratory of Animal Reproduction, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
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Zhang L, Cui Z, Zhou L, Kang Y, Li L, Li J, Dai Y, Yu S, Li N. Developing a Triple Transgenic Cell Line for High-Efficiency Porcine Reproductive and Respiratory Syndrome Virus Infection. PLoS One 2016; 11:e0154238. [PMID: 27182980 PMCID: PMC4868347 DOI: 10.1371/journal.pone.0154238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/11/2016] [Indexed: 11/24/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most devastating pathogens in the swine industry worldwide. Due to the lack of robust cell lines and small animal models, the pathogenesis of PRRSV infection and mechanism for protective vaccination are still not yet well understood. To obtain useful cell lines, several groups have attempted to construct different transgenic cell lines with three PRRSV receptors: CD163, CD169, and CD151. The results showed that CD163 is essential for PRRSV entry into target cells and replication, and both CD169 and CD151 play key roles during PRRSV infection. However, their interplay and combined effect remains unclear. In this study, we generated transgenic BHK-21 derived cell lines co-expressing different combinations of the three receptors, which were transfected with CD163 alone, or the combination of CD163 and CD169, or the combination of CD163 and CD151, or the combination of CD163, CD169, and CD151 using the PiggyBac transposon system. Our results showed that the synergistic interaction among the three receptors was important to improve the susceptibility of cells during PRRSV infection. Through a series of comparable analyses, we confirmed that the cell line co-expressing triple receptors sustained viral infection and replication, and was superior to the current cell platform used for the PRRSV study, MARC-145 cells. Moreover, we found that PRRSV infection of the transgenic cell lines could trigger IFN-stimulated gene responses similar to those of porcine alveolar macrophages and MARC-145 cells. In summary, we developed a stable transgenic cell line susceptible to PRRSV, which may not only provide a useful tool for virus propagation, vaccine development, and pathogenesis studies, but also establish the foundation for small animal model development.
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Affiliation(s)
- Linlin Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhengzhi Cui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lei Zhou
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Youmin Kang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Li Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jinxiu Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yunping Dai
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shuyang Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- * E-mail: (SY); (NL)
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- * E-mail: (SY); (NL)
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Bronner IF, Otto TD, Zhang M, Udenze K, Wang C, Quail MA, Jiang RHY, Adams JH, Rayner JC. Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants. Genome Res 2016; 26:980-9. [PMID: 27197223 PMCID: PMC4937560 DOI: 10.1101/gr.200279.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 05/04/2016] [Indexed: 01/06/2023]
Abstract
Genetic screening using random transposon insertions has been a powerful tool for uncovering biology in prokaryotes, where whole-genome saturating screens have been performed in multiple organisms. In eukaryotes, such screens have proven more problematic, in part because of the lack of a sensitive and robust system for identifying transposon insertion sites. We here describe quantitative insertion-site sequencing, or QIseq, which uses custom library preparation and Illumina sequencing technology and is able to identify insertion sites from both the 5′ and 3′ ends of the transposon, providing an inbuilt level of validation. The approach was developed using piggyBac mutants in the human malaria parasite Plasmodium falciparum but should be applicable to many other eukaryotic genomes. QIseq proved accurate, confirming known sites in >100 mutants, and sensitive, identifying and monitoring sites over a >10,000-fold dynamic range of sequence counts. Applying QIseq to uncloned parasites shortly after transfections revealed multiple insertions in mixed populations and suggests that >4000 independent mutants could be generated from relatively modest scales of transfection, providing a clear pathway to genome-scale screens in P. falciparum. QIseq was also used to monitor the growth of pools of previously cloned mutants and reproducibly differentiated between deleterious and neutral mutations in competitive growth. Among the mutants with fitness defects was a mutant with a piggyBac insertion immediately upstream of the kelch protein K13 gene associated with artemisinin resistance, implying mutants in this gene may have competitive fitness costs. QIseq has the potential to enable the scale-up of piggyBac-mediated genetics across multiple eukaryotic systems.
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Affiliation(s)
- Iraad F Bronner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Min Zhang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Kenneth Udenze
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Michael A Quail
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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Huang Y, Liu Z, Rong YS. Genome Editing: From Drosophila to Non-Model Insects and Beyond. J Genet Genomics 2016; 43:263-72. [PMID: 27216295 DOI: 10.1016/j.jgg.2016.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/06/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022]
Abstract
Insect is the largest group of animals on land. Many insect species inflict economical and health losses to humans. Yet many more benefit us by helping to maintain balances in our ecosystem. The benefits that insects offer remain largely untapped, justifying our continuing efforts to develop tools to better understand their biology and to better manage their activities. Here we focus on reviewing the progresses made in the development of genome engineering tools for model insects. Instead of detailed descriptions of the molecular mechanisms underlying each technical advance, we focus our discussion on the logistics for implementing similar tools in non-model insects. Since none of the tools were developed specific for insects, similar approaches can be applied to other non-model organisms.
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Affiliation(s)
- Yueping Huang
- Institute of Entomology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiping Liu
- Institute of Entomology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yikang S Rong
- Institute of Entomology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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Abstract
The piggyBac transposon was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and dissimilarity to the other DNA transposon families, the piggyBac transposon was not recognized as a member of a large transposon superfamily for a long time. Initially, the piggyBac transposon was thought to be a rare transposon. This view, however, has now been completely revised as a number of fully sequenced genomes have revealed the presence of piggyBac-like repetitive elements. The isolation of active copies of the piggyBac-like elements from several distinct species further supported this revision. This includes the first isolation of an active mammalian DNA transposon identified in the bat genome. To date, the piggyBac transposon has been deeply characterized and it represents a number of unique characteristics. In general, all members of the piggyBac superfamily use TTAA as their integration target sites. In addition, the piggyBac transposon shows precise excision, i.e., restoring the sequence to its preintegration state, and can transpose in a variety of organisms such as yeasts, malaria parasites, insects, mammals, and even in plants. Biochemical analysis of the chemical steps of transposition revealed that piggyBac does not require DNA synthesis during the actual transposition event. The broad host range has attracted researchers from many different fields, and the piggyBac transposon is currently the most widely used transposon system for genetic manipulations.
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40
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Abstract
Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80-100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.
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Kim SI, Oceguera-Yanez F, Sakurai C, Nakagawa M, Yamanaka S, Woltjen K. Inducible Transgene Expression in Human iPS Cells Using Versatile All-in-One piggyBac Transposons. Methods Mol Biol 2016; 1357:111-31. [PMID: 26025620 DOI: 10.1007/7651_2015_251] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transgenics is a mainstay of functional genomics. Conditionally overexpressing genes of interest (GOIs) helps to reveal their roles in the control of complex biological processes. Complemented by findings in classic animal model systems, recent advances in human embryonic stem cell (hESC) and patient-specific induced pluripotent stem cell (hiPSC) differentiation have led to sophisticated in vitro models of human development and disease. Yet, as transgenic elements encoding inducible systems must be introduced de novo into each genetically unique human stem cell line, robust and straightforward solutions to gene delivery are required. Transposons are a family of mobile DNA elements that have been adapted as experimental tools for stable genomic integration of transgenes. The piggyBac (PB) transposon from Trichoplusia ni presents a number of benefits over classic viral or BAC transgenesis: ease of application, simple integration-site mapping, and the unique capacity for traceless excision. Moreover, their large capacity permits the consolidation of multiple transgene components in a single vector system. In this chapter, we outline the features of a panel of "All-in-One" PB transposons designed for drug-inducible gene expression and provide guidelines to establish and validate populations or clones of transgenic hiPSCs.
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Affiliation(s)
- Shin-Il Kim
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Fabian Oceguera-Yanez
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Chiho Sakurai
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Masato Nakagawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- Gladstone Institutes of Cardiovascular Disease, University of California, San Francisco, CA, 94158, USA
| | - Knut Woltjen
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, 606-8501, Japan.
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Alessio AP, Fili AE, Garrels W, Forcato DO, Olmos Nicotra MF, Liaudat AC, Bevacqua RJ, Savy V, Hiriart MI, Talluri TR, Owens JB, Ivics Z, Salamone DF, Moisyadi S, Kues WA, Bosch P. Establishment of cell-based transposon-mediated transgenesis in cattle. Theriogenology 2015; 85:1297-311.e2. [PMID: 26838464 DOI: 10.1016/j.theriogenology.2015.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/10/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022]
Abstract
Transposon-mediated transgenesis is a well-established tool for genome modification in small animal models. However, translation of this active transgenic method to large animals warrants further investigations. Here, the piggyBac (PB) and sleeping beauty (SB) transposon systems were assessed for stable gene transfer into the cattle genome. Bovine fibroblasts were transfected either with a helper-independent PB system or a binary SB system. Both transposons were highly active in bovine cells increasing the efficiency of DNA integration up to 88 times over basal nonfacilitated integrations in a colony formation assay. SB transposase catalyzed multiplex transgene integrations in fibroblast cells transfected with the helper vector and two donor vectors carrying different transgenes (fluorophore and neomycin resistance). Stably transfected fibroblasts were used for SCNT and on in vitro embryo culture, morphologically normal blastocysts that expressed the fluorophore were obtained with both transposon systems. The data indicate that transposition is a feasible approach for genetic engineering in the cattle genome.
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Affiliation(s)
- Ana P Alessio
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - Alejandro E Fili
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - Wiebke Garrels
- Department of Biotechnology, Friedrich-Loeffler-Institut, Institut für Nutztiergenetik, Neustadt, Germany
| | - Diego O Forcato
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - María F Olmos Nicotra
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - Ana C Liaudat
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina
| | - Romina J Bevacqua
- Laboratorio de Biotecnología Animal, Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, República Argentina
| | - Virginia Savy
- Laboratorio de Biotecnología Animal, Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, República Argentina
| | - María I Hiriart
- Laboratorio de Biotecnología Animal, Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, República Argentina
| | - Thirumala R Talluri
- Department of Biotechnology, Friedrich-Loeffler-Institut, Institut für Nutztiergenetik, Neustadt, Germany
| | - Jesse B Owens
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Daniel F Salamone
- Laboratorio de Biotecnología Animal, Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, República Argentina
| | - Stefan Moisyadi
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Wilfried A Kues
- Department of Biotechnology, Friedrich-Loeffler-Institut, Institut für Nutztiergenetik, Neustadt, Germany
| | - Pablo Bosch
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, República Argentina.
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CAMSAP3 orients the apical-to-basal polarity of microtubule arrays in epithelial cells. Proc Natl Acad Sci U S A 2015; 113:332-7. [PMID: 26715742 DOI: 10.1073/pnas.1520638113] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Polarized epithelial cells exhibit a characteristic array of microtubules that are oriented along the apicobasal axis of the cells. The minus-ends of these microtubules face apically, and the plus-ends face toward the basal side. The mechanisms underlying this epithelial-specific microtubule assembly remain unresolved, however. Here, using mouse intestinal cells and human Caco-2 cells, we show that the microtubule minus-end binding protein CAMSAP3 (calmodulin-regulated-spectrin-associated protein 3) plays a pivotal role in orienting the apical-to-basal polarity of microtubules in epithelial cells. In these cells, CAMSAP3 accumulated at the apical cortices, and tethered the longitudinal microtubules to these sites. Camsap3 mutation or depletion resulted in a random orientation of these microtubules; concomitantly, the stereotypic positioning of the nucleus and Golgi apparatus was perturbed. In contrast, the integrity of the plasma membrane was hardly affected, although its structural stability was decreased. Further analysis revealed that the CC1 domain of CAMSAP3 is crucial for its apical localization, and that forced mislocalization of CAMSAP3 disturbs the epithelial architecture. These findings demonstrate that apically localized CAMSAP3 determines the proper orientation of microtubules, and in turn that of organelles, in mature mammalian epithelial cells.
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Henssen AG, Henaff E, Jiang E, Eisenberg AR, Carson JR, Villasante CM, Ray M, Still E, Burns M, Gandara J, Feschotte C, Mason CE, Kentsis A. Genomic DNA transposition induced by human PGBD5. eLife 2015; 4. [PMID: 26406119 PMCID: PMC4625184 DOI: 10.7554/elife.10565] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/23/2015] [Indexed: 11/13/2022] Open
Abstract
Transposons are mobile genetic elements that are found in nearly all organisms, including humans. Mobilization of DNA transposons by transposase enzymes can cause genomic rearrangements, but our knowledge of human genes derived from transposases is limited. In this study, we find that the protein encoded by human PGBD5, the most evolutionarily conserved transposable element-derived gene in vertebrates, can induce stereotypical cut-and-paste DNA transposition in human cells. Genomic integration activity of PGBD5 requires distinct aspartic acid residues in its transposase domain, and specific DNA sequences containing inverted terminal repeats with similarity to piggyBac transposons. DNA transposition catalyzed by PGBD5 in human cells occurs genome-wide, with precise transposon excision and preference for insertion at TTAA sites. The apparent conservation of DNA transposition activity by PGBD5 suggests that genomic remodeling contributes to its biological function.
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Affiliation(s)
- Anton G Henssen
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Elizabeth Henaff
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Eileen Jiang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Amy R Eisenberg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Julianne R Carson
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Camila M Villasante
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Mondira Ray
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Eric Still
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Melissa Burns
- Boston Children's Hospital, Harvard Medical School, Boston, United States
| | - Jorge Gandara
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Cedric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Christopher E Mason
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States.,Department of Pediatrics, Memorial Sloan Kaettering Cancer Center, New York, United States.,Weill Cornell Medical College, Cornell University, New York, United States
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45
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Inada E, Saitoh I, Watanabe S, Aoki R, Miura H, Ohtsuka M, Murakami T, Sawami T, Yamasaki Y, Sato M. PiggyBac transposon-mediated gene delivery efficiently generates stable transfectants derived from cultured primary human deciduous tooth dental pulp cells (HDDPCs) and HDDPC-derived iPS cells. Int J Oral Sci 2015. [PMID: 26208039 PMCID: PMC4582557 DOI: 10.1038/ijos.2015.18] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The ability of human deciduous tooth dental pulp cells (HDDPCs) to differentiate into odontoblasts that generate mineralized tissue holds immense potential for therapeutic use in the field of tooth regenerative medicine. Realization of this potential depends on efficient and optimized protocols for the genetic manipulation of HDDPCs. In this study, we demonstrate the use of a PiggyBac (PB)-based gene transfer system as a method for introducing nonviral transposon DNA into HDDPCs and HDDPC-derived inducible pluripotent stem cells. The transfection efficiency of the PB-based system was significantly greater than previously reported for electroporation-based transfection of plasmid DNA. Using the neomycin resistance gene as a selection marker, HDDPCs were stably transfected at a rate nearly 40-fold higher than that achieved using conventional methods. Using this system, it was also possible to introduce two constructs simultaneously into a single cell. The resulting stable transfectants, expressing tdTomato and enhanced green fluorescent protein, exhibited both red and green fluorescence. The established cell line did not lose the acquired phenotype over three months of culture. Based on our results, we concluded that PB is superior to currently available methods for introducing plasmid DNA into HDDPCs. There may be significant challenges in the direct clinical application of this method for human dental tissue engineering due to safety risks and ethical concerns. However, the high level of transfection achieved with PB may have significant advantages in basic scientific research for dental tissue engineering applications, such as functional studies of genes and proteins. Furthermore, it is a useful tool for the isolation of genetically engineered HDDPC-derived stem cells for studies in tooth regenerative medicine.
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Affiliation(s)
- Emi Inada
- Department of Pediatric Dentistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Issei Saitoh
- Division of Pediatric Dentistry, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Satoshi Watanabe
- Animal Genome Research Unit, Division of Animal Science, National Institute of Agrobiological Sciences, Ibaraki, Japan
| | - Reiji Aoki
- Functional Biomolecules Research Group, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Hiromi Miura
- Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa, Japan
| | - Masato Ohtsuka
- Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa, Japan
| | - Tomoya Murakami
- Division of Pediatric Dentistry, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Tadashi Sawami
- Division of Pediatric Dentistry, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Youichi Yamasaki
- Department of Pediatric Dentistry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, Kagoshima, Japan
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46
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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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47
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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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48
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Gee JM, Gibbons MB, Taheri M, Palumbos S, Morris SC, Smeal RM, Flynn KF, Economo MN, Cizek CG, Capecchi MR, Tvrdik P, Wilcox KS, White JA. Imaging activity in astrocytes and neurons with genetically encoded calcium indicators following in utero electroporation. Front Mol Neurosci 2015; 8:10. [PMID: 25926768 PMCID: PMC4397926 DOI: 10.3389/fnmol.2015.00010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 03/23/2015] [Indexed: 11/13/2022] Open
Abstract
Complex interactions between networks of astrocytes and neurons are beginning to be appreciated, but remain poorly understood. Transgenic mice expressing fluorescent protein reporters of cellular activity, such as the GCaMP family of genetically encoded calcium indicators (GECIs), have been used to explore network behavior. However, in some cases, it may be desirable to use long-established rat models that closely mimic particular aspects of human conditions such as Parkinson's disease and the development of epilepsy following status epilepticus. Methods for expressing reporter proteins in the rat brain are relatively limited. Transgenic rat technologies exist but are fairly immature. Viral-mediated expression is robust but unstable, requires invasive injections, and only works well for fairly small genes (<5 kb). In utero electroporation (IUE) offers a valuable alternative. IUE is a proven method for transfecting populations of astrocytes and neurons in the rat brain without the strict limitations on transgene size. We built a toolset of IUE plasmids carrying GCaMP variants 3, 6s, or 6f driven by CAG and targeted to the cytosol or the plasma membrane. Because low baseline fluorescence of GCaMP can hinder identification of transfected cells, we included the option of co-expressing a cytosolic tdTomato protein. A binary system consisting of a plasmid carrying a piggyBac inverted terminal repeat (ITR)-flanked CAG-GCaMP-IRES-tdTomato cassette and a separate plasmid encoding for expression of piggyBac transposase was employed to stably express GCaMP and tdTomato. The plasmids were co-electroporated on embryonic days 13.5-14.5 and astrocytic and neuronal activity was subsequently imaged in acute or cultured brain slices prepared from the cortex or hippocampus. Large spontaneous transients were detected in slices obtained from rats of varying ages up to 127 days. In this report, we demonstrate the utility of this toolset for interrogating astrocytic and neuronal activity in the rat brain.
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Affiliation(s)
- J Michael Gee
- Neuronal Dynamics Laboratory, Department of Bioengineering, University of Utah Salt Lake City, UT, USA ; MD-PhD Program, University of Utah Salt Lake City, UT, USA
| | - Meredith B Gibbons
- Glial-Neuronal Interactions in Epilepsy Laboratory, Department of Pharmacology and Toxicology, University of Utah Salt Lake City, UT, USA ; Interdepartmental Program in Neuroscience, University of Utah Salt Lake City, UT, USA
| | - Marsa Taheri
- Neuronal Dynamics Laboratory, Department of Bioengineering, University of Utah Salt Lake City, UT, USA
| | - Sierra Palumbos
- Mario Capecchi Laboratory, Department of Human Genetics, University of Utah Salt Lake City, UT, USA
| | - S Craig Morris
- Neuronal Dynamics Laboratory, Department of Bioengineering, University of Utah Salt Lake City, UT, USA ; Mario Capecchi Laboratory, Department of Human Genetics, University of Utah Salt Lake City, UT, USA
| | - Roy M Smeal
- Glial-Neuronal Interactions in Epilepsy Laboratory, Department of Pharmacology and Toxicology, University of Utah Salt Lake City, UT, USA
| | - Katherine F Flynn
- Glial-Neuronal Interactions in Epilepsy Laboratory, Department of Pharmacology and Toxicology, University of Utah Salt Lake City, UT, USA
| | - Michael N Economo
- Neuronal Dynamics Laboratory, Department of Bioengineering, University of Utah Salt Lake City, UT, USA
| | - Christian G Cizek
- Neuronal Dynamics Laboratory, Department of Bioengineering, University of Utah Salt Lake City, UT, USA ; Mario Capecchi Laboratory, Department of Human Genetics, University of Utah Salt Lake City, UT, USA
| | - Mario R Capecchi
- Mario Capecchi Laboratory, Department of Human Genetics, University of Utah Salt Lake City, UT, USA ; Department of Human Genetics, Howard Hughes Medical Institute, University of Utah Salt Lake City, UT, USA
| | - Petr Tvrdik
- Mario Capecchi Laboratory, Department of Human Genetics, University of Utah Salt Lake City, UT, USA
| | - Karen S Wilcox
- Glial-Neuronal Interactions in Epilepsy Laboratory, Department of Pharmacology and Toxicology, University of Utah Salt Lake City, UT, USA
| | - John A White
- Neuronal Dynamics Laboratory, Department of Bioengineering, University of Utah Salt Lake City, UT, USA
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49
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Haghighat-Khah RE, Scaife S, Martins S, St John O, Matzen KJ, Morrison N, Alphey L. Site-specific cassette exchange systems in the Aedes aegypti mosquito and the Plutella xylostella moth. PLoS One 2015; 10:e0121097. [PMID: 25830287 PMCID: PMC4382291 DOI: 10.1371/journal.pone.0121097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/09/2015] [Indexed: 12/02/2022] Open
Abstract
Genetically engineered insects are being evaluated as potential tools to decrease the economic and public health burden of mosquitoes and agricultural pest insects. Here we describe a new tool for the reliable and targeted genome manipulation of pest insects for research and field release using recombinase mediated cassette exchange (RMCE) mechanisms. We successfully demonstrated the established ΦC31-RMCE method in the yellow fever mosquito, Aedes aegypti, which is the first report of RMCE in mosquitoes. A new variant of this RMCE system, called iRMCE, combines the ΦC31-att integration system and Cre or FLP-mediated excision to remove extraneous sequences introduced as part of the site-specific integration process. Complete iRMCE was achieved in two important insect pests, Aedes aegypti and the diamondback moth, Plutella xylostella, demonstrating the transferability of the system across a wide phylogenetic range of insect pests.
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Affiliation(s)
- Roya Elaine Haghighat-Khah
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | - Sara Martins
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | - Oliver St John
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | | | - Luke Alphey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
- * E-mail: (LA); (KJM)
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50
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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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