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Avilan L. Assembling Multiple Fragments: The Gibson Assembly. Methods Mol Biol 2023; 2633:45-53. [PMID: 36853455 DOI: 10.1007/978-1-0716-3004-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The Gibson Assembly is a popular method for molecular cloning which has been developed specifically to join several fragments together in a specific order, without the constraint of restriction enzyme sites. This method is based on the assembly of overlapping fragments, generally produced by PCR, and then combining them using three enzymes: a 5' exonuclease, a DNA polymerase, and a DNA ligase, in an isothermal reaction. Here, we describe this method, including the design of primers for the generation of the overlapping fragments and the assembly; to this end, we provide an example involving joining two fragments in a single plasmid.
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2
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Costa TM, Brandt LCP, Maachi A, Nagata T. Construction of an infectious full-length cDNA clone of a recombinant isolate of cucurbit aphid-borne yellows virus from Brazil. Virus Genes 2023; 59:163-166. [PMID: 36306006 DOI: 10.1007/s11262-022-01948-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/16/2022] [Indexed: 01/13/2023]
Abstract
In Brazil, the main viral disease of melon plant is severe yellowing disease called "Amarelão do Meloeiro," and a polerovirus, cucurbit aphid-borne yellows virus (CABYV) was considered one of the etiological agents. This virus is a recombinant strain originated from CABYV and unknown polerovirus. Due to unsuccessful mechanical inoculations of CABYV to host plants, the study of its biological characterization is hampered. Therefore, an infectious clone of the recombinant strain of CABYV was constructed using the Gibson Assembly technology. The full-length cDNA clones produced in this study showed to be infectious in three cucurbit species; melon (Cucumis melo), squash (a hybrid of Cucurbita maxima × C. moschata), and West Indian gherkin (Cucumis anguria) plants, but not in watermelon, cucumber, and zucchini plants. This insusceptibility of watermelon plants to the infectious clone corroborates the observation that this virus was never found in watermelon plants often located next to the infected melon plants. This infectious clone provides important tools for future study in developing resistant melon variety to CABYV infection.
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Affiliation(s)
- Thiago Marques Costa
- Laboratório de Microscopia Eletrônica e Virologia, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil.,Pós-graduação em Biologia Celular e Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Lizandra Costa Pereira Brandt
- Laboratório de Microscopia Eletrônica e Virologia, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Ayoub Maachi
- Abiopep S.L., Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, 30100, Espinardo, Murcia, Spain
| | - Tatsuya Nagata
- Laboratório de Microscopia Eletrônica e Virologia, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil. .,Pós-graduação em Biologia Celular e Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil.
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3
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Li L, Changrob S, Fu Y, Stovicek O, Guthmiller JJ, McGrath JJC, Dugan HL, Stamper CT, Zheng NY, Huang M, Wilson PC. Librator: a platform for the optimized analysis, design, and expression of mutable influenza viral antigens. Brief Bioinform 2022; 23:6532539. [PMID: 35183062 PMCID: PMC8921739 DOI: 10.1093/bib/bbac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Artificial mutagenesis and protein engineering have laid the foundation for antigenic characterization and universal vaccine design for influenza viruses. However, many methods used in this process require manual sequence editing and protein expression, limiting their efficiency and utility in high-throughput applications. More streamlined in silico tools allowing researchers to properly analyze and visualize influenza viral protein sequences with accurate nomenclature are necessary to improve antigen design and productivity. To address this need, we developed Librator, a system for analyzing and designing custom protein sequences of influenza virus hemagglutinin (HA) and neuraminidase (NA) glycoproteins. Within Librator's graphical interface, users can easily interrogate viral sequences and phylogenies, visualize antigen structures and conservation, mutate target residues and design custom antigens. Librator also provides optimized fragment design for Gibson Assembly of HA and NA expression constructs based on peptide conservation of all historical HA and NA sequences, ensuring fragments are reusable and compatible across related subtypes, thereby promoting reagent savings. Finally, the program facilitates single-cell immune profiling, epitope mapping of monoclonal antibodies and mosaic protein design. Using Librator-based antigen construction, we demonstrate that antigenicity can be readily transferred between HA molecules of H3, but not H1, lineage viruses. Altogether, Librator is a valuable tool for analyzing influenza virus HA and NA proteins and provides an efficient resource for optimizing recombinant influenza antigen synthesis.
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Affiliation(s)
| | | | | | - Olivia Stovicek
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jenna J Guthmiller
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Joshua J C McGrath
- Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | | | - Nai-Ying Zheng
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA,Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Min Huang
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Patrick C Wilson
- Corresponding author: Patrick C. Wilson, Drukier Institute for Children’s Health, Weill Cornell Medicine, New York, NY 10021, USA. E-mail:
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4
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Ni N, Deng F, He F, Wang H, Shi D, Liao J, Zou Y, Wang H, Zhao P, Hu X, Chen C, Hu DA, Sabharwal M, Qin KH, Wagstaff W, Qin D, Hendren-Santiago B, Haydon RC, Luu HH, Reid RR, Shen L, He TC, Fan J. A one-step construction of adenovirus (OSCA) system using the Gibson DNA Assembly technology. Mol Ther Oncolytics 2021; 23:602-611. [PMID: 34977337 PMCID: PMC8666640 DOI: 10.1016/j.omto.2021.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/16/2021] [Indexed: 02/07/2023] Open
Abstract
Adenovirus (Ad) is a non-enveloped linear double-stranded DNA virus with >50 serotypes in humans. Ad vectors have been used as gene delivery vehicles to express transgenes, small interfering RNAs (siRNAs) for gene silencing, or CRISPR/Cas and designer nucleases for genome editing. Although several methods are used to generate Ad vectors, the Ad-making process remains technically challenging and time consuming. Moreover, the Ad-making techniques have not been improved for the past two decades. Gibson DNA Assembly (GDA) technology allows one-step isothermal DNA assembly of multiple overlapping fragments. Here, we developed a one-step construction of Ad (OSCA) system using GDA technology. Specifically, we first engineered several adenoviral recipient vectors that contain the ccdB suicide gene flanked with two 20-bp unique sequences, which serve as universal sites for GDA reactions in the Ad genome ΔE1 region. In two proof-of-principle experiments, we demonstrated that the GDA reactions were highly efficient and that the resulting Ad plasmids could be effectively packaged into Ads. Ad-mediated expression of mouse BMP9 in mesenchymal stem cells was shown to effectively induce osteogenic differentiation both in vitro and in vivo. Collectively, our results demonstrate that the OSCA system drastically streamlines the Ad-making process and should facilitate Ad-based applications in basic, translational, and clinical research.
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Affiliation(s)
- Na Ni
- Ministry of Education Key Laboratory of Diagnostic Medicine, and Department of Clinical Biochemistry, The School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Fang Deng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Pathophysiology, and Key Laboratory of High Altitude Medicine, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Departments of Gastroenterology, Blood Transfusion, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Hao Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine, and Department of Clinical Biochemistry, The School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Junyi Liao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Departments of Gastroenterology, Blood Transfusion, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yulong Zou
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Hongwei Wang
- Division of Research and Development, Decoding Therapeutics, Inc., Mt Prospect, IL 60056, USA
| | - Piao Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Departments of Gastroenterology, Blood Transfusion, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xue Hu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Departments of Gastroenterology, Blood Transfusion, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Daniel A Hu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Maya Sabharwal
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Kevin H Qin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - David Qin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Bryce Hendren-Santiago
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rex C Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jiaming Fan
- Ministry of Education Key Laboratory of Diagnostic Medicine, and Department of Clinical Biochemistry, The School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
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5
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Hamdan F, Martins B, Feodoroff M, Giannoula Y, Feola S, Fusciello M, Chiaro J, Antignani G, Grönholm M, Ylösmäki E, Cerullo V. GAMER-Ad: a novel and rapid method for generating recombinant adenoviruses. Mol Ther Methods Clin Dev 2021; 20:625-634. [PMID: 33718513 PMCID: PMC7907680 DOI: 10.1016/j.omtm.2021.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/27/2021] [Indexed: 12/18/2022]
Abstract
Oncolytic adenoviruses have become ideal agents in the path toward treating cancer. Such viruses have been engineered to conditionally replicate in malignant cells in which certain signaling pathways have been disrupted. Other than such oncolytic properties, the viruses need to activate the immune system in order to sustain a long-term response. Therefore, oncolytic adenoviruses have been genetically modified to express various immune-stimulatory agents to achieve this. However, genetically modifying adenoviruses is very time consuming and labor intensive with the current available methods. In this paper, we describe a novel method we have called GAMER-Ad to genetically modify adenovirus genomes within 2 days. Our method entails the replacement of the gp19k gene in the E3 region with any given gene of interest (GOI) using Gibson Assembly avoiding the homologous recombination between the shuttle and the parental plasmid. In this manuscript as proof of concept we constructed and characterized three oncolytic adenoviruses expressing CXCL9, CXCL10, and interleukin-15 (IL-15). We demonstrate that our novel method is fast, reliable, and simple compared to other methods. We anticipate that our method will be used in the future to genetically engineer oncolytic but also other adenoviruses used for gene therapy as well.
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Affiliation(s)
- Firas Hamdan
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Beatriz Martins
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Michaela Feodoroff
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Yvonne Giannoula
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Sara Feola
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Manlio Fusciello
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Jacopo Chiaro
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Gabriella Antignani
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Mikaela Grönholm
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Erkko Ylösmäki
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Vincenzo Cerullo
- Laboratory of Immunovirotherapy (IVTLab), Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.,Department of Molecular Medicine and Medical Biotechnology and CEINGE, Naples University 24 Federico II, 80131 Naples, Italy
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6
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De Munter S, Van Parys A, Bral L, Ingels J, Goetgeluk G, Bonte S, Pille M, Billiet L, Weening K, Verhee A, Van der Heyden J, Taghon T, Leclercq G, Kerre T, Tavernier J, Vandekerckhove B. Rapid and Effective Generation of Nanobody Based CARs using PCR and Gibson Assembly. Int J Mol Sci 2020; 21:ijms21030883. [PMID: 32019116 PMCID: PMC7037261 DOI: 10.3390/ijms21030883] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/25/2022] Open
Abstract
Recent approval of chimeric antigen receptor (CAR) T cell therapy by the European Medicines Agency (EMA)/Federal and Drug Administration (FDA) and the remarkable results of CAR T clinical trials illustrate the curative potential of this therapy. While CARs against a multitude of different antigens are being developed and tested (pre)clinically, there is still a need for optimization. The use of single-chain variable fragments (scFvs) as targeting moieties hampers the quick generation of functional CARs and could potentially limit the efficacy. Instead, nanobodies may largely circumvent these difficulties. We used an available nanobody library generated after immunization of llamas against Cluster of Differentiation (CD) 20 through DNA vaccination or against the ectodomain of CD33 using soluble protein. The nanobody specific sequences were amplified by PCR and cloned by Gibson Assembly into a retroviral vector containing two different second-generation CAR constructs. After transduction in T cells, we observed high cell membrane nanoCAR expression in all cases. Following stimulation of nanoCAR-expressing T cells with antigen-positive cell lines, robust T cell activation, cytokine production and tumor cell lysis both in vitro and in vivo was observed. The use of nanobody technology in combination with PCR and Gibson Assembly allows for the rapid and effective generation of compact CARs.
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Affiliation(s)
- Stijn De Munter
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Alexander Van Parys
- Cytokine Receptor Laboratory, Flanders Institute of Biotechnology, VIB-UGent Center for Medical Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Layla Bral
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Joline Ingels
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Glenn Goetgeluk
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sarah Bonte
- Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium
| | - Melissa Pille
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Lore Billiet
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Karin Weening
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Annick Verhee
- Cytokine Receptor Laboratory, Flanders Institute of Biotechnology, VIB-UGent Center for Medical Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jose Van der Heyden
- Cytokine Receptor Laboratory, Flanders Institute of Biotechnology, VIB-UGent Center for Medical Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Tessa Kerre
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium
| | - Jan Tavernier
- Cytokine Receptor Laboratory, Flanders Institute of Biotechnology, VIB-UGent Center for Medical Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
- Correspondence:
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7
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Yamaguchi H, de Lecea L. Construction of Viral Vectors for Cell Type-specific CRISPR Gene Editing in the Adult Mouse Brain. Bio Protoc 2019; 9:e3334. [PMID: 33654839 DOI: 10.21769/bioprotoc.3334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/27/2019] [Accepted: 07/11/2019] [Indexed: 11/02/2022] Open
Abstract
Recently developed gene editing technologies based on engineered CRISPR/Cas9 systems enables researchers to disrupt genes in a cell type-specific manner in the adult mouse brain. Using these technologies, we recently showed that the dopamine beta-hydroxylase gene in Locus Coeruleus (LC) norepinephrine neurons plays a vital role in the maintenance of wakefulness. Our method consists of four steps, (1) crossing Cre-dependent spCas9 knockin mice with a Cre-driver mouse line to express spCas9 in the target neural populations, (2) cloning of sgRNA, (3) construction of an AAV (adeno associated virus) vector expressing dual sgRNA, and (4) virus packaging and stereotaxic injection of the virus into the target brain area. Here, we describe a detailed protocol of AAV vector construction for cell type-specific CRISPR gene editing in the adult mouse brain. The method adopts a dual-sgRNA strategy for efficient disruption of the target gene. At first, a few different sgRNAs targeting the same gene are cloned into a plasmid expressing spCas9. After evaluation of the sgRNAs by a T7 endonuclease assay, the two most efficient sgRNAs are cloned in tandem into an AAV vector using the Gibson Assembly method.
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Affiliation(s)
- Hiroshi Yamaguchi
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Luis de Lecea
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305, USA
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8
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Ferro MMM, Ramos-Sobrinho R, Xavier CAD, Zerbini FM, Lima GSA, Nagata T, Assunção IP. New approach for the construction of infectious clones of a circular DNA plant virus using Gibson Assembly. J Virol Methods 2018; 263:20-23. [PMID: 30366017 DOI: 10.1016/j.jviromet.2018.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/20/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
Abstract
Viruses belonging to the genus Begomovirus (family Geminiviridae) have circular single-strand DNA genomes encapsidated into quasi-icosahedral particles, and are transmitted by whiteflies of the Bemisia tabaci complex. Biological and molecular properties of begomoviruses have been studied efficiently with infectious clones containing dimeric genomic components. However, current approaches employing enzymatic digestion and ligation to binary vectors are laborious, mostly due to many cloning steps or partial digestion by restriction enzyme. Here, an infectious clone of the bipartite begomovirus Bean golden mosaic virus (BGMV) was obtained using PCR and Gibson Assembly (GA). Common bean (Phaseolus vulgaris) seedlings displayed severe yellow mosaic and stunt symptoms 15 days after agroinoculation with DNA-A and DNA-B of BGMV. The approach based on PCR-GA protocol is a fast and useful tool to obtain infectious clones of a circular DNA plant virus.
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Affiliation(s)
- M M M Ferro
- Setor de Fitossanidade/Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - R Ramos-Sobrinho
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
| | - C A D Xavier
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - F M Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - G S A Lima
- Setor de Fitossanidade/Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - T Nagata
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - I P Assunção
- Setor de Fitossanidade/Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
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9
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Pan H, Yan Y, Zhang J, Zhao S, Feng L, Ou J, Cao N, Li M, Zhao W, Wan C, Ismail AM, Rajaiya J, Chodosh J, Zhang Q. Rapid Construction of a Replication-Competent Infectious Clone of Human Adenovirus Type 14 by Gibson Assembly. Viruses 2018; 10:E568. [PMID: 30340336 DOI: 10.3390/v10100568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Abstract
In 1955, Human adenovirus type 14 (HAdV-B14p) was firstly identified in a military trainee diagnosed as acute respiratory disease (ARD) in the Netherlands. Fifty years later, a genomic variant, HAdV-B14p1, re-emerged in the U.S. and caused large and fatal ARD outbreaks. Subsequently, more and more ARD outbreaks occurred in Canada, the UK, Ireland, and China, in both military and civil settings. To generate a tool for the efficient characterization of this new genomic variant, a full-length infectious genomic clone of HAdV-B14 was successfully constructed using one-step Gibson Assembly method in this study. Firstly, the full genome of HAdV-B14p1 strain GZ01, the first HAdV-B14 isolate in China, was assembled into pBR322 plasmid by Gibson Assembly. The pBRAdV14 plasmid, generated by Gibson Assembly, was analyzed and verified by PCR, restriction enzymes digestion and the sequencing. Secondly, viruses were rescued from pBRAdV14-transfected A549 cells. The integrity of the rescued viruses was identified by restriction enzyme analysis. The complete sequence of the infectious clone was further sequenced. No mutation was found in the infectious clone during the construction when compared with the parental virus and pBR322 sequences. The direct immunofluorescence assay indicated the expression of the hexon protein. Finally, typical virions were observed; the one-step growth curves further showed that the DNA replication and viral reproduction efficiency of pBRAd14 derived viruses was similar with that of wild-type HAdV-B14 strain. The successful construction of the replication-competent infectious clone of pBRAdV14 facilitates the development of vaccine and antiviral drugs against HAdV-B14, as well as provides a novel strategy for rapid construction of infectious viral clones for other large-genome DNA viruses.
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Rudenko O, Barnes AC. Gibson Assembly facilitates bacterial allelic exchange mutagenesis. J Microbiol Methods 2018; 144:157-63. [PMID: 29196271 DOI: 10.1016/j.mimet.2017.11.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 02/01/2023]
Abstract
Allelic exchange mutagenesis that relies on RecA-mediated homologous recombination up- and downstream from the targeted gene is a generalizable method of site-specific bacterial gene knock-out and knock-in. However, generation of a mutagenic DNA construct (alternative allele flanked by regions surrounding the gene target) and subsequent mutant selection are laborious procedures. Here we demonstrate allelic exchange knock-out facilitated by Gibson Assembly in Streptococcus iniae. Gibson Assembly allows rapid construction of a large allelic exchange cassette simultaneous with cloning, as well as rapid reconstruction of complete recombinant vector sequence when required. Additionally, we show that during two-step mutant selection, absence of recombination at one of the homologous regions (single cross-over) might be rapidly detected by colony PCR of meroploid clones and resolved by extension/shifting of corresponding sequence in DNA construct. The combination of Gibson Assembly for mutagenic DNA construction/redesign with colony PCR screening of meroploids to detect recombination at both sides of the exchange target may significantly accelerate generation of chromosomal mutants in a wide range of bacterial taxa.
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Blawid R, Nagata T. Construction of an infectious clone of a plant RNA virus in a binary vector using one-step Gibson Assembly. J Virol Methods 2015; 222:11-5. [PMID: 25986144 DOI: 10.1016/j.jviromet.2015.05.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/06/2015] [Accepted: 05/07/2015] [Indexed: 11/29/2022]
Abstract
The construction of full-length infectious clones of RNA viruses is often laborious due to the many cloning steps required and the DNA exclusion within the plasmid during Escherichia coli transformation. We demonstrate single-step cloning procedure of an infectious cDNA of the tomato blistering mosaic virus (ToBMV) using Gibson Assembly (GA), which drastically reduces the number of cloning steps. By agro-inoculation with the construct obtained by this procedure, ToBMV was recovered six days post-inoculation in Nicotiana benthamiana plants. The symptoms induced by the recovered virus were indistinguishable from those caused by the wild-type virus. We conclude that the GA is very useful method particularly to construct a full-length cDNA clone of a plant RNA virus in a binary vector.
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Affiliation(s)
- Rosana Blawid
- Universidade de Brasília, Department of Cell Biology, Campus Universitário Darcy Ribeiro, 70910-900 Brasília, DF, Brazil
| | - Tatsuya Nagata
- Universidade de Brasília, Department of Cell Biology, Campus Universitário Darcy Ribeiro, 70910-900 Brasília, DF, Brazil.
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