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Siddiqui AA, Peter S, Ngoh EZX, Wang CI, Ng S, Dangerfield JA, Gunzburg WH, Dröge P, Makhija H. A versatile genomic transgenesis platform with enhanced λ integrase for human Expi293F cells. Front Bioeng Biotechnol 2023; 11:1198465. [PMID: 37425360 PMCID: PMC10325659 DOI: 10.3389/fbioe.2023.1198465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Reliable cell-based platforms to test and/or produce biologics in a sustainable manner are important for the biotech industry. Utilizing enhanced λ integrase, a sequence-specific DNA recombinase, we developed a novel transgenesis platform involving a fully characterized single genomic locus as an artificial landing pad for transgene insertion in human Expi293F cells. Importantly, transgene instability and variation in expression were not observed in the absence of selection pressure, thus enabling reliable long-term biotherapeutics testing or production. The artificial landing pad for λ integrase can be targeted with multi-transgene constructs and offers future modularity involving additional genome manipulation tools to generate sequential or nearly seamless insertions. We demonstrated broad utility with expression constructs for anti PD-1 monoclonal antibodies and showed that the orientation of heavy and light chain transcription units profoundly affected antibody expression levels. In addition, we demonstrated encapsulation of our PD-1 platform cells into bio-compatible mini-bioreactors and the continued secretion of antibodies, thus providing a basis for future cell-based applications for more effective and affordable therapies.
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Affiliation(s)
- Asim Azhar Siddiqui
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Sabrina Peter
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Eve Zi Xian Ngoh
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Cheng-I. Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shirelle Ng
- Austrianova Singapore Pte. Ltd., Singapore, Singapore
| | | | - Walter H. Gunzburg
- Austrianova Singapore Pte. Ltd., Singapore, Singapore
- Department of Pathobiology, Institute of Virology, University of Veterinary Medicine, Vienna, Austria
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Brown DM, Glass JI. Technology used to build and transfer mammalian chromosomes. Exp Cell Res 2020; 388:111851. [PMID: 31952951 DOI: 10.1016/j.yexcr.2020.111851] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 01/05/2023]
Abstract
In the near twenty-year existence of the human and mammalian artificial chromosome field, the technologies for artificial chromosome construction and installation into desired cell types or organisms have evolved with the rest of modern molecular and synthetic biology. Medical, industrial, pharmaceutical, agricultural, and basic research scientists seek the as yet unrealized promise of human and mammalian artificial chromosomes. Existing technologies for both top-down and bottom-up approaches to construct these artificial chromosomes for use in higher eukaryotes are very different but aspire to achieve similar results. New capacity for production of chromosome sized synthetic DNA will likely shift the field towards more bottom-up approaches, but not completely. Similarly, new approaches to install human and mammalian artificial chromosomes in target cells will compete with the microcell mediated cell transfer methods that currently dominate the field.
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Flexible pseudotyping of retrovirus using recombinase-mediated cassette exchange. Biotechnol Lett 2018; 40:633-639. [PMID: 29353442 PMCID: PMC5862940 DOI: 10.1007/s10529-018-2515-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/11/2018] [Indexed: 10/27/2022]
Abstract
OBJECTIVE Develop an engineered cell line containing two flexible gene expression systems enabling the continuous production of tailor-made recombinant gammaretrovirus with predictable productivities through targeted integration. RESULTS Dual-FLEX cells (dFLEX) contain two independent recombinase-mediated cassette exchange (RMCE) systems which confer flexibility to the expression of different transgene and envelope combinations. The flexible envelope expression in dFLEX cells was validated by pseudotyping retrovirus particles with three different viral envelope proteins-GaLV, 4070A and VSV-G. Our results show that dFLEX cells are able to provide high titers of infectious retroviral particles with a single-copy integration of the envelope constructs after RMCE. The integrated CRE/Lox tagging cassette was amenable to express envelope proteins both using constitutive (i.e. CMV) and inducible (i.e. Tet-on) promoters. CONCLUSIONS dFLEX cell line provides predictable productivities of recombinant retrovirus pseudotyped with different envelope proteins broadening the tropism of particles that can be generated and thus accelerating the research and development of retrovirus-based products.
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Vidigal J, Fernandes B, Dias MM, Patrone M, Roldão A, Carrondo MJT, Alves PM, Teixeira AP. RMCE-based insect cell platform to produce membrane proteins captured on HIV-1 Gag virus-like particles. Appl Microbiol Biotechnol 2017; 102:655-666. [DOI: 10.1007/s00253-017-8628-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/03/2017] [Accepted: 11/05/2017] [Indexed: 12/20/2022]
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LiPS-A3S, a human genomic site for robust expression of inserted transgenes. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e394. [PMID: 27898090 PMCID: PMC5155331 DOI: 10.1038/mtna.2016.99] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 10/06/2016] [Indexed: 01/14/2023]
Abstract
Transgenesis of human pluripotent stem cells (hPSCs) can enable and empower a variety of studies in stem cell research, including lineage tracing and functional genetics studies. While in recent years much progress has been made in the development of tools for gene targeting, little attention has been given to the identification of sites in the human genome where transgenes can be inserted and reliably expressed. In order to find human genomic sites capable of supporting long-term and high-level transgene expression in hPSCs, we performed a lentiviral screen in human induced pluripotent stem cells (iPSCs). We isolated 40 iPSC clones each harboring a single vector copy and characterized the level of transgene expression afforded by each unique integration site. We selected one clone, LiPS-A3 with an integration site in chromosome 15 maintaining robust expression without silencing and demonstrate that different transgenes can be inserted therein rapidly and efficiently through recombinase-mediated cassette exchange (RMCE). The LiPS-A3 line can greatly facilitate the insertion of reporter and other genes in hPSCs. Targeting transgenes in the LiPS-A3S genomic locus can find broad applications in stem cell research and possibly cell and gene therapy.
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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Papapetrou EP, Schambach A. Gene Insertion Into Genomic Safe Harbors for Human Gene Therapy. Mol Ther 2016; 24:678-84. [PMID: 26867951 DOI: 10.1038/mt.2016.38] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 02/05/2016] [Indexed: 12/14/2022] Open
Abstract
Genomic safe harbors (GSHs) are sites in the genome able to accommodate the integration of new genetic material in a manner that ensures that the newly inserted genetic elements: (i) function predictably and (ii) do not cause alterations of the host genome posing a risk to the host cell or organism. GSHs are thus ideal sites for transgene insertion whose use can empower functional genetics studies in basic research and therapeutic applications in human gene therapy. Currently, no fully validated GSHs exist in the human genome. Here, we review our formerly proposed GSH criteria and discuss additional considerations on extending these criteria, on strategies for the identification and validation of GSHs, as well as future prospects on GSH targeting for therapeutic applications. In view of recent advances in genome biology, gene targeting technologies, and regenerative medicine, gene insertion into GSHs can potentially catalyze nearly all applications in human gene therapy.
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Affiliation(s)
- Eirini P Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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