1
|
Xu L, Zheng S, Witzel K, Van De Slijke E, Baekelandt A, Mylle E, Van Damme D, Cheng J, De Jaeger G, Inzé D, Jiang H. Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana. Nat Commun 2024; 15:1286. [PMID: 38346986 PMCID: PMC10861482 DOI: 10.1038/s41467-024-45577-5] [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: 07/03/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The nuclear matrix is a nuclear compartment that has diverse functions in chromatin regulation and transcription. However, how this structure influences epigenetic modifications and gene expression in plants is largely unknown. In this study, we show that a nuclear matrix binding protein, AHL22, together with the two transcriptional repressors FRS7 and FRS12, regulates hypocotyl elongation by suppressing the expression of a group of genes known as SMALL AUXIN UP RNAs (SAURs) in Arabidopsis thaliana. The transcriptional repression of SAURs depends on their attachment to the nuclear matrix. The AHL22 complex not only brings these SAURs, which contain matrix attachment regions (MARs), to the nuclear matrix, but it also recruits the histone deacetylase HDA15 to the SAUR loci. This leads to the removal of H3 acetylation at the SAUR loci and the suppression of hypocotyl elongation. Taken together, our results indicate that MAR-binding proteins act as a hub for chromatin and epigenetic regulators. Moreover, we present a mechanism by which nuclear matrix attachment to chromatin regulates histone modifications, transcription, and hypocotyl elongation.
Collapse
Affiliation(s)
- Linhao Xu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Shiwei Zheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, 14979, Germany
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Jinping Cheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany.
| |
Collapse
|
2
|
Hamaker NK, Lee KH. High-efficiency and multilocus targeted integration in CHO cells using CRISPR-mediated donor nicking and DNA repair inhibitors. Biotechnol Bioeng 2023; 120:2419-2440. [PMID: 37039773 PMCID: PMC10524319 DOI: 10.1002/bit.28393] [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: 11/23/2022] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 04/12/2023]
Abstract
Efforts to leverage clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) for targeted genomic modifications in mammalian cells are limited by low efficiencies and heterogeneous outcomes. To aid method optimization, we developed an all-in-one reporter system, including a novel superfolder orange fluorescent protein (sfOrange), to simultaneously quantify gene disruption, site-specific integration (SSI), and random integration (RI). SSI strategies that utilize different donor plasmid formats and Cas9 nuclease variants were evaluated for targeting accuracy and efficiency in Chinese hamster ovary cells. Double-cut and double-nick donor formats significantly improved targeting accuracy by 2.3-8.3-fold and 19-22-fold, respectively, compared to standard circular donors. Notably, Cas9-mediated donor linearization was associated with increased RI events, whereas donor nicking minimized RI without sacrificing SSI efficiency and avoided low-fidelity outcomes. A screen of 10 molecules that modulate the major mammalian DNA repair pathways identified two inhibitors that further enhance targeting accuracy and efficiency to achieve SSI in 25% of transfected cells without selection. The optimized methods integrated transgene expression cassettes with 96% efficiency at a single locus and with 53%-55% efficiency at two loci simultaneously in selected clones. The CRISPR-based tools and methods developed here could inform the use of CRISPR/Cas9 in mammalian cell lines, accelerate mammalian cell line engineering, and support advanced recombinant protein production applications.
Collapse
Affiliation(s)
- Nathaniel K. Hamaker
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Kelvin H. Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- The National Institute for Innovation in Manufacturing Biopharmaceuticals (NIIMBL), University of Delaware, Newark, DE, 19713, USA
| |
Collapse
|
3
|
Huhn SC, Chang M, Jiang B, Tang X, Betenbaugh M, Du Z. Genomic features of recombinant CHO clones arising from transposon-based and randomized integration. J Biotechnol 2023; 373:73-81. [PMID: 37271453 DOI: 10.1016/j.jbiotec.2023.05.009] [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: 03/10/2023] [Revised: 05/04/2023] [Accepted: 05/28/2023] [Indexed: 06/06/2023]
Abstract
The use of transposase in cell line development (CLD) programs has experienced increased popularity over the past decade. However, few studies have described the mechanism of action and the genomic and phenotypic characteristics of clones derived from transposase. Additionally, how these traits impact long-term bioproduction is unknown. Here, we use chromosome painting, deep sequencing, and ddPCR to characterize the unique fingerprints associated with transposase-derived clones. Transposase reduces the cellular pool of transient vector as early as three days post transfection following transfection and expedites stable pool establishment by up to two weeks. Furthermore, recombinant DNA expression is significantly improved up to ∼3 fold along with a greater balance of antibody heavy and light chain transcripts, resulting in higher titers in transposase generated pools. Transposase derived pools contained an often innumerable number of integration sites, representing a vast increase in integration site diversity over randomly generated pools, which were bottlenecked at 1-3 integration sites per pool. These transposase mediated integrations typically occurred in clean singlets, free of genomic scars such as deletions, inversions, and other modifications associated with legacy transfection methods which exhibited higher copy numbers per integration site. Relative declines in gene expression occur with copy number increase in the randomly generated, but not the transposase derived clones. Furthermore, transposase-derived clones were more likely to exhibit enhanced a long term stability profile, including product quality attributes such as mannose-5. This improved stability may result from circumventing mechanisms associated with the silencing of tandem repeats. Thus, transposase-mediated approaches can provide multifaceted molecular and phenotypic advantages in cell line development when compared to legacy random-integration methods.
Collapse
Affiliation(s)
- S C Huhn
- Merck Sharp & Dohme LLC, 126 East Lincoln Avenue P.O. Box 2000, Rahway, NJ 07065, USA.
| | - M Chang
- Merck Sharp & Dohme LLC, 126 East Lincoln Avenue P.O. Box 2000, Rahway, NJ 07065, USA
| | - B Jiang
- Merck Sharp & Dohme LLC, 126 East Lincoln Avenue P.O. Box 2000, Rahway, NJ 07065, USA
| | - X Tang
- Merck Sharp & Dohme LLC, 126 East Lincoln Avenue P.O. Box 2000, Rahway, NJ 07065, USA
| | - M Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Z Du
- Merck Sharp & Dohme LLC, 126 East Lincoln Avenue P.O. Box 2000, Rahway, NJ 07065, USA
| |
Collapse
|
4
|
Ma C, Liu J, Tang J, Sun Y, Jiang X, Zhang T, Feng Y, Liu Q, Wang L. Current genetic strategies to investigate gene functions in Trichoderma reesei. Microb Cell Fact 2023; 22:97. [PMID: 37161391 PMCID: PMC10170752 DOI: 10.1186/s12934-023-02104-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 04/21/2023] [Indexed: 05/11/2023] Open
Abstract
The filamentous fungus Trichoderma reesei (teleomorph Hypocrea jecorina, Ascomycota) is a well-known lignocellulolytic enzymes-producing strain in industry. To increase the fermentation titer of lignocellulolytic enzymes, random mutagenesis and rational genetic engineering in T. reesei were carried out since it was initially found in the Solomon Islands during the Second World War. Especially the continuous exploration of the underlying regulatory network during (hemi)cellulase gene expression in the post-genome era provided various strategies to develop an efficient fungal cell factory for these enzymes' production. Meanwhile, T. reesei emerges competitiveness potential as a filamentous fungal chassis to produce proteins from other species (e.g., human albumin and interferon α-2b, SARS-CoV-2 N antigen) in virtue of the excellent expression and secretion system acquired during the studies about (hemi)cellulase production. However, all the achievements in high yield of (hemi)cellulases are impossible to finish without high-efficiency genetic strategies to analyze the proper functions of those genes involved in (hemi)cellulase gene expression or secretion. Here, we in detail summarize the current strategies employed to investigate gene functions in T. reesei. These strategies are supposed to be beneficial for extending the potential of T. reesei in prospective strain engineering.
Collapse
Affiliation(s)
- Chixiang Ma
- China Medical University-The Queen's University of Belfast Joint College, Shenyang, Liaoning, 110122, China
| | - Jialong Liu
- College of Basic Medical Sciences, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Jiaxin Tang
- College of Basic Medical Sciences, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Yuanlu Sun
- China Medical University-The Queen's University of Belfast Joint College, Shenyang, Liaoning, 110122, China
| | - Xiaojie Jiang
- China Medical University-The Queen's University of Belfast Joint College, Shenyang, Liaoning, 110122, China
| | - Tongtong Zhang
- China Medical University-The Queen's University of Belfast Joint College, Shenyang, Liaoning, 110122, China
| | - Yan Feng
- College of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, Shanxi, China
| | - Qinghua Liu
- College of Basic Medical Sciences, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Lei Wang
- College of Basic Medical Sciences, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| |
Collapse
|
5
|
Oliviero C, Hinz SC, Grzeschik J, Hock B, Kolmar H, Hagens G. Cell Line Development Using Targeted Gene Integration into MAR-Rich Landing Pads for Stable Expression of Transgenes. Methods Mol Biol 2023; 2681:343-359. [PMID: 37405657 DOI: 10.1007/978-1-0716-3279-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Integration of a gene of interest (GOI) into the genome of mammalian cells is the first step of cell line development campaigns for the production of biotherapeutics. Besides random integration methods, targeted gene integration approaches have emerged as promising tools over the last few years. In addition to reducing heterogeneity within a pool of recombinant transfectants, this process can also facilitate shorter timelines of the current cell line development process. Herein, we describe protocols for generating host cell lines carrying matrix attachment region (MAR)-rich landing pads (LPs), including BxB1 recombination sites. These LP-containing cell lines allow for site-specific and simultaneous integration of multiple GOIs. The resulting transgene-expressing stable recombinant clones can be used for the production of mono- or multispecific antibodies.
Collapse
Affiliation(s)
- Claudia Oliviero
- Institute of Life Technologies, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Sion, Switzerland
| | - Steffen C Hinz
- Institute of Life Technologies, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Sion, Switzerland
| | | | - Björn Hock
- Aerium Therapeutics, Epalinges, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerrit Hagens
- Institute of Life Technologies, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Sion, Switzerland.
| |
Collapse
|
6
|
Mladenova V, Mladenov E, Chaudhary S, Stuschke M, Iliakis G. The high toxicity of DSB-clusters modelling high-LET-DNA damage derives from inhibition of c-NHEJ and promotion of alt-EJ and SSA despite increases in HR. Front Cell Dev Biol 2022; 10:1016951. [PMID: 36263011 PMCID: PMC9574094 DOI: 10.3389/fcell.2022.1016951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Heavy-ion radiotherapy utilizing high linear energy transfer (high-LET) ionizing radiation (IR) is a promising cancer treatment modality owing to advantageous physical properties of energy deposition and associated toxicity over X-rays. Therapies utilizing high-LET radiation will benefit from a better understanding of the molecular mechanisms underpinning their increased biological efficacy. Towards this goal, we investigate here the biological consequences of well-defined clusters of DNA double-strand breaks (DSBs), a form of DNA damage, which on theoretical counts, has often been considered central to the enhanced toxicity of high-LET IR. We test clonal cell lines harboring in their genomes constructs with appropriately engineered I-SceI recognition sites that convert upon I-SceI expression to individual DSBs, or DSB-clusters comprising known numbers of DSBs with defined DNA-ends. We find that, similarly to high-LET IR, DSB-clusters of increasing complexity, i.e. increasing numbers of DSBs, with compatible or incompatible ends, compromise classical non-homologous end-joining, favor DNA end-resection and promote resection-dependent DSB-processing. Analysis of RAD51 foci shows increased engagement of error-free homologous recombination on DSB-clusters. Multicolor fluorescence in situ hybridization analysis shows that complex DSB-clusters markedly increase the incidence of structural chromosomal abnormalities (SCAs). Since RAD51-knockdown further increases SCAs-incidence, we conclude that homologous recombination suppresses SCAs-formation. Strikingly, CtIP-depletion inhibits SCAs-formation, suggesting that it relies on alternative end-joining or single-strand annealing. Indeed, ablation of RAD52 causes a marked reduction in SCAs, as does also inhibition of PARP1. We conclude that increased DSB-cluster formation that accompanies LET-increases, enhances IR-effectiveness by promoting DNA end-resection, which suppresses c-NHEJ and enhances utilization of alt-EJ or SSA. Although increased resection also favors HR, on balance, error-prone processing dominates, causing the generally observed increased toxicity of high-LET radiation. These findings offer new mechanistic insights into high-LET IR-toxicity and have translational potential in the clinical setting that may be harnessed by combining high-LET IR with inhibitors of PARP1 or RAD52.
Collapse
Affiliation(s)
- Veronika Mladenova
- Department of Radiation Therapy, Division of Experimental Radiation Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Emil Mladenov
- Department of Radiation Therapy, Division of Experimental Radiation Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Shipra Chaudhary
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute for Advanced Biosciences, Inserm U 1209 / CNRS UMR 5309 Joint Research Center, Grenoble Alpes University, Grenoble, France
| | - Martin Stuschke
- Department of Radiation Therapy, Division of Experimental Radiation Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - George Iliakis
- Department of Radiation Therapy, Division of Experimental Radiation Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute of Medical Radiation Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- *Correspondence: George Iliakis,
| |
Collapse
|
7
|
Oliviero C, Hinz SC, Bogen JP, Kornmann H, Hock B, Kolmar H, Hagens G. Generation of a Host Cell line containing a MAR-rich landing pad for site-specific integration and expression of transgenes. Biotechnol Prog 2022; 38:e3254. [PMID: 35396920 PMCID: PMC9539524 DOI: 10.1002/btpr.3254] [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: 01/11/2022] [Revised: 03/22/2022] [Accepted: 03/31/2022] [Indexed: 11/10/2022]
Abstract
In recent years, targeted gene integration (TI) has been introduced as a strategy for the generation of recombinant mammalian cell lines for the production of biotherapeutics. Besides reducing the immense heterogeneity within a pool of recombinant transfectants, TI also aims at shortening the duration of the current cell line development process. Here we describe the generation of a host cell line carrying Matrix‐Attachment Region (MAR)‐rich landing pads (LPs), which allow for the simultaneous and site‐specific integration of multiple genes of interest (GOIs). We show that several copies of each chicken lysozyme 5'MAR‐based LP containing either BxB1 wild type or mutated recombination sites, integrated at one random chromosomal locus of the host cell genome. We further demonstrate that these LP‐containing host cell lines can be used for the site‐specific integration of several GOIs and thus, generation of transgene‐expressing stable recombinant clones. Transgene expression was shown by site‐specific integration of heavy and light chain genes coding for a monospecific antibody (msAb) as well as for a bi‐specific antibody (bsAb). The genetic stability of the herein described LP‐based recombinant clones expressing msAb or bsAb was demonstrated by cultivating the recombinant clones and measuring antibody titers over 85 generations. We conclude that the host cell containing multiple copies of MAR‐rich landing pads can be successfully used for stable expression of one or several GOIs.
Collapse
Affiliation(s)
- Claudia Oliviero
- Institute of Life Technology, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Rue de l'Industrie 19, CH-1950 Sion, Switzerland
| | - Steffen C Hinz
- Institute of Life Technology, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Rue de l'Industrie 19, CH-1950 Sion, Switzerland
| | - Jan P Bogen
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany
| | - Henri Kornmann
- Ferring Biologics Innovation Center, Route de la Corniche 8, CH-1066, Epalinges, Switzerland
| | - Björn Hock
- Ferring Biologics Innovation Center, Route de la Corniche 8, CH-1066, Epalinges, Switzerland.,SwissThera SA, Route de la Corniche 4, CH-1066, Epalinges, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany
| | - Gerrit Hagens
- Institute of Life Technology, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Rue de l'Industrie 19, CH-1950 Sion, Switzerland
| |
Collapse
|
8
|
Stadermann A, Gamer M, Fieder J, Lindner B, Fehrmann S, Schmidt M, Schulz P, Gorr IH. Structural analysis of random transgene integration in CHO manufacturing cell lines by targeted sequencing. Biotechnol Bioeng 2021; 119:868-880. [PMID: 34935125 PMCID: PMC10138747 DOI: 10.1002/bit.28012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/08/2022]
Abstract
Genetically modified CHO cell lines are traditionally used for the production of biopharmaceuticals. However, an in-depth molecular understanding of the mechanism and exact position of transgene integration into the genome of pharmaceutical manufacturing cell lines is still scarce. Next Generation Sequencing (NGS) holds great promise for strongly facilitating the understanding of CHO cell factories, as it has matured to a powerful and affordable technology for cellular genotype analysis. Targeted Locus Amplification (TLA) combined with NGS allows for robust detection of genomic positions of transgene integration and structural genomic changes occurring upon stable integration of expression vectors. TLA was applied to generate comparative genomic fingerprints of several CHO production cell lines expressing different monoclonal antibodies. Moreover, high producers resulting from an additional round of transfection of an existing cell line (supertransfection) were analyzed to investigate the integrity and the number of integration sites. Our analyses enabled detailed genetic characterization of the integration regions with respect to the number of integrates and structural changes of the host cell's genome. Single integration sites per clone with concatenated transgene copies could be detected and were in some cases found to be associated with genomic rearrangements, deletions or translocations. Supertransfection resulted in an increase in titer associated with an additional integration site per clone. Based on the TLA fingerprints, CHO cell lines originating from the same mother clone could clearly be distinguished. Interestingly, two CHO cell lines originating from the same mother clone were shown to differ genetically and phenotypically despite of their identical TLA fingerprints. Taken together, TLA provides an accurate genetic characterization with respect to transgene integration sites compared to conventional methods and represents a valuable tool for a comprehensive evaluation of CHO production clones early in cell line development. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Anna Stadermann
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Martin Gamer
- R&D Project Management NBEs, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Jürgen Fieder
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Benjamin Lindner
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Steffen Fehrmann
- Genedata AG, Selector BU, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - Moritz Schmidt
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Patrick Schulz
- Bioprocess Development Biologicals, Cell Line Development, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| | - Ingo H Gorr
- Analytical Development Biologicals, Boehringer Ingelheim GmbH & Co. KG, Birkendorfer Strasse 65, 88397, Biberach, Germany
| |
Collapse
|
9
|
Smirnov A, Battulin N. Concatenation of Transgenic DNA: Random or Orchestrated? Genes (Basel) 2021; 12:genes12121969. [PMID: 34946918 PMCID: PMC8701086 DOI: 10.3390/genes12121969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022] Open
Abstract
Generation of transgenic organisms by pronuclear microinjection has become a routine procedure. However, while the process of DNA integration in the genome is well understood, we still do not know much about the recombination between transgene molecules that happens in the first moments after DNA injection. Most of the time, injected molecules are joined together in head-to-tail tandem repeats-the so-called concatemers. In this review, we focused on the possible concatenation mechanisms and how they could be studied with genetic reporters tracking individual copies in concatemers. We also discuss various features of concatemers, including palindromic junctions and repeat-induced gene silencing (RIGS). Finally, we speculate how cooperation of DNA repair pathways creates a multicopy concatenated insert.
Collapse
Affiliation(s)
- Alexander Smirnov
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Nariman Battulin
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Institute of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
| |
Collapse
|
10
|
Abstract
Following the success of and the high demand for recombinant protein-based therapeutics during the last 25 years, the pharmaceutical industry has invested significantly in the development of novel treatments based on biologics. Mammalian cells are the major production systems for these complex biopharmaceuticals, with Chinese hamster ovary (CHO) cell lines as the most important players. Over the years, various engineering strategies and modeling approaches have been used to improve microbial production platforms, such as bacteria and yeasts, as well as to create pre-optimized chassis host strains. However, the complexity of mammalian cells curtailed the optimization of these host cells by metabolic engineering. Most of the improvements of titer and productivity were achieved by media optimization and large-scale screening of producer clones. The advances made in recent years now open the door to again consider the potential application of systems biology approaches and metabolic engineering also to CHO. The availability of a reference genome sequence, genome-scale metabolic models and the growing number of various “omics” datasets can help overcome the complexity of CHO cells and support design strategies to boost their production performance. Modular design approaches applied to engineer industrially relevant cell lines have evolved to reduce the time and effort needed for the generation of new producer cells and to allow the achievement of desired product titers and quality. Nevertheless, important steps to enable the design of a chassis platform similar to those in use in the microbial world are still missing. In this review, we highlight the importance of mammalian cellular platforms for the production of biopharmaceuticals and compare them to microbial platforms, with an emphasis on describing novel approaches and discussing still open questions that need to be resolved to reach the objective of designing enhanced modular chassis CHO cell lines.
Collapse
|
11
|
Smirnov A, Fishman V, Yunusova A, Korablev A, Serova I, Skryabin BV, Rozhdestvensky TS, Battulin N. DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote. Nucleic Acids Res 2020; 48:719-735. [PMID: 31740957 PMCID: PMC7145541 DOI: 10.1093/nar/gkz1085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
Mechanisms that ensure repair of double-strand DNA breaks (DSBs) are instrumental in the integration of foreign DNA into the genome of transgenic organisms. After pronuclear microinjection, exogenous DNA is usually found as a concatemer comprising multiple co-integrated transgene copies. Here, we investigated the contribution of various DSB repair pathways to the concatemer formation. We injected mouse zygotes with a pool of linear DNA molecules carrying unique barcodes at both ends and obtained 10 transgenic embryos with 1–300 transgene copies. Sequencing the barcodes allowed us to assign relative positions to the copies in concatemers and detect recombination events that occurred during integration. Cumulative analysis of approximately 1,000 integrated copies reveals that over 80% of them underwent recombination when their linear ends were processed by synthesis-dependent strand annealing (SDSA) or double-strand break repair (DSBR). We also observed evidence of double Holliday junction (dHJ) formation and crossing over during the concatemer formations. Sequencing indels at the junctions between copies shows that at least 10% of DNA molecules introduced into the zygotes are ligated by non-homologous end joining (NHEJ). Our barcoding approach, verified with Pacific Biosciences Single Molecule Real-Time (SMRT) long-range sequencing, documents high activity of homologous recombination after DNA microinjection.
Collapse
Affiliation(s)
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | | | - Alexey Korablev
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Irina Serova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Boris V Skryabin
- Medical Faculty, Core Facility Transgenic animal and genetic engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Timofey S Rozhdestvensky
- Medical Faculty, Core Facility Transgenic animal and genetic engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
12
|
Zhang JH, Zhang JH, Wang XY, Xu DH, Wang TY. Distance effect characteristic of the matrix attachment region increases recombinant protein expression in Chinese hamster ovary cells. Biotechnol Lett 2019; 42:187-196. [PMID: 31776751 DOI: 10.1007/s10529-019-02775-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/24/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVES Previously, we have found that the matrix attachment region (MAR) may confer a 'distance effect' on transgene expression. This work aims to systematically explore the increased transgene expression in transfected Chinese hamster ovary (CHO) cells due to the characteristics of MAR and its mechanism. RESULTS Compared with the control vector, 500 and 1000 bp DNA distances between MAR and the cytomegalovirus promoter can increase transgene expression by 1.77- and 1.56-fold, respectively. Meanwhile, transgene expression was not affected when 2000 and 2500 bp spacer DNAs were inserted, but a declining trend was observed when a 1500 bp spacer DNA was inserted. The vector containing a 500 bp DNA distance significantly increased the expression of the enhanced green fluorescent protein, and this increase was not related to transgene copy numbers. CONCLUSIONS A short DNA distance-containing MAR confers high transgene expression level in transfected CHO cells, but a distance threshold does not exist in the vector system.
Collapse
Affiliation(s)
- Jun-He Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, No. 601 Jinsui Road, Xinxiang, 453003, Henan, China.,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Ji-Hong Zhang
- Department of Histology and Embryology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiao-Yin Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, No. 601 Jinsui Road, Xinxiang, 453003, Henan, China.,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Dan-Hua Xu
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, No. 601 Jinsui Road, Xinxiang, 453003, Henan, China.,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, No. 601 Jinsui Road, Xinxiang, 453003, Henan, China. .,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China.
| |
Collapse
|
13
|
Duroy PO, Bosshard S, Schmid-Siegert E, Neuenschwander S, Arib G, Lemercier P, Masternak J, Roesch L, Buron F, Girod PA, Xenarios I, Mermod N. Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release. Biotechnol Bioeng 2019; 117:466-485. [PMID: 31631325 PMCID: PMC7003738 DOI: 10.1002/bit.27200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/10/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Abstract
The Chinese hamster ovary (CHO) cells used to produce biopharmaceutical proteins are known to contain type‐C endogenous retrovirus (ERV) sequences in their genome and to release retroviral‐like particles. Although evidence for their infectivity is missing, this has raised safety concerns. As the genomic origin of these particles remained unclear, we characterized type‐C ERV elements at the genome, transcriptome, and viral particle RNA levels. We identified 173 type‐C ERV sequences clustering into three functionally conserved groups. Transcripts from one type‐C ERV group were full‐length, with intact open reading frames, and cognate viral genome RNA was loaded into retroviral‐like particles, suggesting that this ERV group may produce functional viruses. CRISPR‐Cas9 genome editing was used to disrupt the gag gene of the expressed type‐C ERV group. Comparison of CRISPR‐derived mutations at the DNA and RNA level led to the identification of a single ERV as the main source of the release of RNA‐loaded viral particles. Clones bearing a Gag loss‐of‐function mutation in this ERV showed a reduction of RNA‐containing viral particle release down to detection limits, without compromising cell growth or therapeutic protein production. Overall, our study provides a strategy to mitigate potential viral particle contaminations resulting from ERVs during biopharmaceutical manufacturing.
Collapse
Affiliation(s)
- Pierre-Olivier Duroy
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Present address: Selexis SA, Plan-les-Ouates, Switzerland
| | - Sandra Bosshard
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Present address: Lonza AG, Visp, Switzerland
| | | | | | | | - Philippe Lemercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Jacqueline Masternak
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Lucien Roesch
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Flavien Buron
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Ioannis Xenarios
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Present address: Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Mermod
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
14
|
Bosshard S, Duroy PO, Mermod N. A role for alternative end-joining factors in homologous recombination and genome editing in Chinese hamster ovary cells. DNA Repair (Amst) 2019; 82:102691. [PMID: 31476574 DOI: 10.1016/j.dnarep.2019.102691] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022]
Abstract
CRISPR technologies greatly foster genome editing in mammalian cells through site-directed DNA double strand breaks (DSBs). However, precise editing outcomes, as mediated by homologous recombination (HR) repair, are typically infrequent and outnumbered by undesired genome alterations. By using knockdown and overexpression studies in Chinese hamster ovary (CHO) cells as well as characterizing repaired DNA junctions, we found that efficient HR-mediated genome editing depends on alternative end-joining (alt-EJ) DNA repair activities, a family of incompletely characterized DNA repair pathways traditionally considered to oppose HR. This dependency was influenced by the CRISPR nuclease type and the DSB-to-mutation distance, but not by the DNA sequence surrounding the DSBs or reporter cell line. We also identified elevated Mre11 and Pari, and low Rad51 expression levels as the most rate-limiting factors for HR in CHO cells. Counteracting these three bottlenecks improved precise genome editing by up to 75%. Altogether, our study provides novel insights into the complex interplay of alt-EJ and HR repair pathways, highlighting their relevance for developing improved genome editing strategies.
Collapse
Affiliation(s)
- Sandra Bosshard
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Pierre-Olivier Duroy
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Mermod
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
| |
Collapse
|
15
|
Mohammadian O, Rajabibazl M, Pourmaleki E, Bayat H, Ahani R, Rahimpour A. Development of an improved lentiviral based vector system for the stable expression of monoclonal antibody in CHO cells. Prep Biochem Biotechnol 2019; 49:822-829. [PMID: 31156045 DOI: 10.1080/10826068.2019.1621893] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Therapeutic monoclonal antibodies (mAbs) have become the dominant products in biopharmaceutical industry. Mammalian cell expression systems including Chinese hamster ovary (CHO) cells are the most commonly used hosts for the production of complex recombinant proteins. However, development of stable, high producing CHO cell lines suffers from the low expression level and instability of the transgene. The increasing efforts in the development of novel therapeutic antibodies and the advent of biosimilars have revealed the necessity for the development of improved platforms for rapid production of products for initial characterization and testing. In line with this premise, vector design and engineering has been applied to improve the expression level and stability of the transgene. This study reports the application of an improved lentiviral vector system containing the human interferon-β scaffold attachment region (IFN-SAR) for the development of antibody producing stable CHO cells. mAb expressing clones producing 1100 µg/L of IgG1 monoclonal antibody were isolated without extensive screening of a large number of clones. Our results here indicate the positive effects of IFN-SAR on stable mAb expression using lentiviral based expression vectors. We also observed that although IFN-SAR can improve light chain (LC) and heavy chain (HC) gene copy numbers in stable cell pools, mAb expression in single cell clones was not affected by the transgene copy number.
Collapse
Affiliation(s)
- Omid Mohammadian
- a Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Masoumeh Rajabibazl
- a Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran.,b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Es'hagh Pourmaleki
- b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran.,c Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Hadi Bayat
- b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran.,d Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University , Tehran , Iran
| | - Roshanak Ahani
- b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Azam Rahimpour
- b Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences , Tehran , Iran.,c Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| |
Collapse
|
16
|
Efficient episomal gene transfer to human hepatic cells using the pFAR4–S/MAR vector. Mol Biol Rep 2019; 46:3203-3211. [DOI: 10.1007/s11033-019-04777-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/20/2019] [Indexed: 12/16/2022]
|
17
|
Hamaker NK, Lee KH. Site-specific Integration Ushers in a New Era of Precise CHO Cell Line Engineering. Curr Opin Chem Eng 2018; 22:152-160. [PMID: 31086757 DOI: 10.1016/j.coche.2018.09.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Chinese hamster ovary (CHO) cells are widely used for the production of therapeutic proteins. Customarily, CHO production cell lines are established through random integration, which requires laborious screening of many clones to isolate suitable producers. In contrast, site-specific integration (SSI) accelerates cell line development by targeting integration of transgenes to pre-validated genomic loci capable of supporting high and stable expression. To date, a relatively small number of these so called 'hot spots' have been identified, mainly through empirical methods. Nevertheless, nuclease-mediated and recombinase-mediated SSI have revolutionized cell line engineering by enabling rational and reproducible transgene targeting.
Collapse
Affiliation(s)
- Nathaniel K Hamaker
- Delaware Biotechnology Institute, Newark, DE.,Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| | - Kelvin H Lee
- Delaware Biotechnology Institute, Newark, DE.,Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| |
Collapse
|
18
|
Iyer PS, Mavoungou LO, Ronzoni F, Zemla J, Schmid-Siegert E, Antonini S, Neff LA, Dorchies OM, Jaconi M, Lekka M, Messina G, Mermod N. Autologous Cell Therapy Approach for Duchenne Muscular Dystrophy using PiggyBac Transposons and Mesoangioblasts. Mol Ther 2018; 26:1093-1108. [PMID: 29503200 PMCID: PMC6079556 DOI: 10.1016/j.ymthe.2018.01.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 01/24/2018] [Accepted: 01/29/2018] [Indexed: 01/07/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a lethal muscle-wasting disease currently without cure. We investigated the use of the PiggyBac transposon for full-length dystrophin expression in murine mesoangioblast (MABs) progenitor cells. DMD murine MABs were transfected with transposable expression vectors for full-length dystrophin and transplanted intramuscularly or intra-arterially into mdx/SCID mice. Intra-arterial delivery indicated that the MABs could migrate to regenerating muscles to mediate dystrophin expression. Intramuscular transplantation yielded dystrophin expression in 11%-44% of myofibers in murine muscles, which remained stable for the assessed period of 5 months. The satellite cells isolated from transplanted muscles comprised a fraction of MAB-derived cells, indicating that the transfected MABs may colonize the satellite stem cell niche. Transposon integration site mapping by whole-genome sequencing indicated that 70% of the integrations were intergenic, while none was observed in an exon. Muscle resistance assessment by atomic force microscopy indicated that 80% of fibers showed elasticity properties restored to those of wild-type muscles. As measured in vivo, transplanted muscles became more resistant to fatigue. This study thus provides a proof-of-principle that PiggyBac transposon vectors may mediate full-length dystrophin expression as well as functional amelioration of the dystrophic muscles within a potential autologous cell-based therapeutic approach of DMD.
Collapse
Affiliation(s)
- Pavithra S Iyer
- Institute of Biotechnology, University of Lausanne, Lausanne, Switzerland
| | - Lionel O Mavoungou
- Institute of Biotechnology, University of Lausanne, Lausanne, Switzerland
| | - Flavio Ronzoni
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Joanna Zemla
- Institute of Nuclear Physics, Polish Academy of Sciences, 31342 Krakow, Poland
| | | | | | - Laurence A Neff
- School of Pharmaceutical Sciences, University of Geneva and University of Lausanne, 1211 Geneva, Switzerland
| | - Olivier M Dorchies
- School of Pharmaceutical Sciences, University of Geneva and University of Lausanne, 1211 Geneva, Switzerland
| | - Marisa Jaconi
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Malgorzata Lekka
- Institute of Nuclear Physics, Polish Academy of Sciences, 31342 Krakow, Poland
| | | | - Nicolas Mermod
- Institute of Biotechnology, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
19
|
Jazayeri SH, Amiri-Yekta A, Bahrami S, Gourabi H, Sanati MH, Khorramizadeh MR. Vector and Cell Line Engineering Technologies Toward Recombinant Protein Expression in Mammalian Cell Lines. Appl Biochem Biotechnol 2018; 185:986-1003. [PMID: 29396733 DOI: 10.1007/s12010-017-2689-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/29/2017] [Indexed: 11/26/2022]
Abstract
The rapid growth of global biopharmaceutical market in the recent years has been a good indication of its significance in biotechnology industry. During a long period of time in recombinant protein production from 1980s, optimizations in both upstream and downstream processes were launched. In this regard, one of the most promising strategies is expression vector engineering technology based on incorporation of DNA opening elements found in the chromatin border regions of vectors as well as targeting gene integration. Along with these approaches, cell line engineering has revealed convenient outcomes in isolating high-producing clones. According to the fact that more than 50% of the approved therapeutic proteins is being manufactured in mammalian cell lines, in this review, we focus on several approaches and developments in vector and cell line engineering technologies in mammalian cell culture.
Collapse
Affiliation(s)
- Seyedeh Hoda Jazayeri
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran
| | - Amir Amiri-Yekta
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran
| | - Salahadin Bahrami
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran
| | - Hamid Gourabi
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran
| | - Mohammad Hossein Sanati
- Department of Genetics, Reproductive Biomedicine Research Center, ACECR, Royan Institute for Reproductive Biomedicine, P.O. Box: 14155-6343, Tehran, Iran.
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
| | - Mohammad Reza Khorramizadeh
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, P.O. Box: 1411413137, Tehran, Iran.
| |
Collapse
|
20
|
Smirnov AV, Kontsevaya GV, Feofanova NA, Anisimova MV, Serova IA, Gerlinskaya LA, Battulin NR, Moshkin MP, Serov OL. Unexpected phenotypic effects of a transgene integration causing a knockout of the endogenous Contactin-5 gene in mice. Transgenic Res 2017; 27:1-13. [PMID: 29264679 DOI: 10.1007/s11248-017-0053-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/01/2017] [Indexed: 01/06/2023]
Abstract
Contactins (Cntn1-6) are a family of neuronal membrane proteins expressed in the brain. They are required for establishing cell-to-cell contacts between neurons and for the growth and maturation of the axons. In humans, structural genomic variations in the Contactin genes are implicated in neurodevelopmental disorders. In addition, population genetic studies associate Contactins loci with obesity and hypertension. Cntn5 knockout mice were first described in 2003, but showed no gross physiological or behavioral abnormalities (just minor auditory defects). We report a novel Cntn5 knockout mouse line generated by a random transgene integration as an outcome of pronuclear microinjection. Investigation of the transgene integration site revealed that the 6Kbp transgene construct coding for the human granulocyte-macrophage colony-stimulating factor (hGMCSF) replaced 170 Kbp of the Cntn5 gene, including four exons. Reverse transcription PCR analysis of the Cntn5 transcripts in the wild-type and transgenic mouse lines showed that splicing of the transgene leads to a set of chimeric hGMCSF-Cntn5 transcript variants, none of which encode functional Cntn5 protein due to introduction of stop codons. Although Cntn5 knockout animals displayed no abnormalities in behavior, we noted that they were leaner, with less body mass and fat percentage than wild-type animals. Their cardiovascular parameters (heart rate, blood pressure and blood flow speed) were elevated compared to controls. These findings link Cntn5 deficiency to obesity and hypertension.
Collapse
Affiliation(s)
- Alexander V Smirnov
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - Galina V Kontsevaya
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia A Feofanova
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Margarita V Anisimova
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina A Serova
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lyudmila A Gerlinskaya
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nariman R Battulin
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Mikhail P Moshkin
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg L Serov
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
| |
Collapse
|
21
|
Chen SJ, Wang W, Zhang FY, Jia YL, Wang XY, Guo X, Chen SN, Gao JH, Wang TY. A chimeric HS4 insulator-scaffold attachment region enhances transgene expression in transfected Chinese hamster ovary cells. FEBS Open Bio 2017; 7:2021-2030. [PMID: 29226088 PMCID: PMC5715248 DOI: 10.1002/2211-5463.12335] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/23/2017] [Accepted: 10/03/2017] [Indexed: 11/12/2022] Open
Abstract
Chinese hamster ovary (CHO) cells are one of the most commonly used expression systems for the production of recombinant proteins but low levels of transgene expression and transgene silencing are frequently encountered. Epigenetic regulatory elements such as the chicken β-globin locus control region hypersensitive site 4 (HS4) and scaffold/matrix attachment regions (S/MARs) have positive effects on transgene expression. In this study, a chimeric HS4-SAR was cloned upstream or downstream of an enhanced green fluorescent protein (eGFP) expression cassette in a eukaryotic vector, and the resulting vectors were transfected into CHO cells. eGFP was detected by flow cytometry. Real-time quantitative PCR (qPCR) was used to determine copy numbers of the stably transfected cells. And fluorescence in situ hybridization (FISH) was used to detect the status of vector in the host cell chromosome. The results showed that HS4-SAR positioned downstream of the expression cassette could enhance eGFP expression by 4.83-fold compared with the control vector. There may not be a relationship between transgene copy number and gene expression level. HS4-SAR did not appear to alter the integration of the transgene into the host cell chromosome or its position in the chromosome. We found a synthetic chimeric HS4-SAR positively increased transgene expression in CHO cells.
Collapse
Affiliation(s)
- Si-Jia Chen
- Department of Biochemistry and Molecular Biology Xinxiang Medical University Henan China
| | - Wen Wang
- Pharmacy Collage Xinxiang Medical University Henan China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine Xinxiang Medical University China
| | - Feng-Yi Zhang
- Grade 2012 The Third Clinical Medical College of Xinxiang Medical University Henan China
| | - Yan-Long Jia
- Pharmacy Collage Xinxiang Medical University Henan China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine Xinxiang Medical University China
| | - Xiao-Yin Wang
- Department of Biochemistry and Molecular Biology Xinxiang Medical University Henan China
| | - Xiao Guo
- Pharmacy Collage Xinxiang Medical University Henan China
| | - Shao-Nan Chen
- Department of Biochemistry and Molecular Biology Xinxiang Medical University Henan China
| | - Jian-Hui Gao
- Department of Biochemistry and Molecular Biology Xinxiang Medical University Henan China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology Xinxiang Medical University Henan China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine Xinxiang Medical University China
| |
Collapse
|