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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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2
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Xu Y, Crowe KB, Lieske PL, Barnes M, Bandara K, Chu J, Wei W, Scarcelli JJ, Zhang L. A high-fidelity, dual site-specific integration system in CHO cells by a Bxb1 recombinase. Biotechnol J 2024; 19:e2300410. [PMID: 38375559 DOI: 10.1002/biot.202300410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/16/2023] [Accepted: 12/06/2023] [Indexed: 02/21/2024]
Abstract
Site-specific integration (SSI) via recombinase mediated cassette exchange (RMCE) has shown advantages over random integration methods for expression of biotherapeutics. As an extension of our previous work developing SSI host cells, we developed a dual-site SSI system having two independent integration sites at different genomic loci, each containing a unique landing pad (LP). This system was leveraged to generate and compare two RMCE hosts, one (dFRT) compatible with the Flp recombinase, the other (dBxb1) compatible with the Bxb1 recombinase. Our comparison demonstrated that the dBxb1 host was able to generate stable transfectant pools in a shorter time frame, and cells within the dBxb1 transfectant pools were more phenotypically and genotypically stable. We further improved process performance of the dBxb1 host, resulting in desired fed batch performance attributes. Clones derived from this improved host (referred as 41L-11) maintained stable expression profiles over extended generations. While the data represents a significant improvement in the efficiency of our cell line development process, the dual LP architecture also affords a high degree of flexibility for development of complex protein modalities.
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Affiliation(s)
- Yifeng Xu
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Kerstin B Crowe
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Paulena L Lieske
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Michael Barnes
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Kalpanie Bandara
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Jianlin Chu
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Wei Wei
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - John J Scarcelli
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Lin Zhang
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
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3
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Huang Z, Habib A, Zhao G, Ding X. CRISPR-Cas9 Mediated Stable Expression of Exogenous Proteins in the CHO Cell Line through Site-Specific Integration. Int J Mol Sci 2023; 24:16767. [PMID: 38069090 PMCID: PMC10706275 DOI: 10.3390/ijms242316767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are a popular choice in biopharmaceuticals because of their beneficial traits, including high-density suspension culture, safety, and exogenously produced proteins that closely resemble natural proteins. Nevertheless, a decline in the expression of exogenous proteins is noted as culture time progresses. This is a consequence of foreign gene recombination into chromosomes by random integration. The current investigation employs CRISPR-Cas9 technology to integrate foreign genes into a particular chromosomal location for sustained expression. Results demonstrate the successful integration of enhanced green fluorescent protein (EGFP) and human serum albumin (HSA) near base 434814407 on chromosome NC_048595.1 of CHO-K1 cells. Over 60 successive passages, monoclonal cell lines were produced that consistently expressed all relevant external proteins without discernible variation in expression levels. In conclusion, the CHO-K1 cell locus, NC_048595.1, proves an advantageous locus for stable exogenous protein expression. This study provides a viable approach to establishing a CHO cell line capable of enduring reliable exogenous protein expression.
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Affiliation(s)
- Zhipeng Huang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Arslan Habib
- Laboratory of Molecular Immunology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Guoping Zhao
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, China
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4
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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.
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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
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5
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Leitner K, Motheramgari K, Borth N, Marx N. Nanopore Cas9-targeted sequencing enables accurate and simultaneous identification of transgene integration sites, their structure and epigenetic status in recombinant Chinese hamster ovary cells. Biotechnol Bioeng 2023; 120:2403-2418. [PMID: 36938677 DOI: 10.1002/bit.28382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/27/2023] [Accepted: 03/12/2023] [Indexed: 03/21/2023]
Abstract
The integration of a transgene expression construct into the host genome is the initial step for the generation of recombinant cell lines used for biopharmaceutical production. The stability and level of recombinant gene expression in Chinese hamster ovary (CHO) can be correlated to the copy number, its integration site as well as the epigenetic context of the transgene vector. Also, undesired integration events, such as concatemers, truncated, and inverted vector repeats, are impacting the stability of recombinant cell lines. Thus, to characterize cell clones and to isolate the most promising candidates, it is crucial to obtain information on the site of integration, the structure of integrated sequence and the epigenetic status. Current sequencing techniques allow to gather this information separately but do not offer a comprehensive and simultaneous resolution. In this study, we present a fast and robust nanopore Cas9-targeted sequencing (nCats) pipeline to identify integration sites, the composition of the integrated sequence as well as its DNA methylation status in CHO cells that can be obtained simultaneously from the same sequencing run. A Cas9-enrichment step during library preparation enables targeted and directional nanopore sequencing with up to 724× median on-target coverage and up to 153 kb long reads. The data generated by nCats provides sensitive, detailed, and correct information on the transgene integration sites and the expression vector structure, which could only be partly produced by traditional Targeted Locus Amplification-seq data. Moreover, with nCats the DNA methylation status can be analyzed from the same raw data without prior DNA amplification.
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Affiliation(s)
- Klaus Leitner
- Austrian Center of Industrial Biotechnology GmbH, Vienna, Austria
| | | | - Nicole Borth
- Austrian Center of Industrial Biotechnology GmbH, Vienna, Austria
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicolas Marx
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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6
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Glinšek K, Bozovičar K, Bratkovič T. CRISPR Technologies in Chinese Hamster Ovary Cell Line Engineering. Int J Mol Sci 2023; 24:ijms24098144. [PMID: 37175850 PMCID: PMC10179654 DOI: 10.3390/ijms24098144] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The Chinese hamster ovary (CHO) cell line is a well-established platform for the production of biopharmaceuticals due to its ability to express complex therapeutic proteins with human-like glycopatterns in high amounts. The advent of CRISPR technology has opened up new avenues for the engineering of CHO cell lines for improved protein production and enhanced product quality. This review summarizes recent advances in the application of CRISPR technology for CHO cell line engineering with a particular focus on glycosylation modulation, productivity enhancement, tackling adventitious agents, elimination of problematic host cell proteins, development of antibiotic-free selection systems, site-specific transgene integration, and CRISPR-mediated gene activation and repression. The review highlights the potential of CRISPR technology in CHO cell line genome editing and epigenetic engineering for the more efficient and cost-effective development of biopharmaceuticals while ensuring the safety and quality of the final product.
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Affiliation(s)
- Katja Glinšek
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Krištof Bozovičar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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7
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Kalkan AK, Palaz F, Sofija S, Elmousa N, Ledezma Y, Cachat E, Rios-Solis L. Improving recombinant protein production in CHO cells using the CRISPR-Cas system. Biotechnol Adv 2023; 64:108115. [PMID: 36758652 DOI: 10.1016/j.biotechadv.2023.108115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/28/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Chinese hamster ovary (CHO) cells are among the most widely used mammalian cell lines in the biopharmaceutical industry. Therefore, it is not surprising that significant efforts have been made around the engineering of CHO cells using genetic engineering methods such as the CRISPR-Cas system. In this review, we summarize key recent studies that have used different CRISPR-Cas systems such as Cas9, Cas13 or dCas9 fused with effector domains to improve recombinant protein (r-protein) production in CHO cells. Here, every relevant stage of production was considered, underscoring the advantages and limitations of these systems, as well as discussing their bottlenecks and probable solutions. A special emphasis was given on how these systems could disrupt and/or regulate genes related to glycan composition, which has relevant effects over r-protein properties and in vivo activity. Furthermore, the related promising future applications of CRISPR to achieve a tunable, reversible, or highly stable editing of CHO cells are discussed. Overall, the studies covered in this review show that despite the complexity of mammalian cells, the synthetic biology community has developed many mature strategies to improve r-protein production using CHO cells. In this regard, CRISPR-Cas technology clearly provides efficient and flexible genetic manipulation and allows for the generation of more productive CHO cell lines, leading to more cost-efficient production of biopharmaceuticals, however, there is still a need for many emerging techniques in CRISPR to be reported in CHO cells; therefore, more research in these cells is needed to realize the full potential of this technology.
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Affiliation(s)
- Ali Kerem Kalkan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Environmental Engineering Department, Gebze Technical University, Turkey
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Semeniuk Sofija
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nada Elmousa
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Yuri Ledezma
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; Biology Department, Faculty of Pure and Natural Sciences, Universidad Mayor de San Andrés, Bolivia
| | - Elise Cachat
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK; UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Leonardo Rios-Solis
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
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8
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Amiri S, Adibzadeh S, Ghanbari S, Rahmani B, Kheirandish MH, Farokhi-Fard A, Dastjerdeh MS, Davami F. CRISPR-interceded CHO cell line development approaches. Biotechnol Bioeng 2023; 120:865-902. [PMID: 36597180 DOI: 10.1002/bit.28329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/28/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
For industrial production of recombinant protein biopharmaceuticals, Chinese hamster ovary (CHO) cells represent the most widely adopted host cell system, owing to their capacity to produce high-quality biologics with human-like posttranslational modifications. As opposed to random integration, targeted genome editing in genomic safe harbor sites has offered CHO cell line engineering a new perspective, ensuring production consistency in long-term culture and high biotherapeutic expression levels. Corresponding the remarkable advancements in knowledge of CRISPR-Cas systems, the use of CRISPR-Cas technology along with the donor design strategies has been pushed into increasing novel scenarios in cell line engineering, allowing scientists to modify mammalian genomes such as CHO cell line quickly, readily, and efficiently. Depending on the strategies and production requirements, the gene of interest can also be incorporated at single or multiple loci. This review will give a gist of all the most fundamental recent advancements in CHO cell line development, such as different cell line engineering approaches along with donor design strategies for targeted integration of the desired construct into genomic hot spots, which could ultimately lead to the fast-track product development process with consistent, improved product yield and quality.
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Affiliation(s)
- Shahin Amiri
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Setare Adibzadeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Samaneh Ghanbari
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behnaz Rahmani
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad H Kheirandish
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies, Tehran University of Medical Sciences, Tehran, Iran
| | - Aref Farokhi-Fard
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mansoureh S Dastjerdeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Davami
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Durrant MG, Fanton A, Tycko J, Hinks M, Chandrasekaran SS, Perry NT, Schaepe J, Du PP, Lotfy P, Bassik MC, Bintu L, Bhatt AS, Hsu PD. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat Biotechnol 2023; 41:488-499. [PMID: 36217031 PMCID: PMC10083194 DOI: 10.1038/s41587-022-01494-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 09/01/2022] [Indexed: 11/09/2022]
Abstract
Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold and enabling the prediction of their insertion site specificities. We tested their recombination activity in human cells, classifying them as landing pad, genome-targeting or multi-targeting LSRs. Overall, we achieved up to seven-fold higher recombination than Bxb1 and genome integration efficiencies of 40-75% with cargo sizes over 7 kb. We also demonstrate virus-free, direct integration of plasmid or amplicon libraries for improved functional genomics applications. This systematic discovery of recombinases directly from microbial sequencing data provides a resource of over 60 LSRs experimentally characterized in human cells for large-payload genome insertion without exposed DNA double-stranded breaks.
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Affiliation(s)
- Matthew G Durrant
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michaela Hinks
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sita S Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Nicholas T Perry
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Julia Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Peter P Du
- Department of Genetics, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Peter Lotfy
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA.
| | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
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10
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Introduction of the FecG F mutation in GDF9 gene via CRISPR/Cas9 system with single-stranded oligodeoxynucleotide. Theriogenology 2023; 197:177-185. [PMID: 36525857 DOI: 10.1016/j.theriogenology.2022.11.044] [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: 05/02/2022] [Revised: 11/21/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) 9 system has been a recent focus of breeders owing to its potential to improve economically significant traits of livestock. The introduction of defined point mutations into the ovine genome via CRISPR/Cas9-mediated homology-directed repair has been reported; however, indel and mosaic events observed in genetically modified animals limit the practical application of this system in sheep breeding. The FecGF mutation (g. G1111A, p. V371 M) in the growth differentiation factor 9 (GDF9) gene is strongly associated with litter size in Belclare and Norwegian White Sheep. In the present study, we introduced the FecGF mutation in GDF9 by co-injecting the CRISPR/Cas9 system, single-stranded oligodeoxynucleotide (ssODN), and Scr7 into ovine zygotes. Scr7 at various concentrations (0 μM, 1 μM, and 2 μM) had no adverse effects on embryonic development in vitro. No significant differences in total mutation, point mutation, and indel rates in embryos were observed among groups treated with different concentrations of Scr7. However, the mosaicism rates of embryos from zygotes microinjected with 1 and 2 μM Scr7 were significantly lower than that for 0 μM Scr7 (7.7% and 7.5% vs. 19.7%). We successfully obtained lambs with defined nucleotide substitutions by the coinjection of Cas9 mRNA, sgRNA, ssODN, and 1 μM Scr7 into Altay sheep zygotes. The single nucleotide mutation efficiency was 7.69% (3/39) in newborn lambs, with one mosaic. Our findings provide evidence that Scr7 could improve the specificity of the CRISPR/Cas9 system for the introduction of a defined point mutation in livestock to some extent.
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11
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Tanihara F, Hirata M, Namula Z, Do LTK, Yoshimura N, Lin Q, Takebayashi K, Sakuma T, Yamamoto T, Otoi T. Pigs with an INS point mutation derived from zygotes electroporated with CRISPR/Cas9 and ssODN. Front Cell Dev Biol 2023; 11:884340. [PMID: 36711037 PMCID: PMC9880039 DOI: 10.3389/fcell.2023.884340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Just one amino acid at the carboxy-terminus of the B chain distinguishes human insulin from porcine insulin. By introducing a precise point mutation into the porcine insulin (INS) gene, we were able to generate genetically modified pigs that secreted human insulin; these pigs may be suitable donors for islet xenotransplantation. The electroporation of the CRISPR/Cas9 gene-editing system into zygotes is frequently used to establish genetically modified rodents, as it requires less time and no micromanipulation. However, electroporation has not been used to generate point-mutated pigs yet. In the present study, we introduced a point mutation into porcine zygotes via electroporation using the CRISPR/Cas9 system to generate INS point-mutated pigs as suitable islet donors. We first optimized the efficiency of introducing point mutations by evaluating the effect of Scr7 and the homology arm length of ssODN on improving homology-directed repair-mediated gene modification. Subsequently, we prepared electroporated zygotes under optimized conditions and transferred them to recipient gilts. Two recipients became pregnant and delivered five piglets. Three of the five piglets carried only the biallelic frame-shift mutation in the INS gene, whereas the other two successfully carried the desired point mutation. One of the two pigs mated with a WT boar, and this desired point mutation was successfully inherited in the next F1 generation. In conclusion, we successfully established genetically engineered pigs with the desired point mutation via electroporation-mediated introduction of the CRISPR/Cas9 system into zygotes, thereby avoiding the time-consuming and complicated micromanipulation method.
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Affiliation(s)
- Fuminori Tanihara
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Maki Hirata
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan,Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
| | - Zhao Namula
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan,College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Lanh Thi Kim Do
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan,Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Naoaki Yoshimura
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan,Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
| | - Qingyi Lin
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan,Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
| | - Koki Takebayashi
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan,Bio-Innovation Research Center, Tokushima University, Tokushima, Japan
| | - Tetsushi Sakuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takeshige Otoi
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan,Bio-Innovation Research Center, Tokushima University, Tokushima, Japan,*Correspondence: Takeshige Otoi,
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12
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Targeted integration in CHO cells using CRIS-PITCh/Bxb1 recombinase-mediated cassette exchange hybrid system. Appl Microbiol Biotechnol 2023; 107:769-783. [PMID: 36536089 PMCID: PMC9763083 DOI: 10.1007/s00253-022-12322-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/27/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
Recombinant Chinese hamster ovary (CHO) cell line development for complex biotherapeutic production is conventionally based on the random integration (RI) approach. Due to the lack of control over the integration site and copy number, RI-generated cell pools are always coupled with rigorous screening to find clones that satisfy requirements for production titers, quality, and stability. Targeted integration into a well-defined genomic site has been suggested as a possible strategy to mitigate the drawbacks associated with RI. In this work, we employed the CRISPR-mediated precise integration into target chromosome (CRIS-PITCh) system in combination with the Bxb1 recombinase-mediated cassette exchange (RMCE) system to generate an isogenic transgene-expressing cell line. We successfully utilized the CRIS-PITCh system to target a 2.6 kb Bxb1 landing pad with homology arms as short as 30 bp into the upstream region of the S100A gene cluster, achieving a targeting efficiency of 10.4%. The platform cell line (PCL) with a single copy of the landing pad was then employed for the Bxb1-mediated landing pad exchange with an EGFP encoding cassette to prove its functionality. Finally, to accomplish the main goal of our cell line development method, the PCL was applied for the expression of a secretory glycoprotein, human recombinant soluble angiotensin-converting enzyme 2 (hrsACE2). Taken together, on-target, single-copy, and stable expression of the transgene over long-term cultivation demonstrated our CRIS-PITCh/RMCE hybrid approach might possibly improve the cell line development process in terms of timeline, specificity, and stability. KEY POINTS: • CRIS-PITCh system is an efficient method for single copy targeted integration of the landing pad and generation of platform cell line • Upstream region of the S100A gene cluster of CHO-K1 is retargetable by recombinase-mediated cassette exchange (RMCE) approach and provides a stable expression of the transgene • CRIS-PITCh/Bxb1 RMCE hybrid system has the potential to overcome some limitations of the random integration approach and accelerate the cell line development timeline.
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13
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Novel CRISPR/Cas9-mediated knockout of LIG4 increases efficiency of site-specific integration in Chinese hamster ovary cell line. Biotechnol Lett 2022; 44:1063-1072. [PMID: 35918621 DOI: 10.1007/s10529-022-03282-7] [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: 03/29/2022] [Accepted: 07/11/2022] [Indexed: 11/02/2022]
Abstract
AIM To investigate the impact of deficiency of LIG4 gene on site-specific integration in CHO cells. RESULTS CHO cells are considered the most valuable mammalian cells in the manufacture of biological medicines, and genetic engineering of CHO cells can improve product yield and stability. The traditional method of inserting foreign genes by random integration (RI) requires multiple rounds of screening and selection, which may lead to location effects and gene silencing, making it difficult to obtain stable, high-yielding cell lines. Although site-specific integration (SSI) techniques may overcome the challenges with RI, its feasibility is limited by the very low efficiency of the technique. Recently, SSI efficiency has been enhanced in other mammalian cell types by inhibiting DNA ligase IV (Lig4) activity, which is indispensable in DNA double-strand break repair by NHEJ. However, this approach has not been evaluated in CHO cells. In this study, the LIG4 gene was knocked out of CHO cells using CRISPR/Cas9-mediated genome editing. Efficiency of gene targeting in LIG4-/--CHO cell lines was estimated by a green fluorescence protein promoterless reporter system. Notably, the RI efficiency, most likely mediated by NHEJ in CHO, was inhibited by LIG4 knockout, whereas SSI efficiency strongly increased 9.2-fold under the precise control of the promoter in the ROSA26 site in LIG4-/--CHO cells. Moreover, deletion of LIG4 had no obvious side effects on CHO cell proliferation. CONCLUSIONS Deficiency of LIG4 represents a feasible strategy to improve SSI efficiency and suggests it can be applied to develop and engineer CHO cell lines in the future.
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14
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Shams F, Bayat H, Mohammadian O, Mahboudi S, Vahidnezhad H, Soosanabadi M, Rahimpour A. Advance trends in targeting homology-directed repair for accurate gene editing: An inclusive review of small molecules and modified CRISPR-Cas9 systems. BIOIMPACTS 2022; 12:371-391. [PMID: 35975201 PMCID: PMC9376165 DOI: 10.34172/bi.2022.23871] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
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Introduction: Clustered regularly interspaced short palindromic repeat and its associated protein (CRISPR-Cas)-based technologies generate targeted modifications in host genome by inducing site-specific double-strand breaks (DSBs) that can serve as a substrate for homology-directed repair (HDR) in both in vitro and in vivo models. HDR pathway could enhance incorporation of exogenous DNA templates into the CRISPR-Cas9-mediated DSB site. Owing to low rate of HDR pathway, the efficiency of accurate genome editing is diminished. Enhancing the efficiency of HDR can provide fast, easy, and accurate technologies based on CRISPR-Cas9 technologies.
Methods: The current study presents an overview of attempts conducted on the precise genome editing strategies based on small molecules and modified CRISPR-Cas9 systems.
Results: In order to increase HDR rate in targeted cells, several logical strategies have been introduced such as generating CRISPR effector chimeric proteins, anti-CRISPR proteins, modified Cas9 with donor template, and using validated synthetic or natural small molecules for either inhibiting non-homologous end joining (NHEJ), stimulating HDR, or synchronizing cell cycle. Recently, high-throughput screening methods have been applied for identification of small molecules which along with the CRISPR system can regulate precise genome editing through HDR.
Conclusion: The stimulation of HDR components or inhibiting NHEJ can increase the accuracy of CRISPR-Cas-mediated engineering systems. Generating chimeric programmable endonucleases provide this opportunity to direct DNA template close proximity of CRISPR-Cas-mediated DSB. Small molecules and their derivatives can also proficiently block or activate certain DNA repair pathways and bring up novel perspectives for increasing HDR efficiency, especially in human cells. Further, high throughput screening of small molecule libraries could result in more discoveries of promising chemicals that improve HDR efficiency and CRISPR-Cas9 systems.
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Affiliation(s)
- Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mahboudi
- Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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15
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Small-molecule enhancers of CRISPR-induced homology-directed repair in gene therapy: A medicinal chemist's perspective. Drug Discov Today 2022; 27:2510-2525. [PMID: 35738528 DOI: 10.1016/j.drudis.2022.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/19/2022] [Accepted: 06/16/2022] [Indexed: 11/20/2022]
Abstract
CRISPR technologies are increasingly being investigated and utilized for the treatment of human genetic diseases via genome editing. CRISPR-Cas9 first generates a targeted DNA double-stranded break, and a functional gene can then be introduced to replace the defective copy in a precise manner by templated repair via the homology-directed repair (HDR) pathway. However, this is challenging owing to the relatively low efficiency of the HDR pathway compared with a rival random repair pathway known as non-homologous end joining (NHEJ). Small molecules can be employed to increase the efficiency of HDR and decrease that of NHEJ to improve the efficiency of precise knock-in genome editing. This review discusses the potential usage of such small molecules in the context of gene therapy and their drug-likeness, from a medicinal chemist's perspective.
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16
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Factors affecting the quality of therapeutic proteins in recombinant Chinese hamster ovary cell culture. Biotechnol Adv 2021; 54:107831. [PMID: 34480988 DOI: 10.1016/j.biotechadv.2021.107831] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/21/2021] [Accepted: 08/30/2021] [Indexed: 12/17/2022]
Abstract
Chinese hamster ovary (CHO) cells are the most widely used mammalian host cells for the commercial production of therapeutic proteins. Fed-batch culture is widely used to produce therapeutic proteins, including monoclonal antibodies, because of its operational simplicity and high product titer. Despite technical advances in the development of culture media and cell cultures, it is still challenging to maintain high productivity in fed-batch cultures while also ensuring good product quality. In this review, factors that affect the quality attributes of therapeutic proteins in recombinant CHO (rCHO) cell culture, such as glycosylation, charge variation, aggregation, and degradation, are summarized and categorized into three groups: culture environments, chemical additives, and host cell proteins accumulated in culture supernatants. Understanding the factors that influence the therapeutic protein quality in rCHO cell culture will facilitate the development of large-scale, high-yield fed-batch culture processes for the production of high-quality therapeutic proteins.
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17
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Wittayarat M, Hirata M, Namula Z, Sato Y, Nguyen NT, Le QA, Lin Q, Takebayashi K, Tanihara F, Otoi T. Introduction of a point mutation in the KRAS gene of in vitro fertilized porcine zygotes via electroporation of the CRISPR/Cas9 system with single-stranded oligodeoxynucleotides. Anim Sci J 2021; 92:e13534. [PMID: 33638256 DOI: 10.1111/asj.13534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/21/2020] [Accepted: 02/08/2021] [Indexed: 01/02/2023]
Abstract
This study aimed to investigate the efficiency of KRAS gene editing via CRISPR/Cas9 delivery by electroporation and analyzed the effects of the non-homologous end-joining pathway inhibitor Scr7 and single-stranded oligodeoxynucleotide (ssODN) homology arm length on introducing a point mutation in KRAS. Various concentrations (0-2 µM) of Scr7 were evaluated; all concentrations of Scr7 including 0 µM resulted in the generation of blastocysts with a point mutation and the wild-type sequence or indels. No significant differences in the blastocyst formation rates of electroporated zygotes were observed among ssODN homology arm lengths, irrespective of the gRNA (gRNA1 and gRNA2). The proportion of blastocysts carrying a point mutation with or without the wild-type sequence and indels was significantly higher in the ssODN20 group (i.e., the group with a ssODN homology arm of 20 bp) than in the ssODN60 group (gRNA1: 25.7% vs. 5.4% and gRNA2: 45.5% vs. 5.9%, p < .05). In conclusion, the CRISPR/Cas9 delivery with ssODN via electroporation is feasible for the generation of point mutations in porcine embryos. Further studies are required to improve the efficiency and accuracy of the homology-directed repair.
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Affiliation(s)
- Manita Wittayarat
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan.,Faculty of Veterinary Science, Prince of Songkla University, Songkhla, Thailand
| | - Maki Hirata
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Zhao Namula
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan.,College of Agricultural Science, Guangdong Ocean University, Guangdong, China
| | - Yoko Sato
- School of Biological Science, Tokai University, Sapporo, Japan
| | - Nhien T Nguyen
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Quynh A Le
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Qingyi Lin
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Koki Takebayashi
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Fuminori Tanihara
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Takeshige Otoi
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
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18
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Tevelev B, Patel H, Shields K, Wei W, Cooley C, Zhang S, Bitzas G, Duan W, Khetemenee L, Jackobek R, D'Antona A, Sievers A, King A, Tam A, Zhang Y, Sousa E, Cohen J, Wroblewska L, Marshall J, Jackson M, Scarcelli JJ. Genetic rearrangement during site specific integration event facilitates cell line development of a bispecific molecule. Biotechnol Prog 2021; 37:e3158. [PMID: 33891804 PMCID: PMC8459265 DOI: 10.1002/btpr.3158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022]
Abstract
Site specific integration (SSI) expression systems offer robust means of generating highly productive and stable cell lines for traditional monoclonal antibodies. As complex modalities such as antibody‐like molecules comprised of greater than two peptides become more prevalent, greater emphasis needs to be placed on the ability to produce appreciable quantities of the correct product of interest (POI). The ability to screen several transcript stoichiometries could play a large role in ensuring high amounts of the correct POI. Here we illustrate implementation of an SSI expression system with a single site of integration for development and production of a multi‐chain, bi‐specific molecule. A SSI vector with a single copy of all of the genes of interest was initially selected for stable Chinese hamster ovary transfection. While the resulting transfection pools generated low levels of the desired heterodimer, utilizing an intensive clone screen strategy, we were able to identify clones having significantly higher levels of POI. In‐depth genotypic characterization of clones having the desirable phenotype revealed that a duplication of the light chain within the landing pad was responsible for producing the intended molecule. Retrospective transfection pool analysis using a vector configuration mimicking the transgene configuration found in the clones, as well as other vector configurations, yielded more favorable results with respect to % POI. Overall, the study demonstrated that despite the theoretical static nature of the SSI expression system, enough heterogeneity existed to yield clones having significantly different transgene phenotypes/genotypes and support production of a complex multi‐chain molecule.
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Affiliation(s)
- Barbara Tevelev
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Himakshi Patel
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Kathleen Shields
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Wei Wei
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Cecilia Cooley
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Sam Zhang
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | | | - Weili Duan
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Lam Khetemenee
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Ryan Jackobek
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Aaron D'Antona
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Annette Sievers
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Amy King
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Amy Tam
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Yan Zhang
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Eric Sousa
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Justin Cohen
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Lila Wroblewska
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Jeffrey Marshall
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Martha Jackson
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - John J Scarcelli
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
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19
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Shin SW, Kim D, Lee JS. Controlling Ratios of Plasmid-Based Double Cut Donor and CRISPR/Cas9 Components to Enhance Targeted Integration of Transgenes in Chinese Hamster Ovary Cells. Int J Mol Sci 2021; 22:ijms22052407. [PMID: 33673701 PMCID: PMC7957797 DOI: 10.3390/ijms22052407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
Chinese hamster ovary (CHO) cells are the most valuable expression host for the commercial production of biotherapeutics. Recent trends in recombinant CHO cell-line development have focused on the site-specific integration of transgenes encoding recombinant proteins over random integration. However, the low efficiency of homology-directed repair upon transfection of Cas9, single-guide RNA (sgRNA), and the donor template has limited its feasibility. Previously, we demonstrated that a double-cut donor (DCD) system enables highly efficient CRISPR/Cas9-mediated targeted integration (TI) in CHO cells. Here, we describe several CRISPR/Cas9 vector systems based on DCD templates using a promoter trap-based TI monitoring cell line. Among them, a multi-component (MC) system consisting of an sgRNA/DCD vector and Cas9 expression vector showed an approximate 1.5-fold increase in knock-in (KI) efficiency compared to the previous DCD system, when a systematically optimized relative ratio of sgRNA/DCD and Cas9 vector was applied. Our optimization efforts revealed that concurrently increasing sgRNA and DCD components relative to Cas9 correlated positively with KI efficiency at a single KI site. Furthermore, we explored component bottlenecks, such as effects of sgRNA components and applicability of the MC system on simultaneous double KI. Taken together, we improved the DCD vector design by tailoring plasmid constructs and relative component ratios, and this system can be widely used in the TI strategy of transgenes, particularly in CHO cell line development and engineering.
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20
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Kwak JM, Lee Y, Shin SW, Lee JS. Hydroxyurea selection for enhancement of homology-directed targeted integration of transgenes in CHO cells. N Biotechnol 2021; 62:26-31. [PMID: 33484867 DOI: 10.1016/j.nbt.2021.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 01/06/2021] [Accepted: 01/17/2021] [Indexed: 12/23/2022]
Abstract
Site-specific integration via genome editing technologies has been implemented in Chinese hamster ovary (CHO) cells for predictable and efficient cell line development and engineering. Various strategies have been employed to enhance knock-in (KI) efficiency for precise homology-directed repair (HDR)-mediated targeted integration of transgenes in CHO cells. Given the cell cycle-dependent regulation of the DNA damage repair pathway, cell cycle synchronization to the HDR-favored S/G2 phase has been successfully utilized in mammalian cells, but the effect is limited in CHO cells. Here, we describe a cell cycle enrichment method to increase HDR-mediated KI efficiency in CHO cells. Existing G1 cell cycle synchronization methods showed transient cell cycle arrest and did not improve KI efficiency. Rather than cell cycle arrest with a high concentration of chemicals followed by a release step, cells were incubated in the presence of a lower concentration of hydroxyurea (HU) to enrich cells in the S phase. HU selection allowed for robust S phase enrichment of CHO cells by up to 70 % and maintained cell viability. This short-term selection resulted in improved KI efficiency by 1.2-1.5 fold compared with cells in the control condition. Overall, this approach serves as a simple and effective strategy for enhancement of site-specific genome engineering in CHO cells.
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Affiliation(s)
- Jin Myeong Kwak
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, 16499, Republic of Korea; Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Youngsik Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Sung Wook Shin
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Jae Seong Lee
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, 16499, Republic of Korea; Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea.
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21
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Shin SW, Lee JS. CHO Cell Line Development and Engineering via Site-specific Integration: Challenges and Opportunities. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0093-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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22
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Guo X, Wang C, Wang TY. Chromatin-modifying elements for recombinant protein production in mammalian cell systems. Crit Rev Biotechnol 2020; 40:1035-1043. [PMID: 32777953 DOI: 10.1080/07388551.2020.1805401] [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] [Indexed: 02/07/2023]
Abstract
Mammalian cells are the preferred choice system for the production of complex molecules, such as recombinant therapeutic proteins. Although the technology for increasing the yield of proteins has improved rapidly, the process of selecting, identifying as well as maintaining high-yield cell clones is still troublesome, time-consuming and usually uncertain. Optimization of expression vectors is one of the most effective methods for enhancing protein expression levels. Several commonly used chromatin-modifying elements, including the matrix attachment region, ubiquitous chromatin opening elements, insulators, stabilizing anti-repressor elements can be used to increase the expression level and stability of recombinant proteins. In this review, these chromatin-modifying elements used for the expression vector optimization in mammalian cells are summarized, and future strategies for the utilization of expression cassettes are also discussed.
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Affiliation(s)
- Xiao Guo
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China.,Perildicals Publishing House, Xinxiang Medical University, Xinxiang, China
| | - Chong Wang
- School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China.,Perildicals Publishing House, Xinxiang Medical University, Xinxiang, China
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23
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Hamaker NK, Lee KH. A Site-Specific Integration Reporter System That Enables Rapid Evaluation of CRISPR/Cas9-Mediated Genome Editing Strategies in CHO Cells. Biotechnol J 2020; 15:e2000057. [PMID: 32500600 DOI: 10.1002/biot.202000057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/09/2020] [Indexed: 12/12/2022]
Abstract
Targeted gene knockout and site-specific integration (SSI) are powerful genome editing techniques to improve the development of industrially relevant Chinese hamster ovary (CHO) cell lines. However, past efforts to perform SSI in CHO cells are characterized by low efficiencies. Moreover, numerous strategies proposed to boost SSI efficiency in mammalian cell types have yet to be evaluated head to head or in combination to appreciably boost efficiencies in CHO. To enable systematic and rapid optimization of genome editing methods, the SSIGNAL (site-specific integration and genome alteration) reporter system is developed. This tool can analyze CRISPR (clustered regularly interspaced palindromic repeats)/Cas9 (CRISPR-associated protein 9)-mediated disruption activity alone or in conjunction with SSI efficiency. The reporter system uses green and red dual-fluorescence signals to indicate genotype states within four days following transfection, facilitating rapid data acquisition via standard flow cytometry instrumentation. In addition to describing the design and development of the system, two of its applications are demonstrated by first comparing transfection conditions to maximize CRISPR/Cas9 activity and subsequently assessing the efficiency of several promising SSI strategies. Due to its sensitivity and versatility, the SSIGNAL reporter system may serve as a tool to advance genome editing technology.
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Affiliation(s)
- Nathaniel K Hamaker
- Biopharmaceutical Innovation Center, Newark, DE, 19713, USA.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Kelvin H Lee
- Biopharmaceutical Innovation Center, Newark, DE, 19713, USA.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
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24
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Shin SW, Lee JS. Optimized CRISPR/Cas9 strategy for homology-directed multiple targeted integration of transgenes in CHO cells. Biotechnol Bioeng 2020; 117:1895-1903. [PMID: 32086804 DOI: 10.1002/bit.27315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
Site-specific integration has emerged as a promising strategy for precise Chinese hamster ovary (CHO) cell line engineering and predictable cell line development (CLD). CRISPR/Cas9 with the homology-directed repair (HDR) pathway enables precise integration of transgenes into target genomic sites. However, inherent recalcitrance to HDR-mediated targeted integration (TI) of transgenes results in low targeting efficiency, thus requiring a selection process to find a targeted integrant in CHO cells. Here, we explored several parameters that influence the targeting efficiency using a promoter-trap-based single- or double-knock-in (KI) monitoring system. A simple change in the donor template design by the addition of single-guide RNA recognition sequences strongly increased KI efficiency (2.9-36.0 fold), depending on integration sites and cell culture mode, compared to conventional circular donor plasmids. Furthermore, sequential and simultaneous KI strategies enabled us to obtain populations with ~1-4% of double-KI cells without additional enrichment procedures. Thus, this simple optimized strategy not only allows efficient CRISPR/Cas9-mediated TI in CHO cells but also paves the way for the applicability of multiplexed KIs in one experimental step without the need for sequential and independent CHO-CLD procedures.
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Affiliation(s)
- Sung Wook Shin
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
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25
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Wang TY, Guo X. Expression vector cassette engineering for recombinant therapeutic production in mammalian cell systems. Appl Microbiol Biotechnol 2020; 104:5673-5688. [PMID: 32372203 DOI: 10.1007/s00253-020-10640-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/13/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
Human tissue plasminogen activator was the first recombinant therapy protein that successfully produced in Chinese hamster ovary cells in 1986 and approved for clinical use. Since then, more and more therapeutic proteins are being manufactured in mammalian cells, and the technologies for recombinant protein production in this expression system have developed rapidly, with the optimization of both upstream and downstream processes. One of the most promising strategies is expression vector cassette optimization based on the expression vector cassette. In this review paper, these approaches and developments are summarized, and the future strategy on the utilizing of expression cassettes for the production of recombinant therapeutic proteins in mammalian cells is discussed.
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Affiliation(s)
- Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
| | - Xiao Guo
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- Perildicals Publishing House, Xinxiang Medical University, Xinxiang, Henan, China
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Lamas‐Toranzo I, Martínez‐Moro A, O´Callaghan E, Millán‐Blanca G, Sánchez J, Lonergan P, Bermejo‐Álvarez P. RS-1 enhances CRISPR-mediated targeted knock-in in bovine embryos. Mol Reprod Dev 2020; 87:542-549. [PMID: 32227559 PMCID: PMC7496720 DOI: 10.1002/mrd.23341] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/08/2020] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Targeted knock-in (KI) can be achieved in embryos by clustered regularly interspaced short palindromic repeats (CRISPR)-assisted homology directed repair (HDR). However, HDR efficiency is constrained by the competition of nonhomologous end joining. The objective of this study was to explore whether CRISPR-assisted targeted KI rates can be improved in bovine embryos by exposure to the HDR enhancer RS-1. In vitro produced zygotes were injected with CRISPR components (300 ng/µl Cas9 messenger RNA and 100 ng/µl single guide RNA against a noncoding region) and a single-stranded DNA (ssDNA) repair template (100 ng/µl). ssDNA template contained a 6 bp XbaI site insert, allowing targeted KI detection by restriction analysis, flanked by 50 bp homology arms. Following microinjection, zygotes were exposed to 0, 3.75, or 7.5 µM RS-1 for 24 hr. No differences were noted between groups in terms of development or genome edition rates. However, targeted KI rates were doubled in the group exposed to 7.5 µM RS-1 compared to the others (52.8% vs. 25% and 23.1%, for 7.5, 0, and 3.75 µM, respectively). In conclusion, transient exposure to 7.5 µM RS-1 enhances targeted KI rates resulting in approximately half of the embryos containing the intended mutation, hence allowing direct KI generation in embryos.
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Affiliation(s)
| | - A. Martínez‐Moro
- Animal Reproduction DepartmentINIAMadridSpain
- ProcreatecMadridSpain
| | - E. O´Callaghan
- School of Agriculture and Food ScienceUniversity College DublinDublinIreland
| | | | - J.M. Sánchez
- School of Agriculture and Food ScienceUniversity College DublinDublinIreland
| | - P. Lonergan
- School of Agriculture and Food ScienceUniversity College DublinDublinIreland
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27
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Henry MN, MacDonald MA, Orellana CA, Gray PP, Gillard M, Baker K, Nielsen LK, Marcellin E, Mahler S, Martínez VS. Attenuating apoptosis in Chinese hamster ovary cells for improved biopharmaceutical production. Biotechnol Bioeng 2020; 117:1187-1203. [DOI: 10.1002/bit.27269] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/25/2019] [Accepted: 01/04/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Matthew N. Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
| | - Michael A. MacDonald
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
| | - Camila A. Orellana
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
| | - Peter P. Gray
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
| | - Marianne Gillard
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
| | - Kym Baker
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
- Patheon Biologics—A Part of Thermo Fisher Scientific Brisbane Queensland Australia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
- Metabolomics Australia The University of Queensland Brisbane Queensland Australia
- The Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kgs. Lyngby Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland Brisbane Queensland Australia
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
- Metabolomics Australia The University of Queensland Brisbane Queensland Australia
| | - Stephen Mahler
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
| | - Verónica S. Martínez
- ARC Training Centre for Biopharmaceutical Innovation (CBI) Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane Queensland Australia
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28
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Schweickert PG, Cheng Z. Application of Genetic Engineering in Biotherapeutics Development. J Pharm Innov 2019. [DOI: 10.1007/s12247-019-09411-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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29
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Mitigating Clonal Variation in Recombinant Mammalian Cell Lines. Trends Biotechnol 2019; 37:931-942. [DOI: 10.1016/j.tibtech.2019.02.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 12/27/2022]
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30
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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.
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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.
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31
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Aksoy YA, Nguyen DT, Chow S, Chung RS, Guillemin GJ, Cole NJ, Hesselson D. Chemical reprogramming enhances homology-directed genome editing in zebrafish embryos. Commun Biol 2019; 2:198. [PMID: 31149642 PMCID: PMC6533270 DOI: 10.1038/s42003-019-0444-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/15/2019] [Indexed: 12/26/2022] Open
Abstract
Precise genome editing is limited by the inefficiency of homology-directed repair (HDR) compared to the non-homologous end-joining (NHEJ) of double strand breaks (DSBs). The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 system generates precise, locus-specific DSBs that can serve as substrates for HDR. We developed an in vivo visual reporter assay to quantify HDR-mediated events at single-cell resolution in zebrafish and used this system to identify small-molecule modulators that shift the DNA repair equilibrium in favor of HDR. By further optimizing the reaction environment and repair template, we achieved dramatic enhancement of HDR-mediated repair efficiency in zebrafish. Accordingly, under optimized conditions, inhibition of NHEJ with NU7441 enhanced HDR-mediated repair up to 13.4-fold. Importantly, we demonstrate that the increase in somatic HDR events correlates directly with germline transmission, permitting the efficient recovery of large seamlessly integrated DNA fragments in zebrafish.
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Affiliation(s)
- Yagiz A. Aksoy
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW Australia
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - David T. Nguyen
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW Australia
| | - Sharron Chow
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - Roger S. Chung
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - Gilles J. Guillemin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - Nicholas J. Cole
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW Australia
| | - Daniel Hesselson
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, NSW Australia
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32
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Raab N, Mathias S, Alt K, Handrick R, Fischer S, Schmieder V, Jadhav V, Borth N, Otte K. CRISPR/Cas9-Mediated Knockout of MicroRNA-744 Improves Antibody Titer of CHO Production Cell Lines. Biotechnol J 2019; 14:e1800477. [PMID: 30802343 DOI: 10.1002/biot.201800477] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are noncoding RNAs that serve as versatile molecular engineering tools to improve production cells by overexpression or knockdown of miRNAs showing beneficial or adverse effects on cell-culture performance. The genomic knockout (KO) of noncoding RNAs in Chinese hamster ovary (CHO) production cells has not been reported. However, given the significant number of miRNAs showing negative effects on CHO-bioprocess performance and the development of clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR/Cas9), genome editing tools facilitate precise optimization of CHO cells via modulation of noncoding RNAs. In a previous high-content miRNA screen, miR-744 was identified as a potential target associated with reduced productivity. Hence, the genomic miR-744 precursor sequence is deleted by two single guide RNA (sgRNA)-Cas9-mediated DNA double-strand breaks (DSB) flanking the miR-744 locus. After fluorescence-activated cell sorting (FACS), clonal miR-744 KO cell lines are recovered and three of them are confirmed as miR-744 KOs. Impacts of CRISPR/Cas9 editing are characterized at the genetic, transcript, and phenotypic levels. During batch cultivation, antibody titers of miR-744 KOs are significantly increased to 190-311 mg L-1 compared to a nontargeting (NT) sgRNA transfected clonal control with 156 mg L-1 , pointing towards the potential of miRNA KO for cell line engineering.
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Affiliation(s)
- Nadja Raab
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
| | - Sven Mathias
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
| | - Kerstin Alt
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
- Genetikum, Wegenerstraße 15, Neu-Ulm, 89231, Germany
| | - René Handrick
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
| | - Simon Fischer
- Boehringer Ingelheim Pharma GmbH & Co KG, Cell Line Development CMB, Birkendorfer Str. 65, Biberach, 88397, Germany
| | - Valerie Schmieder
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Vaibhav Jadhav
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Nicole Borth
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
- BOKU Vienna, Institute of Biotechnology, Gregor-Mendel-Straße 33, Vienna, 1180, Austria
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
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33
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Zhou S, Ding X, Yang L, Chen Y, Gong X, Jin J, Li H. Discovery of a stable expression hot spot in the genome of Chinese hamster ovary cells using lentivirus-based random integration. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1601998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Songtao Zhou
- Department of Fermentation Engineering, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Xuefeng Ding
- Department of Fermentation Engineering, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Lei Yang
- Department of Fermentation Engineering, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Yun Chen
- Department of Drug Design and Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, PR China
| | - Xiaohai Gong
- Department of Drug Design and Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, PR China
| | - Jian Jin
- Department of Drug Design and Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, PR China
| | - Huazhong Li
- Department of Fermentation Engineering, School of Biotechnology, Jiangnan University, Wuxi, PR China
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34
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Pristovšek N, Nallapareddy S, Grav LM, Hefzi H, Lewis NE, Rugbjerg P, Hansen HG, Lee GM, Andersen MR, Kildegaard HF. Systematic Evaluation of Site-Specific Recombinant Gene Expression for Programmable Mammalian Cell Engineering. ACS Synth Biol 2019; 8:758-774. [PMID: 30807689 DOI: 10.1021/acssynbio.8b00453] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many branches of biology depend on stable and predictable recombinant gene expression, which has been achieved in recent years through targeted integration of the recombinant gene into defined integration sites. However, transcriptional levels of recombinant genes in characterized integration sites are controlled by multiple components of the integrated expression cassette. Lack of readily available tools has inhibited meaningful experimental investigation of the interplay between the integration site and the expression cassette components. Here we show in a systematic manner how multiple components contribute to final net expression of recombinant genes in a characterized integration site. We develop a CRISPR/Cas9-based toolbox for construction of mammalian cell lines with targeted integration of a landing pad, containing a recombinant gene under defined 5' proximal regulatory elements. Generated site-specific recombinant cell lines can be used in a streamlined recombinase-mediated cassette exchange for fast screening of different expression cassettes. Using the developed toolbox, we show that different 5' proximal regulatory elements generate distinct and robust recombinant gene expression patterns in defined integration sites of CHO cells with a wide range of transcriptional outputs. This approach facilitates the generation of user-defined and product-specific gene expression patterns for programmable mammalian cell engineering.
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Affiliation(s)
- Nuša Pristovšek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Saranya Nallapareddy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Hooman Hefzi
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, La Jolla, California 92093, United States
| | - Nathan E. Lewis
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, La Jolla, California 92093, United States
| | - Peter Rugbjerg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Henning Gram Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, KAIST, 291 Daehak-ro,
Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
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35
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Zhou S, Chen Y, Gong X, Jin J, Li H. Site-specific integration of light chain and heavy chain genes of antibody into CHO-K1 stable hot spot and detection of antibody and fusion protein expression level. Prep Biochem Biotechnol 2019; 49:384-390. [DOI: 10.1080/10826068.2019.1573196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Songtao Zhou
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yun Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Xiaohai Gong
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Huazhong Li
- School of Biotechnology, Jiangnan University, Wuxi, China
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36
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Abstract
The emergence of CRISPR/Cas9 system as a precise and affordable method for genome editing has prompted its rapid adoption for the targeted integration of transgenes in Chinese hamster ovary (CHO) cells. Targeted gene integration allows the generation of stable cell lines with a controlled and predictable behavior, which is an important feature for the rational design of cell factories aimed at the large-scale production of recombinant proteins. Here we present the protocol for CRISPR/Cas9-mediated integration of a gene expression cassette into a specific genomic locus in CHO cells using homology-directed DNA repair.
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37
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Bandyopadhyay AA, O’Brien SA, Zhao L, Fu HY, Vishwanathan N, Hu WS. Recurring genomic structural variation leads to clonal instability and loss of productivity. Biotechnol Bioeng 2019; 116:41-53. [PMID: 30144379 PMCID: PMC7058117 DOI: 10.1002/bit.26823] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/13/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022]
Abstract
Chinese hamster ovary cells, commonly used in the production of therapeutic proteins, are aneuploid. Their chromosomes bear structural abnormality and undergo changes in structure and number during cell proliferation. Some production cell lines are unstable and lose their productivity over time in the manufacturing process and during the product's life cycle. To better understand the link between genomic structural changes and productivity stability, an immunoglobulin G producing cell line was successively single-cell cloned to obtain subclones that retained or lost productivity, and their genomic features were compared. Although each subclone started with a single karyotype, the progeny quickly diversified to a population with a distribution of chromosome numbers that is not distinctive from the parent and among subclones. The comparative genomic hybridization (CGH) analysis showed that the extent of copy variation of gene coding regions among different subclones stayed at levels of a few percent. Genome regions that were prone to loss of copies, including one with a product transgene integration site, were identified in CGH. The loss of the transgene copy was accompanied by loss of transgene transcript level. Sequence analysis of the host cell and parental producing cell showed prominent structural variations within the regions prone to loss of copies. Taken together, we demonstrated the transient nature of clonal homogeneity in cell line development and the retention of a population distribution of chromosome numbers; we further demonstrated that structural variation in the transgene integration region caused cell line instability. Future cell line development may target the transgene into structurally stable regions.
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Affiliation(s)
| | | | | | | | | | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN 55455-0132 USA
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38
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39
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Kelly PS, Alarcon Miguez A, Alves C, Barron N. From media to mitochondria–rewiring cellular energy metabolism of Chinese hamster ovary cells for the enhanced production of biopharmaceuticals. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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40
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Smirnikhina SA, Anuchina AA, Lavrov AV. Ways of improving precise knock-in by genome-editing technologies. Hum Genet 2018; 138:1-19. [DOI: 10.1007/s00439-018-1953-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/29/2018] [Indexed: 02/07/2023]
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41
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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.
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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
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42
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Debottlenecking protein secretion and reducing protein aggregation in the cellular host. Curr Opin Biotechnol 2018; 53:151-157. [DOI: 10.1016/j.copbio.2018.01.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 01/05/2023]
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43
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Grav LM, Sergeeva D, Lee JS, Marin de Mas I, Lewis NE, Andersen MR, Nielsen LK, Lee GM, Kildegaard HF. Minimizing Clonal Variation during Mammalian Cell Line Engineering for Improved Systems Biology Data Generation. ACS Synth Biol 2018; 7:2148-2159. [PMID: 30060646 DOI: 10.1021/acssynbio.8b00140] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Mammalian cells are widely used to express genes for basic biology studies and biopharmaceuticals. Current methods for generation of engineered cell lines introduce high genomic and phenotypic diversity, which hamper studies of gene functions and discovery of novel cellular mechanisms. Here, we minimized clonal variation by integrating a landing pad for recombinase-mediated cassette exchange site-specifically into the genome of CHO cells using CRISPR and generated subclones expressing four different recombinant proteins. The subclones showed low clonal variation with high consistency in growth, transgene transcript levels and global transcriptional response to recombinant protein expression, enabling improved studies of the impact of transgenes on the host transcriptome. Little variation over time in subclone phenotypes and transcriptomes was observed when controlling environmental culture conditions. The platform enables robust comparative studies of genome engineered CHO cell lines and can be applied to other mammalian cells for diverse biological, biomedical and biotechnological applications.
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Affiliation(s)
- Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Daria Sergeeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jae Seong Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Igor Marin de Mas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
- The Novo Nordisk Foundation Center for Biosustatainability, University of California, San Diego, La Jolla, California 92093, United States
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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44
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Jia Y, Guo X, Lu J, Wang X, Qiu L, Wang T. CRISPR/Cas9-mediated gene knockout for DNA methyltransferase Dnmt3a in CHO cells displays enhanced transgenic expression and long-term stability. J Cell Mol Med 2018; 22:4106-4116. [PMID: 29851281 PMCID: PMC6111867 DOI: 10.1111/jcmm.13687] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/23/2018] [Indexed: 12/14/2022] Open
Abstract
CHO cells are the preferred host for the production of complex pharmaceutical proteins in the biopharmaceutical industry, and genome engineering of CHO cells would benefit product yield and stability. Here, we demonstrated the efficacy of a Dnmt3a-deficient CHO cell line created by CRISPR/Cas9 genome editing technology through gene disruptions in Dnmt3a, which encode the proteins involved in DNA methyltransferases. The transgenes, which were driven by the 2 commonly used CMV and EF1α promoters, were evaluated for their expression level and stability. The methylation levels of CpG sites in the promoter regions and the global DNA were compared in the transfected cells. The Dnmt3a-deficent CHO cell line based on Dnmt3a KO displayed an enhanced long-term stability of transgene expression under the control of the CMV promoter in transfected cells in over 60 passages. Under the CMV promoter, the Dnmt3a-deficent cell line with a high transgene expression displayed a low methylation rate in the promoter region and global DNA. Under the EF1α promoter, the Dnmt3a-deficient and normal cell lines with low transgene expression exhibited high DNA methylation rates. These findings provide insight into cell line modification and design for improved recombinant protein production in CHO and other mammalian cells.
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Affiliation(s)
- Yan‐Long Jia
- College of PharmacyXinxiang Medical UniversityXinxiangHenanChina
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of HenanXinxiang Medical UniversityXinxiangHenanChina
| | - Xiao Guo
- College of PharmacyXinxiang Medical UniversityXinxiangHenanChina
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of HenanXinxiang Medical UniversityXinxiangHenanChina
| | - Jiang‐Tao Lu
- College of PharmacyXinxiang Medical UniversityXinxiangHenanChina
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of HenanXinxiang Medical UniversityXinxiangHenanChina
| | - Xiao‐Yin Wang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of HenanXinxiang Medical UniversityXinxiangHenanChina
- School of Basic MedicineXinxiang Medical UniversityXinxiangHenanChina
| | - Le‐Le Qiu
- School of Basic MedicineXinxiang Medical UniversityXinxiangHenanChina
| | - Tian‐Yun Wang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of HenanXinxiang Medical UniversityXinxiangHenanChina
- School of Basic MedicineXinxiang Medical UniversityXinxiangHenanChina
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45
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Zhao M, Wang J, Luo M, Luo H, Zhao M, Han L, Zhang M, Yang H, Xie Y, Jiang H, Feng L, Lu H, Zhu J. Rapid development of stable transgene CHO cell lines by CRISPR/Cas9-mediated site-specific integration into C12orf35. Appl Microbiol Biotechnol 2018; 102:6105-6117. [PMID: 29789882 DOI: 10.1007/s00253-018-9021-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/16/2022]
Abstract
Chinese hamster ovary (CHO) cells are the most widely used mammalian hosts for recombinant protein production. However, by conventional random integration strategy, development of a high-expressing and stable recombinant CHO cell line has always been a difficult task due to the heterogenic insertion and its caused requirement of multiple rounds of selection. Site-specific integration of transgenes into CHO hot spots is an ideal strategy to overcome these challenges since it can generate isogenic cell lines with consistent productivity and stability. In this study, we investigated three sites with potential high transcriptional activities: C12orf35, HPRT, and GRIK1, to determine the possible transcriptional hot spots in CHO cells, and further construct a reliable site-specific integration strategy to develop recombinant cell lines efficiently. Genes encoding representative proteins mCherry and anti-PD1 monoclonal antibody were targeted into these three loci respectively through CRISPR/Cas9 technology. Stable cell lines were generated successfully after a single round of selection. In comparison with a random integration control, all the targeted integration cell lines showed higher productivity, among which C12orf35 locus was the most advantageous in both productivity and cell line stability. Binding affinity and N-glycan analysis of the antibody revealed that all batches of product were of similar quality independent on integrated sites. Deep sequencing demonstrated that there was low level of off-target mutations caused by CRISPR/Cas9, but none of them contributed to the development process of transgene cell lines. Our results demonstrated the feasibility of C12orf35 as the target site for exogenous gene integration, and strongly suggested that C12orf35 targeted integration mediated by CRISPR/Cas9 is a reliable strategy for the rapid development of recombinant CHO cell lines.
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Affiliation(s)
- Menglin Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jiaxian Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.,Department of Hematology, VU University Medical Center, Amsterdam, the Netherlands
| | - Manyu Luo
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Han Luo
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Meiqi Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Lei Han
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Mengxiao Zhang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hui Yang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yueqing Xie
- Jecho Laboratories, Inc., 7320 Executive Way, Frederick, MD, 21704, USA
| | - Hua Jiang
- Jecho Laboratories, Inc., 7320 Executive Way, Frederick, MD, 21704, USA
| | - Lei Feng
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huili Lu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Jianwei Zhu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China. .,Jecho Laboratories, Inc., 7320 Executive Way, Frederick, MD, 21704, USA.
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46
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Wang W, Zheng W, Hu F, He X, Wu D, Zhang W, Liu H, Ma X. Enhanced Biosynthesis Performance of Heterologous Proteins in CHO-K1 Cells Using CRISPR-Cas9. ACS Synth Biol 2018; 7:1259-1268. [PMID: 29683658 DOI: 10.1021/acssynbio.7b00375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chinese hamster ovary (CHO) cells are the famous expression system for industrial production of recombinant proteins, such as therapeutic antibodies. However, there still remain bottlenecks in protein quality and weakness in expression efficiency because of the intrinsic genetic properties of the cell. Here we have enhanced biosynthesis performance of heterologous proteins in CHO-K1 cells using CRISPR-Cas9 by editing the genome precisely with two genes for improving ER microenvironment and reinforcing antiapoptotic ability. A linear donor plasmid harboring eGFP-HsQSOX1b and Survivin genes was knocked in specific locus in CHO-K1 genome by the CRISPR-Cas9 RNA guided nucleases via NHEJ with efficiencies of up to 3.85% in the CHO-K1 cell pools following FACS, and the hQSOX1 and hSurvivin genes were integrated into expected genome locus successfully. Compared with control, the antiapoptotic viability of edited CHO-K1 cells was increased by 6.40 times, and the yield has been raised by 5.55 times with GLuc as model protein. The possible molecular mechanisms and pathways of remarkable antiapoptotic ability and protein biosynthesis in modified CHO-K1 cells have been elucidated reasonably. In conclusion, the novel ideas and reliable techniques for obtaining foreign proteins more efficiently in engineered animal cells were very valuable to meet large clinical needs.
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Affiliation(s)
- Wenpeng Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Wenyun Zheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
| | - Fengzhi Hu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
| | - Xiujuan He
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
| | - Dong Wu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Wenliang Zhang
- Center of Translational Biomedical Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27310, United States
| | - Haipeng Liu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Xingyuan Ma
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
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47
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Subramanian J, Aulakh RPS, Grewal PS, Sanford M, Pynn AFJ, Yuk IH. Short- and long-term effects on mAb-producing CHO cell lines after cryopreservation. Biotechnol Prog 2018; 34:463-477. [DOI: 10.1002/btpr.2599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/04/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Jayashree Subramanian
- Early Stage Cell Culture, Pharma Technical Development, Genentech, 1 DNA Way; South San Francisco CA 94080
| | - Rigzen P. S. Aulakh
- Early Stage Cell Culture, Pharma Technical Development, Genentech, 1 DNA Way; South San Francisco CA 94080
| | - Parbir S. Grewal
- Early Stage Cell Culture, Pharma Technical Development, Genentech, 1 DNA Way; South San Francisco CA 94080
| | - Mark Sanford
- Early Stage Cell Culture, Pharma Technical Development, Genentech, 1 DNA Way; South San Francisco CA 94080
| | - Abigail F. J. Pynn
- Early Stage Cell Culture, Pharma Technical Development, Genentech, 1 DNA Way; South San Francisco CA 94080
| | - Inn H. Yuk
- Late Stage Cell Culture, Pharma Technical Development, Genentech, 1 DNA Way; South San Francisco CA 94080
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48
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Abstract
Macrophages play essential roles in the response to injury and infection and contribute to the development and/or homeostasis of the various tissues they reside in. Conversely, macrophages also influence the pathogenesis of metabolic, neurodegenerative, and neoplastic diseases. Mechanisms that contribute to the phenotypic diversity of macrophages in health and disease remain poorly understood. Here we review the recent application of genome-wide approaches to characterize the transcriptomes and epigenetic landscapes of tissue-resident macrophages. These studies are beginning to provide insights into how distinct tissue environments are interpreted by transcriptional regulatory elements to drive specialized programs of gene expression.
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49
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Pinto R, Hansen L, Hintze J, Almeida R, Larsen S, Coskun M, Davidsen J, Mitchelmore C, David L, Troelsen JT, Bennett EP. Precise integration of inducible transcriptional elements (PrIITE) enables absolute control of gene expression. Nucleic Acids Res 2017; 45:e123. [PMID: 28472465 PMCID: PMC5570051 DOI: 10.1093/nar/gkx371] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/30/2017] [Accepted: 04/27/2017] [Indexed: 12/22/2022] Open
Abstract
Tetracycline-based inducible systems provide powerful methods for functional studies where gene expression can be controlled. However, the lack of tight control of the inducible system, leading to leakiness and adverse effects caused by undesirable tetracycline dosage requirements, has proven to be a limitation. Here, we report that the combined use of genome editing tools and last generation Tet-On systems can resolve these issues. Our principle is based on precise integration of inducible transcriptional elements (coined PrIITE) targeted to: (i) exons of an endogenous gene of interest (GOI) and (ii) a safe harbor locus. Using PrIITE cells harboring a GFP reporter or CDX2 transcription factor, we demonstrate discrete inducibility of gene expression with complete abrogation of leakiness. CDX2 PrIITE cells generated by this approach uncovered novel CDX2 downstream effector genes. Our results provide a strategy for characterization of dose-dependent effector functions of essential genes that require absence of endogenous gene expression.
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Affiliation(s)
- Rita Pinto
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Medicine of the University of Porto, Porto, Portugal
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - John Hintze
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Raquel Almeida
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Medicine of the University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Sylvester Larsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
- Department of Clinical Immunology, Naestved Hospital, Naestved, Denmark
| | - Mehmet Coskun
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Johanne Davidsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Cathy Mitchelmore
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Leonor David
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Medicine of the University of Porto, Porto, Portugal
| | | | - Eric Paul Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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50
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Lee K, Mackley VA, Rao A, Chong AT, Dewitt MA, Corn JE, Murthy N. Synthetically modified guide RNA and donor DNA are a versatile platform for CRISPR-Cas9 engineering. eLife 2017; 6:e25312. [PMID: 28462777 PMCID: PMC5413346 DOI: 10.7554/elife.25312] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/31/2017] [Indexed: 11/18/2022] Open
Abstract
Chemical modification of the gRNA and donor DNA has great potential for improving the gene editing efficiency of Cas9 and Cpf1, but has not been investigated extensively. In this report, we demonstrate that the gRNAs of Cas9 and Cpf1, and donor DNA can be chemically modified at their terminal positions without losing activity. Moreover, we show that 5' fluorescently labeled donor DNA can be used as a marker to enrich HDR edited cells by a factor of two through cell sorting. In addition, we demonstrate that the gRNA and donor DNA can be directly conjugated together into one molecule, and show that this gRNA-donor DNA conjugate is three times better at transfecting cells and inducing HDR, with cationic polymers, than unconjugated gRNA and donor DNA. The tolerance of the gRNA and donor DNA to chemical modifications has the potential to enable new strategies for genome engineering.
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Affiliation(s)
| | | | - Anirudh Rao
- Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| | - Anthony T Chong
- Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| | - Mark A Dewitt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, Berkeley, United States
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