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Kim SH, Park JH, Shin S, Shin S, Chun D, Kim YG, Yoo J, You WK, Lee JS, Lee GM. Genome-Wide CRISPR/Cas9 Screening Unveils a Novel Target ATF7IP-SETDB1 Complex for Enhancing Difficult-to-Express Protein Production. ACS Synth Biol 2024; 13:634-647. [PMID: 38240694 DOI: 10.1021/acssynbio.3c00646] [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] [Indexed: 02/17/2024]
Abstract
With the emerging novel biotherapeutics that are typically difficult-to-express (DTE), improvement is required for high-yield production. To identify novel targets that can enhance DTE protein production, we performed genome-wide fluorescence-activated cell sorting (FACS)-based clustered regularly interspaced short palindromic repeats (CRISPR) knockout screening in bispecific antibody (bsAb)-producing Chinese hamster ovary (CHO) cells. The screen identified the two highest-scoring genes, Atf7ip and Setdb1, which are the binding partners for H3K9me3-mediated transcriptional repression. The ATF7IP-SETDB1 complex knockout in bsAb-producing CHO cells suppressed cell growth but enhanced productivity by up to 2.7-fold. Decreased H3K9me3 levels and an increased transcriptional expression level of the transgene were also observed. Furthermore, perturbation of the ATF7IP-SETDB1 complex in monoclonal antibody (mAb)-producing CHO cells led to substantial improvements in mAb production, increasing the productivity by up to 3.9-fold without affecting the product quality. Taken together, the genome-wide FACS-based CRISPR screen identified promising targets associated with histone methylation, whose perturbation enhanced the productivity by unlocking the transgene expression.
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Affiliation(s)
- Su Hyun Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Jong-Ho Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
- Biotherapeutics Translational Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Sungwook Shin
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Seunghyeon Shin
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Dahyun Chun
- Department of R&D, ABL Bio Inc, Seongnam 13488, Republic of Korea
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, KRIBB, Daejeon 34141, Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, UST, , Daejeon 34113, Republic of Korea
| | - Jiseon Yoo
- Department of R&D, ABL Bio Inc, Seongnam 13488, Republic of Korea
| | - Weon-Kyoo You
- Department of R&D, ABL Bio Inc, Seongnam 13488, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
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2
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Barnard GC, Zhou M, Shen A, Yuk IH, Laird MW. Utilizing targeted integration CHO pools to potentially accelerate the GMP manufacturing of monoclonal and bispecific antibodies. Biotechnol Prog 2024; 40:e3399. [PMID: 37874920 DOI: 10.1002/btpr.3399] [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: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/08/2023] [Indexed: 10/26/2023]
Abstract
Monoclonal antibodies (mAbs) are effective therapeutic agents against many acute infectious diseases including COVID-19, Ebola, RSV, Clostridium difficile, and Anthrax. mAbs can therefore help combat a future pandemic. Unfortunately, mAb development typically takes years, limiting its potential to save lives during a pandemic. Therefore "pandemic mAb" timelines need to be shortened. One acceleration tool is "deferred cloning" and leverages new Chinese hamster ovary (CHO) technology based on targeted gene integration (TI). CHO pools, instead of CHO clones, can be used for Phase I/II clinical material production. A final CHO clone (producing the mAb with a similar product quality profile and preferably with a higher titer) can then be used for Phase III trials and commercial manufacturing. This substitution reduces timelines by ~3 months. We evaluated our novel CHO TI platform to enable deferred cloning. We created four unique CHO pools expressing three unique mAbs (mAb1, mAb2, and mAb3), and a bispecific mAb (BsAb1). We then performed single-cell cloning for mAb1 and mAb2, identifying three high-expressing clones from each pool. CHO pools and clones were inoculated side-by-side in ambr15 bioreactors. CHO pools yielded mAb titers as high as 10.4 g/L (mAb3) and 7.1 g/L (BsAb1). Subcloning yielded CHO clones expressing higher titers relative to the CHO pools while yielding similar product quality profiles. Finally, we showed that CHO TI pools were stable by performing a 3-month cell aging study. In summary, our CHO TI platform can increase the speed to clinic for a future "pandemic mAb."
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Affiliation(s)
- Gavin C Barnard
- Cell Culture and Bioprocess Operations, Genentech, South San Francisco, California, USA
| | - Michelle Zhou
- Cell Culture and Bioprocess Operations, Genentech, South San Francisco, California, USA
| | - Amy Shen
- Cell Culture and Bioprocess Operations, Genentech, South San Francisco, California, USA
| | - Inn H Yuk
- Cell Culture and Bioprocess Operations, Genentech, South San Francisco, California, USA
| | - Michael W Laird
- Cell Culture and Bioprocess Operations, Genentech, South San Francisco, California, USA
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3
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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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4
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Kim SH, Shin S, Baek M, Xiong K, Karottki KJLC, Hefzi H, Grav LM, Pedersen LE, Kildegaard HF, Lewis NE, Lee JS, Lee GM. Identification of hyperosmotic stress-responsive genes in Chinese hamster ovary cells via genome-wide virus-free CRISPR/Cas9 screening. Metab Eng 2023; 80:66-77. [PMID: 37709005 DOI: 10.1016/j.ymben.2023.09.006] [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: 12/13/2022] [Revised: 08/10/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Chinese hamster ovary (CHO) cells are the preferred mammalian host cells for therapeutic protein production that have been extensively engineered to possess the desired attributes for high-yield protein production. However, empirical approaches for identifying novel engineering targets are laborious and time-consuming. Here, we established a genome-wide CRISPR/Cas9 screening platform for CHO-K1 cells with 111,651 guide RNAs (gRNAs) targeting 21,585 genes using a virus-free recombinase-mediated cassette exchange-based gRNA integration method. Using this platform, we performed a positive selection screening under hyperosmotic stress conditions and identified 180 genes whose perturbations conferred resistance to hyperosmotic stress in CHO cells. Functional enrichment analysis identified hyperosmotic stress responsive gene clusters, such as tRNA wobble uridine modification and signaling pathways associated with cell cycle arrest. Furthermore, we validated 32 top-scoring candidates and observed a high rate of hit confirmation, demonstrating the potential of the screening platform. Knockout of the novel target genes, Zfr and Pnp, in monoclonal antibody (mAb)-producing recombinant CHO (rCHO) cells and bispecific antibody (bsAb)-producing rCHO cells enhanced their resistance to hyperosmotic stress, thereby improving mAb and bsAb production. Overall, the collective findings demonstrate the value of the screening platform as a powerful tool to investigate the functions of genes associated with hyperosmotic stress and to discover novel targets for rational cell engineering on a genome-wide scale in CHO cells.
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Affiliation(s)
- Su Hyun Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Seunghyeon Shin
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Minhye Baek
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Kai Xiong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Karen Julie la Cour Karottki
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark; Departments of Pediatrics and Bioengineering, University of California, San Diego, USA
| | - Hooman Hefzi
- Departments of Pediatrics and Bioengineering, University of California, San Diego, USA
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Nathan E Lewis
- Departments of Pediatrics and Bioengineering, University of California, San Diego, USA
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea.
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea.
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5
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Yoon C, Baek KE, Kim D, Lee GM. Mitigating transcriptional bottleneck using a constitutively active transcription factor, VP16-CREB, in mammalian cells. Metab Eng 2023; 80:33-44. [PMID: 37709006 DOI: 10.1016/j.ymben.2023.09.005] [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: 08/13/2022] [Revised: 07/13/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
High-level expression of recombinant proteins in mammalian cells has long been an area of interest. Inefficient transcription machinery is often an obstacle in achieving high-level expression of recombinant proteins in mammalian cells. Synthetic promoters have been developed to improve the transcription efficiency, but have achieved limited success due to the limited availability of transcription factors (TFs). Here, we present a TF-engineering approach to mitigate the transcriptional bottlenecks of recombinant proteins. This includes: (i) identification of cAMP response element binding protein (CREB) as a candidate TF by searching for TFs enriched in the cytomegalovirus (CMV) promoter-driven high-producing recombinant Chinese hamster ovary (rCHO) cell lines via transcriptome analysis, (ii) confirmation of transcriptional limitation of active CREB in rCHO cell lines, and (iii) direct activation of the transgene promoter by expressing constitutively active CREB at non-cytotoxic levels in rCHO cell lines. With the expression of constitutively active VP16-CREB, the production of therapeutic proteins, such as monoclonal antibody and etanercept, in CMV promoter-driven rCHO cell lines was increased up to 3.9-fold. VP16-CREB was also used successfully with synthetic promoters containing cAMP response elements. Taken together, this strategy to introduce constitutively active TFs into cells is a useful means of overcoming the transcriptional limitations in recombinant mammalian cells.
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Affiliation(s)
- Chansik Yoon
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Kyoung Eun Baek
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Dongil Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea.
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6
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Nguyen NTB, Leung HW, Pang KT, Tay SJ, Walsh I, Choo ABH, Yang Y. Optimizing effector functions of monoclonal antibodies via tailored N-glycan engineering using a dual landing pad CHO targeted integration platform. Sci Rep 2023; 13:15620. [PMID: 37731040 PMCID: PMC10511539 DOI: 10.1038/s41598-023-42925-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023] Open
Abstract
Monoclonal antibodies (mAbs) eliminate cancer cells via various effector mechanisms including antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC), which are influenced by the N-glycan structures on the Fc region of mAbs. Manipulating these glycan structures on mAbs allows for optimization of therapeutic benefits associated with effector functions. Traditional approaches such as gene deletion or overexpression often lead to only all-or-nothing changes in gene expression and fail to modulate the expression of multiple genes at defined ratios and levels. In this work, we have developed a CHO cell engineering platform enabling modulation of multiple gene expression to tailor the N-glycan profiles of mAbs for enhanced effector functions. Our platform involves a CHO targeted integration platform with two independent landing pads, allowing expression of multiple genes at two pre-determined genomic sites. By combining with internal ribosome entry site (IRES)-based polycistronic vectors, we simultaneously modulated the expression of α-mannosidase II (MANII) and chimeric β-1,4-N-acetylglucosaminyl-transferase III (cGNTIII) genes in CHO cells. This strategy enabled the production of mAbs carrying N-glycans with various levels of bisecting and non-fucosylated structures. Importantly, these engineered mAbs exhibited different degrees of effector cell activation and CDC, facilitating the identification of mAbs with optimal effector functions. This platform was demonstrated as a powerful tool for producing antibody therapeutics with tailored effector functions via precise engineering of N-glycan profiles. It holds promise for advancing the field of metabolic engineering in mammalian cells.
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Affiliation(s)
- Ngan T B Nguyen
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Hau Wan Leung
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Kuin Tian Pang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Shi Jie Tay
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Ian Walsh
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Andre B H Choo
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Yuansheng Yang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore.
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7
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Bachhav B, de Rossi J, Llanos CD, Segatori L. Cell factory engineering: Challenges and opportunities for synthetic biology applications. Biotechnol Bioeng 2023; 120:2441-2459. [PMID: 36859509 PMCID: PMC10440303 DOI: 10.1002/bit.28365] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/14/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
Abstract
The production of high-quality recombinant proteins is critical to maintaining a continuous supply of biopharmaceuticals, such as therapeutic antibodies. Engineering mammalian cell factories presents a number of limitations typically associated with the proteotoxic stress induced upon aberrant accumulation of off-pathway protein folding intermediates, which eventually culminate in the induction of apoptosis. In this review, we will discuss advances in cell engineering and their applications at different hierarchical levels of control of the expression of recombinant proteins, from transcription and translational to posttranslational modifications and subcellular trafficking. We also highlight challenges and unique opportunities to apply modern synthetic biology tools to the design of programmable cell factories for improved biomanufacturing of therapeutic proteins.
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Affiliation(s)
- Bhagyashree Bachhav
- Department of Chemical and Biochemical Engineering, Rice University, Houston, United States
| | - Jacopo de Rossi
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Carlos D. Llanos
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Laura Segatori
- Department of Chemical and Biochemical Engineering, Rice University, Houston, United States
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
- Department of Bioengineering, Rice University, Houston, United States
- Department of Biosciences, Rice University, Houston, United States
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8
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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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9
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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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10
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Dehdilani N, Goshayeshi L, Yousefi Taemeh S, Bahrami AR, Rival Gervier S, Pain B, Dehghani H. Integrating Omics and CRISPR Technology for Identification and Verification of Genomic Safe Harbor Loci in the Chicken Genome. Biol Proced Online 2023; 25:18. [PMID: 37355580 DOI: 10.1186/s12575-023-00210-5] [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: 02/10/2023] [Accepted: 06/02/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND One of the most prominent questions in the field of transgenesis is 'Where in the genome to integrate a transgene?'. Escape from epigenetic silencing and promoter shutdown of the transgene needs reliable genomic safe harbor (GSH) loci. Advances in genome engineering technologies combined with multi-omics bioinformatics data have enabled rational evaluation of GSH loci in the host genome. Currently, no validated GSH loci have been evaluated in the chicken genome. RESULTS Here, we analyzed and experimentally examined two GSH loci in the genome of chicken cells. To this end, putative GSH loci including chicken HIPP-like (cHIPP; between DRG1 and EIF4ENIF1 genes) and chicken ROSA-like (cROSA; upstream of the THUMPD3 gene) were predicted using multi-omics bioinformatics data. Then, the durable expression of the transgene was validated by experimental characterization of continuously-cultured isogenous cell clones harboring DsRed2-ΔCMV-EGFP cassette in the predicted loci. The weakened form of the CMV promoter (ΔCMV) allowed the precise evaluation of GSH loci in a locus-dependent manner compared to the full-length CMV promoter. CONCLUSIONS cHIPP and cROSA loci introduced in this study can be reliably exploited for consistent bio-manufacturing of recombinant proteins in the genetically-engineered chickens. Also, results showed that the genomic context dictates the expression of transgene controlled by ΔCMV in GSH loci.
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Affiliation(s)
- Nima Dehdilani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Lena Goshayeshi
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sara Yousefi Taemeh
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmad Reza Bahrami
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sylvie Rival Gervier
- Stem Cell and Brain Research Institute, University of Lyon, Université Lyon 1, INSERM, INRAE, U1208, USC1361, 69500, Bron, France
| | - Bertrand Pain
- Stem Cell and Brain Research Institute, University of Lyon, Université Lyon 1, INSERM, INRAE, U1208, USC1361, 69500, Bron, France
| | - Hesam Dehghani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
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11
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Helleckes LM, Hemmerich J, Wiechert W, von Lieres E, Grünberger A. Machine learning in bioprocess development: from promise to practice. Trends Biotechnol 2023; 41:817-835. [PMID: 36456404 DOI: 10.1016/j.tibtech.2022.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022]
Abstract
Fostered by novel analytical techniques, digitalization, and automation, modern bioprocess development provides large amounts of heterogeneous experimental data, containing valuable process information. In this context, data-driven methods like machine learning (ML) approaches have great potential to rationally explore large design spaces while exploiting experimental facilities most efficiently. Herein we demonstrate how ML methods have been applied so far in bioprocess development, especially in strain engineering and selection, bioprocess optimization, scale-up, monitoring, and control of bioprocesses. For each topic, we will highlight successful application cases, current challenges, and point out domains that can potentially benefit from technology transfer and further progress in the field of ML.
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Affiliation(s)
- Laura M Helleckes
- Institute for Bio- and Geosciences (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; RWTH Aachen University, Templergraben 55, 52062 Aachen, Germany
| | - Johannes Hemmerich
- Institute for Bio- and Geosciences (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Wolfgang Wiechert
- Institute for Bio- and Geosciences (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; RWTH Aachen University, Templergraben 55, 52062 Aachen, Germany
| | - Eric von Lieres
- Institute for Bio- and Geosciences (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany; RWTH Aachen University, Templergraben 55, 52062 Aachen, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; Institute of Process Engineering in Life Sciences, Section III: Microsystems in Bioprocess Engineering, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131, Karlsruhe, Germany.
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12
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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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13
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Tanaka A, Kosuda M, Yamana M, Furukawa A, Nagasawa A, Fujishiro M, Kohno G, Ishihara H. A large-scale functional analysis of genes expressed differentially in insulin secreting MIN6 sublines with high versus mildly reduced glucose-responsiveness. Sci Rep 2023; 13:5654. [PMID: 37024560 PMCID: PMC10079668 DOI: 10.1038/s41598-023-32589-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 03/29/2023] [Indexed: 04/08/2023] Open
Abstract
Molecular mechanisms of glucose-stimulated insulin secretion (GSIS) from pancreatic β-cells are not fully understood. GSIS deteriorations are believed to underlie the pathogenesis of type 2 diabetes mellitus. By comparing transcript levels of 3 insulin secreting MIN6 cell sublines with strong glucose-responsiveness and 3 with mildly reduced responsiveness, we identified 630 differentially expressed genes. Using our recently developed system based on recombinase-mediated cassette exchange, we conducted large-scale generation of stable clones overexpressing such genes in the doxycycline-regulated manner. We found that overexpressions of 18, out of 83, genes altered GSIS. Sox11 ((sex determining region Y)-box 11) was selected to confirm its roles in regulating insulin secretion, and the gene was subjected to shRNA-mediated suppression. While Sox11 overexpression decreased GSIS, its suppression increased GSIS, confirming the role of Sox11 as a negative regulator of insulin secretion. Furthermore, metabolic experiments using radiolabelled glucose showed Sox11 to participate in regulating glucose metabolism. Our data suggested that overexpression screening is a feasible option for systemic functional testing to identify important genes in GSIS.
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Affiliation(s)
- Aya Tanaka
- Division of Diabetes and Metabolic Diseases, Nihon University School of Medicine, 30-1 Oyaguchikami-cho, Itabashi, 173-8610, Japan
| | - Minami Kosuda
- Division of Diabetes and Metabolic Diseases, Nihon University School of Medicine, 30-1 Oyaguchikami-cho, Itabashi, 173-8610, Japan
| | - Midori Yamana
- Division of Diabetes and Metabolic Diseases, Nihon University School of Medicine, 30-1 Oyaguchikami-cho, Itabashi, 173-8610, Japan
| | - Asami Furukawa
- Division of Diabetes and Metabolic Diseases, Nihon University School of Medicine, 30-1 Oyaguchikami-cho, Itabashi, 173-8610, Japan
| | - Akiko Nagasawa
- Division of Diabetes and Metabolic Diseases, Nihon University School of Medicine, 30-1 Oyaguchikami-cho, Itabashi, 173-8610, Japan
| | - Midori Fujishiro
- Division of Diabetes and Metabolic Diseases, Nihon University School of Medicine, 30-1 Oyaguchikami-cho, Itabashi, 173-8610, Japan
| | - Genta Kohno
- Division of Diabetes and Metabolic Diseases, Nihon University School of Medicine, 30-1 Oyaguchikami-cho, Itabashi, 173-8610, Japan
| | - Hisamitsu Ishihara
- Division of Diabetes and Metabolic Diseases, Nihon University School of Medicine, 30-1 Oyaguchikami-cho, Itabashi, 173-8610, Japan.
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14
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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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15
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Discovery and optimization of a broadly-neutralizing human monoclonal antibody against long-chain α-neurotoxins from snakes. Nat Commun 2023; 14:682. [PMID: 36755049 PMCID: PMC9908967 DOI: 10.1038/s41467-023-36393-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
Snakebite envenoming continues to claim many lives across the globe, necessitating the development of improved therapies. To this end, broadly-neutralizing human monoclonal antibodies may possess advantages over current plasma-derived antivenoms by offering superior safety and high neutralization capacity. Here, we report the establishment of a pipeline based on phage display technology for the discovery and optimization of high affinity broadly-neutralizing human monoclonal antibodies. This approach yielded a recombinant human antibody with superior broadly-neutralizing capacities in vitro and in vivo against different long-chain α-neurotoxins from elapid snakes. This antibody prevents lethality induced by Naja kaouthia whole venom at an unprecedented low molar ratio of one antibody per toxin and prolongs the survival of mice injected with Dendroaspis polylepis or Ophiophagus hannah whole venoms.
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16
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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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17
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Oliviero C, Hinz SC, Grzeschik J, Hock B, Kolmar H, Hagens G. Cell Line Development Using Targeted Gene Integration into MAR-Rich Landing Pads for Stable Expression of Transgenes. Methods Mol Biol 2023; 2681:343-359. [PMID: 37405657 DOI: 10.1007/978-1-0716-3279-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Integration of a gene of interest (GOI) into the genome of mammalian cells is the first step of cell line development campaigns for the production of biotherapeutics. Besides random integration methods, targeted gene integration approaches have emerged as promising tools over the last few years. In addition to reducing heterogeneity within a pool of recombinant transfectants, this process can also facilitate shorter timelines of the current cell line development process. Herein, we describe protocols for generating host cell lines carrying matrix attachment region (MAR)-rich landing pads (LPs), including BxB1 recombination sites. These LP-containing cell lines allow for site-specific and simultaneous integration of multiple GOIs. The resulting transgene-expressing stable recombinant clones can be used for the production of mono- or multispecific antibodies.
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Affiliation(s)
- Claudia Oliviero
- Institute of Life Technologies, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Sion, Switzerland
| | - Steffen C Hinz
- Institute of Life Technologies, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Sion, Switzerland
| | | | - Björn Hock
- Aerium Therapeutics, Epalinges, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerrit Hagens
- Institute of Life Technologies, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Sion, Switzerland.
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18
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Min H, Kim SM, Kim D, Lee S, Lee S, Lee JS. Hybrid cell line development system utilizing site-specific integration and methotrexate-mediated gene amplification in Chinese hamster ovary cells. Front Bioeng Biotechnol 2022; 10:977193. [PMID: 36185448 PMCID: PMC9521551 DOI: 10.3389/fbioe.2022.977193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Site-specific integration has emerged as a promising strategy for streamlined and predictable Chinese hamster ovary (CHO) cell line development (CLD). However, the low specific productivity of the targeted integrants limits their practical application. In this study, we developed a hybrid CLD platform combining site-specific integration of a transgene and dihydrofolate reductase/methotrexate (DHFR/MTX)-mediated gene amplification to generate high-producing recombinant CHO cell lines. We used the CRISPR/Cas9-based recombinase-mediated cassette exchange landing pad platform to integrate the DHFR expression cassette and transgene landing pad into a CHO genomic hot spot, C12orf35 locus, of DHFR-knockout CHO-K1 host cell lines. When subjected to various MTX concentrations up to 1 μM, EGFP-expressing targeted integrants showed a 3.6-fold increase in EGFP expression in the presence of 200 nM MTX, accompanied by an increase in the DHFR and EGFP copy number. A single-step 200 nM MTX amplification increased the specific monoclonal antibody (mAb) productivity (qmAb) of recombinant mAb-producing targeted integrants by 2.8-folds, reaching a qmAb of 9.1–11.0 pg/cell/day. Fluorescence in situ hybridization analysis showed colocalization of DHFR and mAb sequences at the intended chromosomal locations without clear amplified arrays of signals. Most MTX-amplified targeted integrants sustained recombinant mAb production during long-term culture in the absence of MTX, supporting stable gene expression in the amplified cell lines. Our study provides a new CLD platform that increases the productivity of targeted integrants by amplifying the transgene copies.
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Affiliation(s)
- Honggi Min
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Seul Mi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Dongwoo Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Solhwi Lee
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
| | - Sumin Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
- *Correspondence: Jae Seong Lee,
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19
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Li ZM, Fan ZL, Wang XY, Wang TY. Factors Affecting the Expression of Recombinant Protein and Improvement Strategies in Chinese Hamster Ovary Cells. Front Bioeng Biotechnol 2022; 10:880155. [PMID: 35860329 PMCID: PMC9289362 DOI: 10.3389/fbioe.2022.880155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/01/2022] [Indexed: 01/20/2023] Open
Abstract
Recombinant therapeutic proteins (RTPs) are important parts of biopharmaceuticals. Chinese hamster ovary cells (CHO) have become the main cell hosts for the production of most RTPs approved for marketing because of their high-density suspension growth characteristics, and similar human post-translational modification patterns et al. In recent years, many studies have been performed on CHO cell expression systems, and the yields and quality of recombinant protein expression have been greatly improved. However, the expression levels of some proteins are still low or even difficult-to express in CHO cells. It is urgent further to increase the yields and to express successfully the “difficult-to express” protein in CHO cells. The process of recombinant protein expression of is a complex, involving multiple steps such as transcription, translation, folding processing and secretion. In addition, the inherent characteristics of molecular will also affect the production of protein. Here, we reviewed the factors affecting the expression of recombinant protein and improvement strategies in CHO cells.
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Affiliation(s)
- Zheng-Mei Li
- School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
| | - Zhen-Lin Fan
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- Institutes of Health Central Plain, Xinxiang Medical University, Xinxiang, China
| | - Xiao-Yin Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
| | - Tian-Yun Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
- *Correspondence: Tian-Yun Wang,
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20
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Shin S, Kim SH, Park JH, Lee JS, Lee GM. Recombinase-mediated cassette exchange-based screening of a CRISPR/Cas9 library for enhanced recombinant protein production in human embryonic kidney cells: Improving resistance to hyperosmotic stress. Metab Eng 2022; 72:247-258. [DOI: 10.1016/j.ymben.2022.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 10/18/2022]
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21
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Yang W, Zhang J, Xiao Y, Li W, Wang T. Screening Strategies for High-Yield Chinese Hamster Ovary Cell Clones. Front Bioeng Biotechnol 2022; 10:858478. [PMID: 35782513 PMCID: PMC9247297 DOI: 10.3389/fbioe.2022.858478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/23/2022] [Indexed: 12/20/2022] Open
Abstract
Chinese hamster ovary (CHO) cells are by far the most commonly used mammalian expression system for recombinant expression of therapeutic proteins in the pharmaceutical industry. The development of high-yield stable cell lines requires processes of transfection, selection, screening and adaptation, among which the screening process requires tremendous time and determines the level of forming highly productive monoclonal cell lines. Therefore, how to achieve productive cell lines is a major question prior to industrial manufacturing. Cell line development (CLD) is one of the most critical steps in the production of recombinant therapeutic proteins. Generation of high-yield cell clones is mainly based on the time-consuming, laborious process of selection and screening. With the increase in recombinant therapeutic proteins expressed by CHO cells, CLD has become a major bottleneck in obtaining cell lines for manufacturing. The basic principles for CLD include preliminary screening for high-yield cell pool, single-cell isolation and improvement of productivity, clonality and stability. With the development of modern analysis and testing technologies, various screening methods have been used for CLD to enhance the selection efficiency of high-yield clonal cells. This review provides a comprehensive overview on preliminary screening methods for high-yield cell pool based on drug selective pressure. Moreover, we focus on high throughput methods for isolating high-yield cell clones and increasing the productivity and stability, as well as new screening strategies used for the biopharmaceutical industry.
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Affiliation(s)
- Wenwen Yang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
| | - Junhe Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
- *Correspondence: Tianyun Wang, ; Junhe Zhang,
| | - Yunxi Xiao
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
| | - Wenqing Li
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
| | - Tianyun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- *Correspondence: Tianyun Wang, ; Junhe Zhang,
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22
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Abstract
![]()
Stable cell performance
in a fluctuating environment is essential
for sustainable bioproduction and synthetic cell functionality; however,
microbial robustness is rarely quantified. Here, we describe a high-throughput
strategy for quantifying robustness of multiple cellular functions
and strains in a perturbation space. We evaluated quantification theory
on experimental data and concluded that the mean-normalized Fano factor
allowed accurate, reliable, and standardized quantification. Our methodology
applied to perturbations related to lignocellulosic bioethanol production
showed that the industrial bioethanol producing strain Saccharomyces
cerevisiae Ethanol Red exhibited both higher and more robust
growth rates than the laboratory strain CEN.PK and industrial strain
PE-2, while a more robust product yield traded off for lower mean
levels. The methodology validated that robustness is function-specific
and characterized by positive and negative function-specific trade-offs.
Systematic quantification of robustness to end-use perturbations will
be important to analyze and construct robust strains with more predictable
functions.
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Affiliation(s)
- Cecilia Trivellin
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Peter Rugbjerg
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Enduro Genetics ApS, Copenhagen 2200, Denmark
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23
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Schmieder V, Fieder J, Drerup R, Gutierrez EA, Guelch C, Stolzenberger J, Stumbaum M, Mueller VS, Higel F, Bergbauer M, Bornhoefft K, Wittner M, Gronemeyer P, Braig C, Huber M, Reisenauer-Schaupp A, Mueller MM, Schuette M, Puengel S, Lindner B, Schmidt M, Schulz P, Fischer S. Towards maximum acceleration of monoclonal antibody development: Leveraging transposase-mediated cell line generation to enable GMP manufacturing within 3 months using a stable pool. J Biotechnol 2022; 349:53-64. [PMID: 35341894 DOI: 10.1016/j.jbiotec.2022.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/25/2022] [Accepted: 03/20/2022] [Indexed: 01/24/2023]
Abstract
In recent years, acceleration of development timelines has become a major focus within the biopharmaceutical industry to bring innovative therapies faster to patients. However, in order to address a high unmet medical need even faster further acceleration potential has to be identified to transform "speed-to-clinic" concepts into "warp-speed" development programs. Recombinant Chinese hamster ovary (CHO) cell lines are the predominant expression system for monoclonal antibodies (mAbs) and are routinely generated by random transgene integration (RTI) of the genetic information into the host cell genome. This process, however, exhibits considerable challenges such as the requirement for a time-consuming clone screening process to identify a suitable clonally derived manufacturing cell line. Hence, RTI represents an error prone and tedious method leading to long development timelines until availability of Good Manufacturing Practice (GMP)-grade drug substance (DS). Transposase-mediated semi-targeted transgene integration (STI) has been recently identified as a promising alternative to RTI as it allows for a more rapid generation of high-performing and stable production cell lines. In this report, we demonstrate how a STI technology was leveraged to develop a very robust DS manufacturing process based on a stable pool cell line at unprecedented pace. Application of the novel strategy resulted in the manufacturing of GMP-grade DS at 2,000 L scale in less than three months paving the way for a start of Phase I clinical trials only six months after transfection. Finally, using a clonally derived production cell line, which was established from the parental stable pool, we were able to successfully implement a process with an increased mAb titer of up to 5 g per liter at the envisioned commercial scale (12,000 L) within eight months.
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Affiliation(s)
- Valerie Schmieder
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Juergen Fieder
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Raphael Drerup
- Early Stage Bioprocess Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Erik Arango Gutierrez
- Early Stage Bioprocess Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Carina Guelch
- Late Stage Upstream Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Jessica Stolzenberger
- Late Stage Downstream Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Mihaela Stumbaum
- Early Stage Pharmaceutical Development, Pharmaceutical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Volker Steffen Mueller
- Early Stage Analytics, Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Fabian Higel
- Early Stage Analytics, Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Martin Bergbauer
- Late Stage Analytics, Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Kim Bornhoefft
- Characterization Technologies, Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Manuel Wittner
- Global CMC Experts NBE, Global Quality Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Petra Gronemeyer
- Cell Banking & Inoculum, Focused Factory CS&T, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christian Braig
- CST Transfer, Focused Factory CS&T, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Michaela Huber
- Process Transfer Cell Culture, Focused Factory Drug Substance, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Anita Reisenauer-Schaupp
- R&D PM NBE, Global R&D Project Management and Development Strategies, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Markus Michael Mueller
- CMC PM Process Industrialization Germany, Global Biopharma CMC Project Mgmt&TechRA, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Mark Schuette
- Global Technology Management, Global Innovation & Alliance Management, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sebastian Puengel
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Benjamin Lindner
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Moritz Schmidt
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Patrick Schulz
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Simon Fischer
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany.
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Oliviero C, Hinz SC, Bogen JP, Kornmann H, Hock B, Kolmar H, Hagens G. Generation of a Host Cell line containing a MAR-rich landing pad for site-specific integration and expression of transgenes. Biotechnol Prog 2022; 38:e3254. [PMID: 35396920 PMCID: PMC9539524 DOI: 10.1002/btpr.3254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/22/2022] [Accepted: 03/31/2022] [Indexed: 11/10/2022]
Abstract
In recent years, targeted gene integration (TI) has been introduced as a strategy for the generation of recombinant mammalian cell lines for the production of biotherapeutics. Besides reducing the immense heterogeneity within a pool of recombinant transfectants, TI also aims at shortening the duration of the current cell line development process. Here we describe the generation of a host cell line carrying Matrix‐Attachment Region (MAR)‐rich landing pads (LPs), which allow for the simultaneous and site‐specific integration of multiple genes of interest (GOIs). We show that several copies of each chicken lysozyme 5'MAR‐based LP containing either BxB1 wild type or mutated recombination sites, integrated at one random chromosomal locus of the host cell genome. We further demonstrate that these LP‐containing host cell lines can be used for the site‐specific integration of several GOIs and thus, generation of transgene‐expressing stable recombinant clones. Transgene expression was shown by site‐specific integration of heavy and light chain genes coding for a monospecific antibody (msAb) as well as for a bi‐specific antibody (bsAb). The genetic stability of the herein described LP‐based recombinant clones expressing msAb or bsAb was demonstrated by cultivating the recombinant clones and measuring antibody titers over 85 generations. We conclude that the host cell containing multiple copies of MAR‐rich landing pads can be successfully used for stable expression of one or several GOIs.
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Affiliation(s)
- Claudia Oliviero
- Institute of Life Technology, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Rue de l'Industrie 19, CH-1950 Sion, Switzerland
| | - Steffen C Hinz
- Institute of Life Technology, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Rue de l'Industrie 19, CH-1950 Sion, Switzerland
| | - Jan P Bogen
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany
| | - Henri Kornmann
- Ferring Biologics Innovation Center, Route de la Corniche 8, CH-1066, Epalinges, Switzerland
| | - Björn Hock
- Ferring Biologics Innovation Center, Route de la Corniche 8, CH-1066, Epalinges, Switzerland.,SwissThera SA, Route de la Corniche 4, CH-1066, Epalinges, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany
| | - Gerrit Hagens
- Institute of Life Technology, Haute Ecole d'Ingénierie HES-SO Valais Wallis, Rue de l'Industrie 19, CH-1950 Sion, Switzerland
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25
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Marx N, Eisenhut P, Weinguny M, Klanert G, Borth N. How to train your cell - Towards controlling phenotypes by harnessing the epigenome of Chinese hamster ovary production cell lines. Biotechnol Adv 2022; 56:107924. [PMID: 35149147 DOI: 10.1016/j.biotechadv.2022.107924] [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: 12/28/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in omics technologies and the broad availability of big datasets have revolutionized our understanding of Chinese hamster ovary cells in their role as the most prevalent host for production of complex biopharmaceuticals. In consequence, our perception of this "workhorse of the biopharmaceutical industry" has successively shifted from that of a nicely working, but unknown recombinant protein producing black box to a biological system governed by multiple complex regulatory layers that might possibly be harnessed and manipulated at will. Despite the tremendous progress that has been made to characterize CHO cells on various omics levels, our understanding is still far from complete. The well-known inherent genetic plasticity of any immortalized and rapidly dividing cell line also characterizes CHO cells and can lead to problematic instability of recombinant protein production. While the high mutational frequency has been a focus of CHO cell research for decades, the impact of epigenetics and its role in differential gene expression has only recently been addressed. In this review we provide an overview about the current understanding of epigenetic regulation in CHO cells and discuss its significance for shaping the cell's phenotype. We also look into current state-of-the-art technology that can be applied to harness and manipulate the epigenetic network so as to nudge CHO cells towards a specific phenotype. Here, we revise current strategies on site-directed integration and random as well as targeted epigenome modifications. Finally, we address open questions that need to be investigated to exploit the full repertoire of fine-tuned control of multiplexed gene expression using epigenetic and systems biology tools.
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Affiliation(s)
- Nicolas Marx
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Eisenhut
- Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Marcus Weinguny
- University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Gerald Klanert
- Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Nicole Borth
- University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria.
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26
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Altamura R, Doshi J, Benenson Y. Rational design and construction of multi-copy biomanufacturing islands in mammalian cells. Nucleic Acids Res 2022; 50:561-578. [PMID: 34893882 PMCID: PMC8754653 DOI: 10.1093/nar/gkab1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/21/2021] [Accepted: 11/26/2021] [Indexed: 11/14/2022] Open
Abstract
Cell line development is a critical step in the establishment of a biopharmaceutical manufacturing process. Current protocols rely on random transgene integration and amplification. Due to considerable variability in transgene integration profiles, this workflow results in laborious screening campaigns before stable producers can be identified. Alternative approaches for transgene dosage increase and integration are therefore highly desirable. In this study, we present a novel strategy for the rapid design, construction, and genomic integration of engineered multiple-copy gene constructs consisting of up to 10 gene expression cassettes. Key to this strategy is the diversification, at the sequence level, of the individual gene cassettes without altering their protein products. We show a computational workflow for coding and regulatory sequence diversification and optimization followed by experimental assembly of up to nine gene copies and a sentinel reporter on a contiguous scaffold. Transient transfections in CHO cells indicates that protein expression increases with the gene copy number on the scaffold. Further, we stably integrate these cassettes into a pre-validated genomic locus. Altogether, our findings point to the feasibility of engineering a fully mapped multi-copy recombinant protein 'production island' in a mammalian cell line with greatly reduced screening effort, improved stability, and predictable product titers.
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Affiliation(s)
- Raffaele Altamura
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Jiten Doshi
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Yaakov Benenson
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, 4058, Switzerland
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27
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Kim SH, Baek M, Park S, Shin S, Lee JS, Lee GM. Improving the secretory capacity of CHO producer cells: The effect of controlled Blimp1 expression, a master transcription factor for plasma cells. Metab Eng 2021; 69:73-86. [PMID: 34775077 DOI: 10.1016/j.ymben.2021.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/29/2021] [Accepted: 11/02/2021] [Indexed: 01/23/2023]
Abstract
With the advent of novel therapeutic proteins with complex structures, cellular bottlenecks in secretory pathways have hampered the high-yield production of difficult-to-express (DTE) proteins in CHO cells. To mitigate their limited secretory capacity, recombinant CHO (rCHO) cells were engineered to express Blimp1, a master regulator orchestrating B cell differentiation into professional secretory plasma cells, using the streamlined CRISPR/Cas9-based recombinase-mediated cassette exchange landing pad platform. The expression of Blimp1α or Blimp1β in rCHO cells producing DTE recombinant human bone morphogenetic protein-4 (rhBMP-4) increased specific rhBMP-4 productivity (qrhBMP-4). However, since Blimp1α expression suppressed cell growth more significantly than Blimp1β expression, only Blimp1β expression enhanced rhBMP-4 yield. In serum-free suspension culture, Blimp1β expression significantly increased the rhBMP-4 concentration (>3-fold) and qrhBMP-4 (>4-fold) without significant increase in hBMP-4 transcript levels. In addition, Blimp1β expression facilitated mature rhBMP-4 secretion by active proteolytic cleavage in the secretory pathway. Transcriptomic profiling (RNA-seq) revealed global changes in gene expression patterns that promote protein processing in secretory organelles. In-depth integrative analysis of the current RNA-seq data, public epigenome/RNA-seq data, and in silico analysis identified 45 potential key regulators of Blimp1 that are consistently up- or down-regulated in Blimp1β expressing rCHO cells and plasma cells. Blimp1β expression also enhanced the production of easy-to-express monoclonal antibodies (mAbs) and modulated the expression of key regulators in rCHO cells producing mAb. Taken together, the results show that controlled expression of Blimp1β improves the production capacity of rCHO cells by regulating secretory machinery and suggest new opportunities for engineering promising targets that are resting in CHO cells.
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Affiliation(s)
- Su Hyun Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Minhye Baek
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Sungje Park
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Seunghyeon Shin
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea.
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea.
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28
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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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29
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Arnesen JA, Hoof JB, Kildegaard HF, Borodina I. Genome Editing of Eukarya. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Shin S, Kim SH, Lee JS, Lee GM. Streamlined Human Cell-Based Recombinase-Mediated Cassette Exchange Platform Enables Multigene Expression for the Production of Therapeutic Proteins. ACS Synth Biol 2021; 10:1715-1727. [PMID: 34133132 DOI: 10.1021/acssynbio.1c00113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A platform, based on targeted integration of transgenes using recombinase-mediated cassette exchange (RMCE) coupled with CRISPR/Cas9, is increasingly being used for the development of mammalian cell lines that produce therapeutic proteins, because of reduced clonal variation and predictable transgene expression. However, low efficiency of the RMCE process has hampered its application in multicopy or multisite integration of transgenes. To improve RMCE efficiency, nuclear transport of RMCE components such as site-specific recombinase and donor plasmid was accelerated by incorporation of nuclear localization signal and DNA nuclear-targeting sequence, respectively. Consequently, the efficiency of RMCE in dual-landing pad human embryonic kidney 293 (HEK293) cell lines harboring identical or orthogonal pairs of recombination sites at two well-known human safe harbors (AAVS1 and ROSA26 loci), increased 6.7- and 8.1-fold, respectively. This platform with enhanced RMCE efficiency enabled simultaneous integration of transgenes at the two sites using a single transfection without performing selection and enrichment processes. The use of a homotypic dual-landing pad HEK293 cell line capable of incorporating the same transgenes at two sites resulted in a 2-fold increase in the transgene expression level compared to a single-landing pad HEK293 cell line. In addition, the use of a heterotypic dual-landing pad HEK293 cell line, which can incorporate transgenes for a recombinant protein at one site and an effector transgene for cell engineering at another site, increased recombinant protein production. Overall, a streamlined RMCE platform can be a versatile tool for mammalian cell line development by facilitating multigene expression at genomic safe harbors.
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Affiliation(s)
- Seunghyeon Shin
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Su Hyun Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
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31
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Nguyen NTB, Lin J, Tay SJ, Mariati, Yeo J, Nguyen-Khuong T, Yang Y. Multiplexed engineering glycosyltransferase genes in CHO cells via targeted integration for producing antibodies with diverse complex-type N-glycans. Sci Rep 2021; 11:12969. [PMID: 34155258 PMCID: PMC8217518 DOI: 10.1038/s41598-021-92320-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/09/2021] [Indexed: 02/05/2023] Open
Abstract
Therapeutic antibodies are decorated with complex-type N-glycans that significantly affect their biodistribution and bioactivity. The N-glycan structures on antibodies are incompletely processed in wild-type CHO cells due to their limited glycosylation capacity. To improve N-glycan processing, glycosyltransferase genes have been traditionally overexpressed in CHO cells to engineer the cellular N-glycosylation pathway by using random integration, which is often associated with large clonal variations in gene expression levels. In order to minimize the clonal variations, we used recombinase-mediated-cassette-exchange (RMCE) technology to overexpress a panel of 42 human glycosyltransferase genes to screen their impact on antibody N-linked glycosylation. The bottlenecks in the N-glycosylation pathway were identified and then released by overexpressing single or multiple critical genes. Overexpressing B4GalT1 gene alone in the CHO cells produced antibodies with more than 80% galactosylated bi-antennary N-glycans. Combinatorial overexpression of B4GalT1 and ST6Gal1 produced antibodies containing more than 70% sialylated bi-antennary N-glycans. In addition, antibodies with various tri-antennary N-glycans were obtained for the first time by overexpressing MGAT5 alone or in combination with B4GalT1 and ST6Gal1. The various N-glycan structures and the method for producing them in this work provide opportunities to study the glycan structure-and-function and develop novel recombinant antibodies for addressing different therapeutic applications.
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Affiliation(s)
- Ngan T. B. Nguyen
- grid.452198.30000 0004 0485 9218Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jianer Lin
- grid.452198.30000 0004 0485 9218Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shi Jie Tay
- grid.452198.30000 0004 0485 9218Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mariati
- grid.452198.30000 0004 0485 9218Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jessna Yeo
- grid.452198.30000 0004 0485 9218Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Terry Nguyen-Khuong
- grid.452198.30000 0004 0485 9218Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yuansheng Yang
- grid.452198.30000 0004 0485 9218Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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32
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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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33
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Baik JY, Han HJ, Lee KH. DNA Double-Strand Breaks Affect Chromosomal Rearrangements during Methotrexate-Mediated Gene Amplification in Chinese Hamster Ovary Cells. Pharmaceutics 2021; 13:pharmaceutics13030376. [PMID: 33809068 PMCID: PMC8000239 DOI: 10.3390/pharmaceutics13030376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/28/2021] [Accepted: 03/05/2021] [Indexed: 11/16/2022] Open
Abstract
Methotrexate (MTX)-mediated gene amplification has been widely used in Chinese hamster ovary (CHO) cells for the biomanufacturing of therapeutic proteins. Although many studies have reported chromosomal instability and extensive chromosomal rearrangements in MTX-mediated gene-amplified cells, which may be associated with cell line instability issues, the mechanisms of chromosomal rearrangement formation remain poorly understood. We tested the impact of DNA double-strand breaks (DSBs) on chromosomal rearrangements using bleomycin, a DSB-inducing reagent. Bleomycin-treated CHO-DUK cells, which are one of the host cell lines deficient in dihydrofolate reductase (Dhfr) activity, exhibited a substantial number of cells containing radial formations or non-radial formations with chromosomal rearrangements, suggesting that DSBs may be associated with chromosomal rearrangements. To confirm the causes of DSBs during gene amplification, we tested the effects of MTX treatment and the removal of nucleotide base precursors on DSB formation in Dhfr-deficient (i.e., CHO-DUK) and Dhfr-expressing (i.e., CHO-K1) cells. Immunocytochemistry demonstrated that MTX treatment did not induce DSBs per se, but a nucleotide shortage caused by the MTX-mediated inhibition of Dhfr activity resulted in DSBs. Our data suggest that a nucleotide shortage caused by MTX-mediated Dhfr inhibition in production cell lines is the primary cause of a marked increase in DSBs, resulting in extensive chromosomal rearrangements after gene amplification processes.
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Affiliation(s)
- Jong Youn Baik
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- Department of Biological Engineering, Inha University, Incheon 22212, Korea;
- Correspondence: (J.Y.B.); (K.H.L.); Tel.: +82-32-860-7513 (J.Y.B.); +1-302-831-0344 (K.H.L.)
| | - Hye-Jin Han
- Department of Biological Engineering, Inha University, Incheon 22212, Korea;
| | - Kelvin H. Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- Correspondence: (J.Y.B.); (K.H.L.); Tel.: +82-32-860-7513 (J.Y.B.); +1-302-831-0344 (K.H.L.)
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34
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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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Bryan L, Henry M, Kelly RM, Lloyd M, Frye CC, Osborne MD, Clynes M, Meleady P. Global phosphoproteomic study of high/low specific productivity industrially relevant mAb producing recombinant CHO cell lines. CURRENT RESEARCH IN BIOTECHNOLOGY 2021. [DOI: 10.1016/j.crbiot.2021.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Vasquez CA, Cowan QT, Komor AC. Base Editing in Human Cells to Produce Single-Nucleotide-Variant Clonal Cell Lines. ACTA ACUST UNITED AC 2020; 133:e129. [PMID: 33151638 DOI: 10.1002/cpmb.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Base-editing technologies enable the introduction of point mutations at targeted genomic sites in mammalian cells, with higher efficiency and precision than traditional genome-editing methods that use DNA double-strand breaks, such as zinc finger nucleases (ZFNs), transcription-activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (CRISPR-Cas9) system. This allows the generation of single-nucleotide-variant isogenic cell lines (i.e., cell lines whose genomic sequences differ from each other only at a single, edited nucleotide) in a more time- and resource-effective manner. These single-nucleotide-variant clonal cell lines represent a powerful tool with which to assess the functional role of genetic variants in a native cellular context. Base editing can therefore facilitate genotype-to-phenotype studies in a controlled laboratory setting, with applications in both basic research and clinical applications. Here, we provide optimized protocols (including experimental design, methods, and analyses) to design base-editing constructs, transfect adherent cells, quantify base-editing efficiencies in bulk, and generate single-nucleotide-variant clonal cell lines. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Design and production of plasmids for base-editing experiments Basic Protocol 2: Transfection of adherent cells and harvesting of genomic DNA Basic Protocol 3: Genotyping of harvested cells using Sanger sequencing Alternate Protocol 1: Next-generation sequencing to quantify base editing Basic Protocol 4: Single-cell isolation of base-edited cells using FACS Alternate Protocol 2: Single-cell isolation of base-edited cells using dilution plating Basic Protocol 5: Clonal expansion to generate isogenic cell lines and genotyping of clones.
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Affiliation(s)
- Carlos A Vasquez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
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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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38
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Sergeeva D, Lee GM, Nielsen LK, Grav LM. Multicopy Targeted Integration for Accelerated Development of High-Producing Chinese Hamster Ovary Cells. ACS Synth Biol 2020; 9:2546-2561. [PMID: 32835482 DOI: 10.1021/acssynbio.0c00322] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ever-growing biopharmaceutical industry relies on the production of recombinant therapeutic proteins in Chinese hamster ovary (CHO) cells. The traditional timelines of CHO cell line development can be significantly shortened by the use of targeted gene integration (TI). However, broad use of TI has been limited due to the low specific productivity (qP) of TI-generated clones. Here, we show a 10-fold increase in the qP of therapeutic glycoproteins in CHO cells through the development and optimization of a multicopy TI method. We used a recombinase-mediated cassette exchange (RMCE) platform to investigate the effect of gene copy number, 5' and 3' gene regulatory elements, and landing pad features on qP. We evaluated the limitations of multicopy expression from a single genomic site as well as multiple genomic sites and found that a transcriptional bottleneck can appear with an increase in gene dosage. We created a dual-RMCE system for simultaneous multicopy TI in two genomic sites and generated isogenic high-producing clones with qP of 12-14 pg/cell/day and product titer close to 1 g/L in fed-batch. Our study provides an extensive characterization of the multicopy TI method and elucidates the relationship between gene copy number and protein expression in mammalian cells. Moreover, it demonstrates that TI-generated CHO cells are capable of producing therapeutic proteins at levels that can support their industrial manufacture.
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Affiliation(s)
- Daria Sergeeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane 4072, Australia
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
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Shin S, Kim SH, Shin SW, Grav LM, Pedersen LE, Lee JS, Lee GM. Comprehensive Analysis of Genomic Safe Harbors as Target Sites for Stable Expression of the Heterologous Gene in HEK293 Cells. ACS Synth Biol 2020; 9:1263-1269. [PMID: 32470292 DOI: 10.1021/acssynbio.0c00097] [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] [Indexed: 11/28/2022]
Abstract
Human cell lines are being increasingly used as host cells to produce therapeutic glycoproteins, due to their human glycosylation machinery. In an attempt to develop a platform for generating isogenic human cell lines producing therapeutic proteins based on targeted integration, three well-known human genomic safe harbors (GSHs)-AAVS1, CCR5, and human ROSA26 loci-were evaluated with respect to the transgene expression level and stability in human embryonic kidney (HEK293) cells. Among the three GSHs, the AAVS1 locus showed the highest eGFP expression with the highest homogeneity. Transgene expression at the AAVS1 locus was sustained without selection for approximately 3 months. Furthermore, the CMV promoter showed the highest expression, followed by the EF1α, SV40, and TK promoters at the AAVS1 locus. Master cell lines were created using CRISPR/Cas9-mediated integration of the landing pad into the AAVS1 locus and were used for faster generation of recombinant cell lines that produce therapeutic proteins with recombinase-mediated cassette exchange.
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Affiliation(s)
- Seunghyeon Shin
- Department of Biological Sciences, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Su Hyun Kim
- Department of Biological Sciences, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Sung Wook Shin
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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40
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Dobson PD, Coss KP, Doherty C, Clifford J, Thompson B, James DC. Cell function profiling to assess clone stability. Biotechnol Bioeng 2020; 117:2295-2299. [PMID: 32181887 PMCID: PMC7383652 DOI: 10.1002/bit.27336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/24/2020] [Accepted: 03/16/2020] [Indexed: 01/07/2023]
Abstract
In cell line development the identification of stable Chinese hamster ovary cells for production is a critical but onerous task. The stability trial focus upon high‐level attributes can mask profound underlying cellular changes, leading to unstable clones mistakenly being chosen for production. The challenge is to assay underlying cell pathways and subsystems without pushing up cell line development costs. ChemStress® cell function profiling is a simple, multiwell plate‐based assay that uses a panel of active chemicals to mimic known bioprocess stresses and challenge key pathways. After 3 days of static culture on the plate, functional responses are assayed, for example, titer and growth. Here this approach is used to monitor 131 clones as they change over real stability trials. A novel stability metric is defined over the data to identify stable clones that remain unperturbed across many components of cell function. This allows stability trials to look beneath the titer to identify clones that are internally more stable.
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Affiliation(s)
- Paul D Dobson
- Valitacell Ltd, NIBRT Foster Avenue, Mount Merrion, Blackrock, County Dublin, Ireland
| | - Karen P Coss
- Valitacell Ltd, NIBRT Foster Avenue, Mount Merrion, Blackrock, County Dublin, Ireland
| | - Carolanne Doherty
- Valitacell Ltd, NIBRT Foster Avenue, Mount Merrion, Blackrock, County Dublin, Ireland
| | - Jerry Clifford
- Valitacell Ltd, NIBRT Foster Avenue, Mount Merrion, Blackrock, County Dublin, Ireland
| | - Ben Thompson
- Valitacell Ltd, NIBRT Foster Avenue, Mount Merrion, Blackrock, County Dublin, Ireland
| | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
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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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42
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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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43
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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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44
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Pinu FR, Beale DJ, Paten AM, Kouremenos K, Swarup S, Schirra HJ, Wishart D. Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. Metabolites 2019; 9:E76. [PMID: 31003499 PMCID: PMC6523452 DOI: 10.3390/metabo9040076] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023] Open
Abstract
The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent 'Australian and New Zealand Metabolomics Conference' (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand.
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecosciences Precinct, Dutton Park, Dutton Park, QLD 4102, Australia.
| | - Amy M Paten
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Research and Innovation Park, Acton, ACT 2601, Australia.
| | - Konstantinos Kouremenos
- Trajan Scientific and Medical, Ringwood, VIC 3134, Australia.
- Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Sanjay Swarup
- Department of Biological Sciences, National University of Singapore, Singapore 117411, Singapore.
| | - Horst J Schirra
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - David Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada.
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
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