1
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Lenser M, Ngo HG, Sarrafha L, Rajendra Y. Evaluation of two transposases for improving expression of recombinant proteins in Chinese hamster ovary cell stable pools by co-transfection and supertransfection approaches. Biotechnol Prog 2024:e3496. [PMID: 39016635 DOI: 10.1002/btpr.3496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/13/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
Transposons are genetic elements capable of cutting and pasting genes of interest via the action of a transposase and offer many advantages over random or targeted integration of DNA in the creation of Chinese hamster ovary (CHO) cell lines for recombinant protein expression. Unique transposases have different recognition sites, allowing multiple transposases to be co-transfected together. They also allow for supertransfection (transfection on a previously transfected pool or cell line) with a second transposase to integrate additional copies of the same gene or an additional gene without disruption of the previously integrated DNA which to our knowledge has not been previously described in literature. Two fluorescent proteins, EGFP and tagRFP657, were either co-transfected or supertransfected into CHO cells using two unique transposases and showed high expression efficiency with similar expression levels (measured as mean fluorescence intensity), regardless of whether the genes were co-transfected or supertransfected onto an existing stable pool. Additionally, dual selection of the genes, both in the absence of L-glutamine and the presence of puromycin, led to higher expression levels than single selection alone. These results demonstrate that supertransfection using unique transposases could be a useful strategy for increasing titers of existing cell lines or for overexpressing helper (non-therapeutic) genes to improve expression and/or product quality of existing pools and cell lines, potentially saving significant time and resources.
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Affiliation(s)
- Melina Lenser
- Bioprocess Development, Technical Operations, Denali Therapeutics, Inc., South San Francisco, California, USA
| | - Hanh Giai Ngo
- Bioprocess Development, Technical Operations, Denali Therapeutics, Inc., South San Francisco, California, USA
| | - Lily Sarrafha
- Discovery Biology, Denali Therapeutics, Inc., South San Francisco, California, USA
| | - Yashas Rajendra
- Bioprocess Development, Technical Operations, Denali Therapeutics, Inc., South San Francisco, California, USA
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2
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Bauer N, Oberist C, Poth M, Stingele J, Popp O, Ausländer S. Genomic barcoding for clonal diversity monitoring and control in cell-based complex antibody production. Sci Rep 2024; 14:14587. [PMID: 38918509 PMCID: PMC11199663 DOI: 10.1038/s41598-024-65323-7] [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: 03/25/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024] Open
Abstract
Engineered mammalian cells are key for biotechnology by enabling broad applications ranging from in vitro model systems to therapeutic biofactories. Engineered cell lines exist as a population containing sub-lineages of cell clones that exhibit substantial genetic and phenotypic heterogeneity. There is still a limited understanding of the source of this inter-clonal heterogeneity as well as its implications for biotechnological applications. Here, we developed a genomic barcoding strategy for a targeted integration (TI)-based CHO antibody producer cell line development process. This technology provided novel insights about clone diversity during stable cell line selection on pool level, enabled an imaging-independent monoclonality assessment after single cell cloning, and eventually improved hit-picking of antibody producer clones by monitoring of cellular lineages during the cell line development (CLD) process. Specifically, we observed that CHO producer pools generated by TI of two plasmids at a single genomic site displayed a low diversity (< 0.1% RMCE efficiency), which further depends on the expressed molecules, and underwent rapid population skewing towards dominant clones during routine cultivation. Clonal cell lines from one individual TI event demonstrated a significantly lower variance regarding production-relevant and phenotypic parameters as compared to cell lines from distinct TI events. This implies that the observed cellular diversity lies within pre-existing cell-intrinsic factors and that the majority of clonal variation did not develop during the CLD process, especially during single cell cloning. Using cellular barcodes as a proxy for cellular diversity, we improved our CLD screening workflow and enriched diversity of production-relevant parameters substantially. This work, by enabling clonal diversity monitoring and control, paves the way for an economically valuable and data-driven CLD process.
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Affiliation(s)
- Niels Bauer
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Christoph Oberist
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Michaela Poth
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Oliver Popp
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Simon Ausländer
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany.
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3
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Lee Z, Wan J, Shen A, Barnard G. Gene copy number, gene configuration and LC/HC mRNA ratio impact on antibody productivity and product quality in targeted integration CHO cell lines. Biotechnol Prog 2024; 40:e3433. [PMID: 38321634 DOI: 10.1002/btpr.3433] [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: 10/13/2023] [Revised: 12/01/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
The augmentation of transgene copy numbers is a prevalent approach presumed to enhance transcriptional activity and product yield. CHO cell lines engineered via targeted integration (TI) offer an advantageous platform for investigating the interplay between gene copy number, mRNA abundance, product yield, and product quality. Our investigation revealed that incrementally elevating the gene copy numbers of both IgG heavy chain (HC) and light chain (LC) concurrently resulted in the attainment of plateaus in mRNA levels and product titers, notably occurring beyond four to five gene copies integrated at the same TI site. Furthermore, maintaining a fixed gene copy number while varying the position of genes within the vector influenced the LC/HC mRNA ratio, which subsequently exerted a substantial impact on product titer. Moreover, manipulation of the LC/HC gene ratio through the introduction of surplus LC gene copies led to heightened LC mRNA expression and a reduction in the levels of high molecular weight species. It is noteworthy that the effects of excess LC on product titer were dependent on the specific molecule under consideration. The strategic utilization of PCR tags enabled precise quantification of transcription from each expression slot within the vector, facilitating the identification of highly expressive and less expressive slots. Collectively, these findings significantly enhance our understanding of stable antibody production in TI CHO cell lines.
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Affiliation(s)
- Zion Lee
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
| | - Jun Wan
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
| | - Amy Shen
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
| | - Gavin Barnard
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
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4
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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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5
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Liu H, Zhang W, Xie L, Hu Y. Identification of a New Integration Site and Study on Site-Specific Integration in CHO-K1 Cells. Pharmaceuticals (Basel) 2023; 17:8. [PMID: 38275994 PMCID: PMC10819697 DOI: 10.3390/ph17010008] [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: 11/29/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Site-specific integration is an important approach used to address the problem of unstable cell lines in industry. In this study, we observed a reduction in the gene copy number and antibody production in a CHOK1 cell line BA03 capable of high antibody expression. We identified a new integration site named locus 7 in the intron region of the parva gene through sequencing, FISH, and genome walking. We demonstrate that the integration of the exogenous gene at this locus does not affect the transcription of the parva and, therefore, has a minimal impact on cell growth. We designed sgRNA and donor vectors to integrate the etanercept-coding gene into locus 7 and obtained a cell line, SSI-4. We performed a passaged stability study on SSI-4 and proved the possibility of the stable, site-specific integration of exogenous genes at this locus in terms of integration site, copy number, expression level, and cell growth. In summary, our study has identified a new integration site suitable for site-specific integration, which lays the foundation for the subsequent development of site-specific integration cell lines.
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Affiliation(s)
| | | | - Liping Xie
- Department of Biology, China State Institute of Pharmaceutical Industry, Shanghai 201203, China; (H.L.); (W.Z.)
| | - Youjia Hu
- Department of Biology, China State Institute of Pharmaceutical Industry, Shanghai 201203, China; (H.L.); (W.Z.)
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6
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Castellano BM, Tang D, Marsters S, Lam C, Liu P, Rose CM, Sandoval W, Ashkenazi A, Snedecor B, Misaghi S. Activation of the PERK branch of the unfolded protein response during production reduces specific productivity in CHO cells via downregulation of PDGFRa and IRE1a signaling. Biotechnol Prog 2023; 39:e3354. [PMID: 37161726 DOI: 10.1002/btpr.3354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/13/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
During the course of biopharmaceutical production, heterologous protein expression in Chinese hamster ovary (CHO) cells imposes a high proteostatic burden that requires cellular adaptation. To mitigate such burden, cells utilize the unfolded protein response (UPR), which increases endoplasmic reticulum (ER) capacity to accommodate elevated rates of protein synthesis and folding. In this study, we show that during production the UPR regulates growth factor signaling to modulate growth and protein synthesis. Specifically, the protein kinase R-like ER kinase (PERK) branch of the UPR is responsible for transcriptional down-regulation of platelet-derived growth factor receptor alpha (PDGFRa) and attenuation of the IRE1-alpha (IRE1a) branch of the UPR. PERK knockout (KO) cell lines displayed reduced growth and viability due to higher rates of apoptosis despite having stabilized PDGFRa levels. Knocking out PERK in an apoptosis impaired (Bax/Bak double KO) antibody-expressing cell line prevented apoptotic cell death and revealed that apoptosis was likely triggered by increased ER stress and reactive oxygen species levels in the PERK KO hosts. Our findings suggest that attenuation of IRE1a and PDGFRa signaling by the PERK branch of the UPR reduces ER protein folding capacity and hence specific productivity of CHO cells in order to mitigate UPR and prevent apoptotic cell death. Last, Bax/Bak/PERK triple KO CHO cell lines displayed 2-3 folds higher specific productivity and titer (up to 8 g/L), suggesting that modulation of PERK signaling during production processes can greatly improve specific productivity in CHO cells.
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Affiliation(s)
- Brian M Castellano
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Danming Tang
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Scot Marsters
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, California, USA
| | - Cynthia Lam
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Peter Liu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, California, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, California, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, California, USA
| | - Avi Ashkenazi
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, California, USA
| | - Brad Snedecor
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Shahram Misaghi
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
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7
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Kim SM, Lee J, Lee JS. Implementation of ubiquitous chromatin opening elements as artificial integration sites for CRISPR/Cas9‐mediated knock‐in in mammalian cells. Eng Life Sci 2023; 23:e2200047. [PMID: 37025191 PMCID: PMC10071570 DOI: 10.1002/elsc.202200047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 01/16/2023] [Accepted: 02/07/2023] [Indexed: 03/11/2023] Open
Abstract
CRISPR/Cas9-mediated targeted gene integration (TI) has been used to generate recombinant mammalian cell lines with predictable transgene expression. Identifying genomic hot spots that render high and stable transgene expression and knock-in (KI) efficiency is critical for fully implementing TI-mediated cell line development (CLD); however, such identification is cumbersome. In this study, we developed an artificial KI construct that can be used as a hot spot at different genomic loci. The ubiquitous chromatin opening element (UCOE) was employed because of its ability to open chromatin and enable stable and site-independent transgene expression. UCOE KI cassettes were randomly integrated into CHO-K1 and HEK293T cells, followed by TI of enhanced green fluorescent protein (EGFP) onto the artificial UCOE KI site. The CHO-K1 random pool harboring 5'2.2A2UCOE-CMV displayed a significant increase in EGFP expression level and KI efficiency compared with that of the control without UCOE. In addition, 5'2.2A2UCOE-CMV showed improved Cas9 accessibility in the HEK293T genome, leading to an increase in indel frequency and homology-independent KI. Overall, this assessment revealed the potential of UCOE KI constructs as artificial integration sites in streamlining the screening of high-production targeted integrants by mitigating the selection of genomic hot spots.
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Affiliation(s)
- Seul Mi Kim
- Department of Molecular Science and Technology Ajou University Suwon Republic of Korea
| | - Jaejin Lee
- Department of Molecular Science and Technology Ajou University Suwon Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology Ajou University Suwon Republic of Korea
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8
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Hall CA, Kravitz RH, Johnson KF, Sanek NA, Maiti P, Ziemba KR, Liu J, Andreev DO, Chrostowski VL, Collins IJ, Bleck GT. Shortening the biologics clinical timeline with a novel method for generating stable, high-producing cell pools and clones. Biotechnol Bioeng 2022. [PMID: 36582005 DOI: 10.1002/bit.28323] [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: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 12/31/2022]
Abstract
Reducing drug development timelines is an industry-wide goal to bring medicines to patients in need more quickly. This was exemplified in the coronavirus disease 2019 pandemic where reducing development timelines had a direct impact on the number of lives lost to the disease. The use of drug substances produced using cell pools, as opposed to clones, has the potential to shorten development timelines. Toward this goal, we have developed a novel technology, GPEx® Lightning, that allows for rapid, reproducible, targeted recombination of transgenes into more than 200 Dock sites in the Chinese hamster ovary cell line genome. This allows for rapid production of high-expressing stable cell pools and clones that reach titers of 4-12 g/l in generic fed-batch production. These pools and clones are highly stable in both titer and glycosylation, showing strong similarities in glycosylation profiles.
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Affiliation(s)
- Chad A Hall
- Catalent Pharma Solutions, Somerset, New Jersey, USA
| | | | | | | | - Payel Maiti
- Catalent Pharma Solutions, Somerset, New Jersey, USA
| | | | - Jia Liu
- Catalent Pharma Solutions, Somerset, New Jersey, USA
| | | | | | - Ian J Collins
- Catalent Pharma Solutions, Somerset, New Jersey, USA
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9
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Tevelev B, Chambers A, Ghosh S, Zhang Y, Marzili L, Rouse JC, Han S, Moffat M, Scarcelli JJ. A genetic off-target event in a site-specific integration cell line expressing monoclonal antibody has no impact on commercial suitability. Biotechnol Prog 2022; 39:e3320. [PMID: 36545889 DOI: 10.1002/btpr.3320] [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: 11/03/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Site-specific integration (SSI) cell line systems are gaining popularity for biotherapeutic development and production. Despite the proven advantages for these expression hosts, the SSI system is still susceptible to rare off-target events and potential vector rearrangements. Here we describe the development process of an SSI cell line for production of an IgG1 monoclonal antibody (mAb-086). During cell line generational studies to assess suitability of clone C10 for commercial purposes, restriction fragment lengths of genomic DNA harboring the light chain (LC) were not in agreement with the predicted size. We first confirmed that the SSI landing-pad achieved occupancy of the desired expression plasmid. Additional investigation revealed that random integration had occurred, resulting in the acquisition of a partial copy of the LC and a full-length copy of the heavy chain (HC) at a different locus in the host genome. This off-target event had no impact on the genotypic consistency and phenotypic stability of the cell line, the production process, or the drug substance product quality. Given the genetic, phenotypic, and process consistency of the cell line, clone C10 was deemed suitable as a manufacturing cell line.
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Affiliation(s)
- Barbara Tevelev
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Andre Chambers
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, Missouri, USA
| | - Swap Ghosh
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, Missouri, USA
| | - Ying Zhang
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Lisa Marzili
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Jason C Rouse
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Shu Han
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Mark Moffat
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, Missouri, USA
| | - John J Scarcelli
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
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10
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Tang D, Gunson J, Tran E, Lam C, Shen A, Snedecor B, Barnard G, Misaghi S. Expressing antigen binding fragments with high titers in a targeted integration CHO host by optimizing expression vector gene copy numbers and position: A case study. Biotechnol Prog 2022; 38:e3290. [PMID: 36537257 DOI: 10.1002/btpr.3290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/15/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022]
Abstract
Antigen binding fragments (Fab) are a promising class of therapeutics as they maintain high potency while having significantly smaller size relative to full-length antibodies. Because Fab molecules are aglycosylated, many expression platforms, including prokaryotic, yeast, and mammalian cells, have been developed for their expression, with Escherichia coli being the most commonly used Fab expression system. In this study, we have examined production of a difficult to express Fab molecule in a targeted integration (TI) Chinese Hamster Ovary (CHO) host. Without a need for extensive host or process optimization, as is usually required for E. coli, by simply using different vector configurations, clones with very high Fab expression titers were obtained. In this case, by increasing heavy chain (HC) gene copy numbers, clones with titers of up to 7.4 g/L in the standard fed-batch production culture were obtained. Our findings suggest that having a predetermined transgene integration site, as well as the option to optimize gene copy number/dosage, makes CHO TI hosts an effective system for expression of Fab molecules, allowing Fab expression using platform process and without significant process development efforts.
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Affiliation(s)
- Danming Tang
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA.,Protein Sciences, Proteologix US Inc., Redwood Shores, California, USA
| | - Jane Gunson
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Eric Tran
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Cynthia Lam
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Amy Shen
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Brad Snedecor
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Gavin Barnard
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
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11
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Wu C, Cook R, Wu P, Srikumar N, Chee E, Sawyer WS, Wang H, Hazen M, Hotzel I, N'Diaye EN, Ding N, Liu Y, Tran JC, Ye Z. Using a peptide-based mass spectrometry approach to quantitate proteolysis of an intact heterogeneous procollagen substrate by BMP1 for antagonistic antibody screening. Anal Bioanal Chem 2022; 414:6601-6610. [PMID: 35821276 DOI: 10.1007/s00216-022-04220-2] [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: 04/24/2022] [Revised: 06/24/2022] [Accepted: 06/30/2022] [Indexed: 11/01/2022]
Abstract
Proteases are critical proteins involved in cleaving substrates that may impact biological pathways, cellular processes, or disease progression. In the biopharmaceutical industry, modulating the levels of protease activity is an important strategy for mitigating many types of diseases. While a variety of analytical tools exist for characterizing substrate cleavages, in vitro functional screening for antibody inhibitors of protease activity using physiologically relevant intact protein substrates remains challenging. In addition, detecting such large protein substrates with high heterogeneity using high-throughput mass spectrometry screening has rarely been reported in the literature with concerns for assay robustness and sensitivity. In this study, we established a peptide-based in vitro functional screening assay for antibody inhibitors of mouse bone morphogenic protein 1 (mBMP1) metalloprotease using a heterogeneous recombinant 66-kDa mouse Procollagen I alpha 1 chain (mProcollagen) substrate. We compared several analytical tools including capillary gel electrophoresis Western blot (CE-Western blot), as well as both intact protein and peptide-based mass spectrometry (MS) to quantitate the mBMP1 proteolytic activity and its inhibition by antibodies using this heterogeneous mProcollagen substrate. We concluded that the peptide-based mass spectrometry screening assay was the most suitable approach in terms of throughput, sensitivity, and assay robustness. We then optimized our mBMP1 proteolysis reaction after characterizing the enzyme kinetics using the peptide-based MS assay. This assay resulted in Z' values ranging from 0.6 to 0.8 from the screening campaign. Among over 1200 antibodies screened, IC50 characterization was performed on the top candidate hits, which showed partial or complete inhibitory activities against mBMP1.
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Affiliation(s)
- Cong Wu
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA.
| | - Ryan Cook
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Ping Wu
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | | | - Elin Chee
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - William S Sawyer
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Hua Wang
- Morphic Therapeutic, Waltham, MA, USA
| | - Meredith Hazen
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Isidro Hotzel
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | | | - Ning Ding
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | | | - John C Tran
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Zhengmao Ye
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
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12
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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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13
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Zhang JH, Shan LL, Liang F, Du CY, Li JJ. Strategies and Considerations for Improving Recombinant Antibody Production and Quality in Chinese Hamster Ovary Cells. Front Bioeng Biotechnol 2022; 10:856049. [PMID: 35316944 PMCID: PMC8934426 DOI: 10.3389/fbioe.2022.856049] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/16/2022] [Indexed: 11/30/2022] Open
Abstract
Recombinant antibodies are rapidly developing therapeutic agents; approximately 40 novel antibody molecules enter clinical trials each year, most of which are produced from Chinese hamster ovary (CHO) cells. However, one of the major bottlenecks restricting the development of antibody drugs is how to perform high-level expression and production of recombinant antibodies. The high-efficiency expression and quality of recombinant antibodies in CHO cells is determined by multiple factors. This review provides a comprehensive overview of several state-of-the-art approaches, such as optimization of gene sequence of antibody, construction and optimization of high-efficiency expression vector, using antibody expression system, transformation of host cell lines, and glycosylation modification. Finally, the authors discuss the potential of large-scale production of recombinant antibodies and development of culture processes for biopharmaceutical manufacturing in the future.
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Affiliation(s)
- Jun-He Zhang
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
- Henan International Joint Laboratory of Recombinant Pharmaceutical Protein Expression System, Xinxiang Medical University, Xinxiang, China
- *Correspondence: Jun-He Zhang,
| | - Lin-Lin Shan
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
| | - Fan Liang
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
| | - Chen-Yang Du
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
| | - Jing-Jing Li
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
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14
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Carver J, Kern M, Ko P, Greenwood-Goodwin M, Yu XC, Duan D, Tang D, Misaghi S, Auslaender S, Haley B, Yuk IH, Shen A. A ribonucleoprotein-based decaplex CRISPR/Cas9 knockout strategy for CHO host engineering. Biotechnol Prog 2022; 38:e3212. [PMID: 34538022 DOI: 10.1002/btpr.3212] [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: 07/11/2021] [Revised: 08/24/2021] [Accepted: 09/16/2021] [Indexed: 11/08/2022]
Abstract
Chinese hamster ovary (CHO) cell engineering based on CRISPR/Cas9 knockout (KO) technology requires the delivery of guide RNA (gRNA) and Cas9 enzyme for efficient gene targeting. With an ever-increasing list of promising gene targets, developing, and optimizing a multiplex gene KO protocol is crucial for rapid CHO cell engineering. Here, we describe a method that can support efficient targeting and KO of up to 10 genes through sequential transfections. This method utilizes Cas9 protein to first screen multiple synthetic gRNAs per gene, followed by Sanger sequencing indel analysis, to identify effective gRNA sequences. Using sequential transfections of these potent gRNAs led to the isolation of single cell clones with the targeted deletion of all 10 genes (as confirmed by Sanger sequencing at the DNA level and mass spectrometry at the protein level). Screening 704 single cell clones yielded 6 clones in which all 10 genes were deleted through sequential transfections, demonstrating the success of this decaplex gene editing strategy. This pragmatic approach substantially reduces the time and effort required to generate multiple gene knockouts in CHO cells.
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Affiliation(s)
- Joseph Carver
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Marie Kern
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Peggy Ko
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | | | - X Christopher Yu
- Analytical Development Quality Control, Genentech, Inc., South San Francisco, California, USA
| | - Dana Duan
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Danming Tang
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Simon Auslaender
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
| | - Ben Haley
- Research Biology, Genentech, Inc., South San Francisco, California, USA
| | - Inn H Yuk
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Amy Shen
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
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15
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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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16
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Zhang Z, Chen J, Wang J, Gao Q, Ma Z, Xu S, Zhang L, Cai J, Zhou W. Reshaping cell line development and CMC strategy for fast responses to pandemic outbreak. Biotechnol Prog 2021; 37:e3186. [PMID: 34148295 DOI: 10.1002/btpr.3186] [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: 03/24/2021] [Revised: 06/12/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022]
Abstract
The global pandemic outbreak COVID-19 (SARS-COV-2), has prompted many pharmaceutical companies to develop vaccines and therapeutic biologics for its prevention and treatment. Most of the therapeutic biologics are common human IgG antibodies, which were identified by next-generation sequencing (NGS) with the B cells from the convalescent patients. To fight against pandemic outbreaks like COVID-19, biologics development strategies need to be optimized to speed up the timeline. Since the advent of therapeutic biologics, strategies of transfection and cell line selection have been continuously improved for greater productivity and efficiency. NGS has also been implemented for accelerated cell bank testing. These recent advances enable us to rethink and reshape the chemistry, manufacturing, and controls (CMC) strategy in order to start supplying Good Manufacturing Practices (GMP) materials for clinical trials as soon as possible. We elucidated an accelerated CMC workflow for biologics, including using GMP-compliant pool materials for phase I clinical trials, selecting the final clone with product quality similar to that of phase I materials for late-stage development and commercial production.
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Affiliation(s)
- Zheng Zhang
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Ji Chen
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Junghao Wang
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Qiao Gao
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Zhujun Ma
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Shurong Xu
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Li Zhang
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Jill Cai
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
| | - Weichang Zhou
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
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