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Yamano-Adachi N, Hata H, Nakanishi Y, Omasa T. Effects of genome instability of parental CHO cell clones on chromosome number distribution and recombinant protein production in parent-derived subclones. J Biosci Bioeng 2024; 137:54-63. [PMID: 37981489 DOI: 10.1016/j.jbiosc.2023.10.001] [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: 08/09/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/21/2023]
Abstract
Chinese hamster ovary (CHO) cells are the de facto standard host cells for biopharmaceuticals, and there is great interest in developing methods for constructing stable production cell lines. In this study, clones with a wide chromosome number distribution were selected from isolated antibody-producing strains, and subclones obtained from these clones were evaluated. The transgene copy number varied between the subclones. Even among subclones with similar copy numbers of antibody genes and maintained insertion sites, clones with different productivity were generated. Although the chromosome number distribution differed between these subclones, there was no correlation between the variability in chromosome number after cloning (genome instability) and productivity. Most of the subclones obtained from a parental strain with a wide chromosome number had the same wide chromosome number distribution as the parental strain. Less frequently, cells with less variation (remaining in one distribution) in chromosome number were isolated from cells with a wide chromosome number distribution, from which subclones with less variation in chromosome number were obtained when subcloning was performed again. These results imply that the characteristics of clones with chromosomal instability are inherited by subclones, and thus provide a better understanding of cell line stability/instability.
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Affiliation(s)
- Noriko Yamano-Adachi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hirofumi Hata
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuto Nakanishi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Omasa
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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2
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Torres M, Betts Z, Scholey R, Elvin M, Place S, Hayes A, Dickson AJ. Long term culture promotes changes to growth, gene expression, and metabolism in CHO cells that are independent of production stability. Biotechnol Bioeng 2023; 120:2389-2402. [PMID: 37060548 DOI: 10.1002/bit.28399] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/28/2023] [Accepted: 04/01/2023] [Indexed: 04/16/2023]
Abstract
Phenotypic stability of Chinese hamster ovary (CHO) cells over long term culture (LTC) presents one of the most pressing challenges in the development of therapeutic protein manufacturing processess. However, our current understanding of the consequences of LTC on recombinant (r-) CHO cell lines is still limited, particularly as clonally-derived cell lines present distinct production stability phenotypes. This study evaluated changes of culture performance, global gene expression, and cell metabolism of two clonally-derived CHO cell lines with a stable or unstable phenotype during the LTC (early [EP] vs. late [LP] culture passages). Our findings indicated that LTC altered the behavior of CHO cells in culture, in terms of growth, overall gene expression, and cell metabolism. Regardless whether cells were categorized as stable or unstable in terms of r-protein production, CHO cells at LP presented an earlier decline in cell viability and loss of any observable stationary phase. These changes were parallelled by the upregulation of genes involved in cell proliferation and survival pathways (i.e., MAPK/ERK, PI3K-Akt). Stable and unstable CHO cell lines both showed increased consumption of glucose and amino acids at LP, with a parallel accumulation of greater amounts of lactate and TCA cycle intermediates. In terms of production stability, we found that decreased r-protein production in the unstable cell line directly correlated to the loss in r-gene copy number and r-mRNA expression. Our data revealed that LTC produced ubiquitious effects on CHO cell phenotypes, changes that were rooted in alterations in cell transcriptome and metabolome. Overall, we found that CHO cells adapted their cellular function to proliferation and survival during the LTC, some of these changes may well have limited effects on overall yield or specific productivity of the desired r-product, but they may be critical toward the capacity of cells to handle r-proteins with specific molecular features.
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Affiliation(s)
- Mauro Torres
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK
- Department of Chemical Engineering, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
| | - Zeynep Betts
- Department of Biology, Kocaeli University, İzmit, Turkey
| | - Rachel Scholey
- Bioinformatics Core Facility, University of Manchester, Manchester, UK
| | - Mark Elvin
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK
- Department of Chemical Engineering, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
| | - Svetlana Place
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK
- Department of Chemical Engineering, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
| | - Andrew Hayes
- Genomic Technologies Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Alan J Dickson
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK
- Department of Chemical Engineering, Biochemical and Bioprocess Engineering Group, University of Manchester, Manchester, UK
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3
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Yamano-Adachi N, Nakanishi Y, Tanaka W, Lai Y, Yamazaki M, Zenner L, Hata H, Omasa T. Artificial induction of chromosome aneuploidy in CHO cells alters their function as host cells. Biotechnol Bioeng 2023; 120:659-673. [PMID: 36385243 DOI: 10.1002/bit.28289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/06/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Chinese hamster ovary (CHO) cells are major host cells for biopharmaceuticals. During culture, the chromosome number of CHO cells alters spontaneously. Here, we investigated the effects of artificial changes in the chromosome number on productivity. When cell fusion between antibody-producing CHO-K1-derived cells was induced, we observed a wide range of aneuploidy that was not detected in controls. In particular, antibody productivities were high in clone-derived cell populations that retained a diverse chromosome number distribution. We also induced aneuploid cells using 3-aminobenzamide that causes chromosome non-disjunction. After induction of aneuploidy by 3-aminobenzamide, cells with an increased chromosome number were isolated, but cells with a decreased chromosome number could not be isolated. When antibody expression vectors were introduced into these isolated clones, productivity tended to increase in cells with an increased chromosome number. Further analysis was carried out by focusing on clone 5E8 with an average chromosome number of 37. When 5E8 cells were used as host, the productivity of multiple antibodies, including difficult-to-express antibodies, was improved compared with CHO-K1 cells. The copies of exogenous genes integrated into the genome were significantly increased in 5E8 cells. These findings expand the possibilities for host cell selection and contribute to the efficient construction of cell lines for recombinant protein production.
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Affiliation(s)
- Noriko Yamano-Adachi
- Graduate School of Engineering, Osaka University, Osaka, Japan.,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Yuto Nakanishi
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Wataru Tanaka
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - YuanShan Lai
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima, Japan
| | | | - Laura Zenner
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Hirofumi Hata
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Takeshi Omasa
- Graduate School of Engineering, Osaka University, Osaka, Japan.,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
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4
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Kawabe Y, Kamihira M. Novel cell lines derived from Chinese hamster kidney tissue. PLoS One 2022; 17:e0266061. [PMID: 35358245 PMCID: PMC8970510 DOI: 10.1371/journal.pone.0266061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/13/2022] [Indexed: 01/15/2023] Open
Abstract
Immortalized kidney cell lines are widely used in basic and applied research such as cell permeability tests and drug screening. Although many cell lines have been established from kidney tissues, the immortalization process has not been clarified in these cell lines. In this study, we analyzed the phenotypic changes that occurred during the immortalization of kidney cells derived from Chinese hamster tissue in terms of karyotype and gene expression profiles. In the newly established cell line, designated as CHK-Q, gene expression profiles at each stage of the immortalization process and during the adaptation to serum-free conditions were analyzed by DNA microarray. Renal stem cell markers CD24 and CD133 were expressed in CHK-Q cells, suggesting that CHK-Q cells were transformed from renal stem cells. Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis to identify the pathways of upregulated and downregulated genes revealed that the immortalization of CHK-Q cells was associated with increased fluctuations in the expression of specific proto-oncogenes. Karyotype analysis of spontaneously immortalized CHK-Q cells indicated that CHK-Q chromosomes had a typical modal number of 23 but possessed slight chromosomal abnormalities. In this study, we investigated the mechanism of cell environmental adaptation by analyzing gene expression behavior during the immortalization process and serum-free adaptation. CHK-Q cells are applicable to the fields of biotechnology and biomedical science by utilizing their characteristics as kidney-derived cells.
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Affiliation(s)
- Yoshinori Kawabe
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, Fukuoka, Japan
- Manufacturing Technology Association of Biologics, Kobe, Japan
| | - Masamichi Kamihira
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, Fukuoka, Japan
- Manufacturing Technology Association of Biologics, Kobe, Japan
- * E-mail:
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5
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Trejo-Santillan I, Mendoza-Guevara CC, Ramos-Godinez MDP, Ramon-Gallegos E. Biosecurity test of conjugated nanoparticles of chitosanprotoporphyrin IX-vitamin B9 for their use in photodynamic therapy. IEEE Trans Nanobioscience 2021; 21:149-156. [PMID: 34606461 DOI: 10.1109/tnb.2021.3117747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nanotechnology proposes new applications for the development of nanotransporters and active targeting molecules with the use of biodegradable polymeric nanoparticles to improve the specificity towards target cells. However, these products must comply with safety tests to be endorsed as therapeutic alternatives by regulatory organizations. The goal of this work was to evaluate the biosafety (cytotoxicity and genotoxicity) of chitosan polymeric nanoparticles conjugate with protoporphyrin IX and vitamin B9 (CNPs-PpIX-B9) that were previously optimized from the established protocol by our laboratory and tested in CHO-K1 cells by bioassay following the recommendations of the chromosomal aberrations test by OECD 473 (2016) guideline. The conjugate did not show evidence of genotoxicity (clastogenicity). Surprisingly, the significant differences between the treatments performed and the negative control do not represent increases in chromosomal aberrations, whereby the safe concentrations to use the conjugate without inducing cytotoxic or genotoxic effects are less than 0.25 mg / mL. Since it induced a significant decrease of structural chromosomal aberrations, generating a positive effect on the genomic stability of CHO-K1 cells cultured in this test system.
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6
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Langsdorf E, Yu L, Kanevskaia L, Felkner R, Sturner S, McVey D, Khetan A. Retrospective assessment of clonal origin of cell lines. Biotechnol Prog 2021; 37:e3157. [PMID: 33896120 DOI: 10.1002/btpr.3157] [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: 12/20/2020] [Revised: 04/11/2021] [Accepted: 04/19/2021] [Indexed: 11/08/2022]
Abstract
Cell lines used for the manufacture of recombinant proteins are expected to arise from a single cell as a control strategy to limit variability and ensure consistent protein production. Health authorities require a minimum of two rounds of limiting dilution cloning or its equivalent to meet the requirement of single cell origin. However, many legacy cell lines may not have been generated with process meeting this criteria potentially impeding the path to commercialization. A general monoclonality assessment strategy was developed based on using the site of plasmid integration for a cell's identity. By comparing the identities of subclones from a master cell bank (MCB) to each other and that of the MCB, a probability of monoclonality was established. Two technologies were used for cell identity, Southern blot and a PCR assay based on plasmid-genome junction sequences identified by splinkerette PCR. Southern blot analysis revealed that subclones may have banding patterns that differ from each other and yet indicate monoclonal origin. Splinkerette PCR identifies cellular sequence flanking the point(s) of plasmid integration. The two assays together provide complimentary data for cell identity that enables proper monoclonality assessment and establishes that the three legacy cell lines investigated are all of clonal origin.
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Affiliation(s)
- Erik Langsdorf
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Le Yu
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Lioudmila Kanevskaia
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Roland Felkner
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Stephen Sturner
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Duncan McVey
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
| | - Anurag Khetan
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, New Brunswick, New Jersey, USA
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7
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Turilova VI, Goryachaya TS, Yakovleva TK. Chinese hamster ovary cell line DXB-11: chromosomal instability and karyotype heterogeneity. Mol Cytogenet 2021; 14:11. [PMID: 33596973 PMCID: PMC7888135 DOI: 10.1186/s13039-021-00528-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Chinese hamster ovary cell lines, also known as CHO cells, represent a large family of related, yet quite different, cell lines which are metabolic mutants derived from the original cell line, CHO-ori. Dihydrofolate reductase-deficient DXB-11 cell line, one of the first CHO derivatives, serves as the host cell line for the production of therapeutic proteins. It is generally assumed that DXB-11 is identical to DUKX or CHO-DUK cell lines, but, to our knowledge, DXB-11 karyotype has not been described yet. RESULTS Using differential staining approaches (G-, C-banding and Ag-staining), we presented DXB-11 karyotype and revealed that karyotypes of DXB-11 and CHO-DUK cells have a number of differences. Although the number of chromosomes is equal-20 in each cell line-DXB-11 has normal chromosomes of the 1st and 5th pairs as well as an intact chromosome 8. Besides, in DXB-11 line, chromosome der(Z9) includes the material of chromosomes X and 6, whereas in CHO-DUK it results from the translocation of chromosomes 1 and 6. Ag-positive nucleolar organizer regions were revealed in the long arms of chromosome del(4)(q11q12) and both chromosome 5 homologues, as well as in the short arms of chromosomes 8 and add(8)(q11). Only 19 from 112 (16.96%) DXB-11 cells display identical chromosome complement accepted as the main structural variant of karyotype. The karyotype heterogeneity of all the rest of cells (93, 83.04%) occurs due to clonal and nonclonal additional structural rearrangements of chromosomes. Estimation of the frequency of chromosome involvement in these rearrangements allowed us to reveal that chromosomes 9, der(X)t(X;3;4), del(2)(p21p23), del(2)(q11q22) /Z2, der(4) /Z7, add(6)(p11) /Z8 are the most stable, whereas mar2, probably der(10), is the most unstable chromosome. A comparative analysis of our own and literary data on CHO karyotypes allowed to designate conservative chromosomes, both normal and rearranged, that remain unchanged in different CHO cell lines, as well as variable chromosomes that determine the individuality of karyotypes of CHO derivatives. CONCLUSION DXB-11and CHO-DUK cell lines differ in karyotypes. The revealed differential instability of DXB-11 chromosomes is likely not incidental and results in karyotype heterogeneity of cell population.
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Affiliation(s)
- Victoria I Turilova
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky ave., 4, St Petersburg, Russia, 194064.
| | - Tatyana S Goryachaya
- Centre of Cell Technologies, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky ave., 4, St Petersburg, Russia, 194064
| | - Tatiana K Yakovleva
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky ave., 4, St Petersburg, Russia, 194064
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8
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9
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Establishment of fast-growing serum-free immortalised cells from Chinese hamster lung tissues for biopharmaceutical production. Sci Rep 2020; 10:17612. [PMID: 33077772 PMCID: PMC7572389 DOI: 10.1038/s41598-020-74735-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/15/2020] [Indexed: 11/09/2022] Open
Abstract
Chinese hamster (Cricetulus griseus) ovary-derived Chinese hamster ovary (CHO) cells are the most commonly used mammalian hosts for the industrial production of recombinant therapeutics because of their ability to fold, assemble, and perform post-translational modifications, such as glycosylation, on proteins. They are also valuable for their ability to grow in serum-free suspension cultures. In this study, we established a cell line derived from lung tissue of Chinese hamsters, named Chinese hamster lung (CHL)-YN cells. The biosafety of CHL-YN cells was confirmed by in vitro sterility testing, mycoplasma detection, and reverse transcriptase assays. One of the key characteristics of CHL-YN cells was their doubling time of 8.1 h in chemically defined culture medium; thus, they proliferate much faster than conventional CHO cells and general mammalian cells. Transgenes could be introduced into CHL-YN cells with high efficiency. Finally, between 50% to > 100% of the amount of glycosylated immunoglobulin G (IgG)1 produced by CHO-K1 cells was produced by CHL-YN cells over a shorter period of time. In summary, fast-growing CHL-YN cells are a unique cell line for producing recombinant proteins.
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10
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Heffner K, Hizal DB, Majewska NI, Kumar S, Dhara VG, Zhu J, Bowen M, Hatton D, Yerganian G, Yerganian A, O'Meally R, Cole R, Betenbaugh M. Expanded Chinese hamster organ and cell line proteomics profiling reveals tissue-specific functionalities. Sci Rep 2020; 10:15841. [PMID: 32985598 PMCID: PMC7522264 DOI: 10.1038/s41598-020-72959-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are the predominant production vehicle for biotherapeutics. Quantitative proteomics data were obtained from two CHO cell lines (CHO-S and CHO DG44) and compared with seven Chinese hamster (Cricetulus griseus) tissues (brain, heart, kidney, liver, lung, ovary and spleen) by tandem mass tag (TMT) labeling followed by mass spectrometry, providing a comprehensive hamster tissue and cell line proteomics atlas. Of the 8470 unique proteins identified, high similarity was observed between CHO-S and CHO DG44 and included increases in proteins involved in DNA replication, cell cycle, RNA processing, and chromosome processing. Alternatively, gene ontology and pathway analysis in tissues indicated increased protein intensities related to important tissue functionalities. Proteins enriched in the brain included those involved in acidic amino acid metabolism, Golgi apparatus, and ion and phospholipid transport. The lung showed enrichment in proteins involved in BCAA catabolism, ROS metabolism, vesicle trafficking, and lipid synthesis while the ovary exhibited enrichments in extracellular matrix and adhesion proteins. The heart proteome included vasoconstriction, complement activation, and lipoprotein metabolism enrichments. These detailed comparisons of CHO cell lines and hamster tissues will enhance understanding of the relationship between proteins and tissue function and pinpoint potential pathways of biotechnological relevance for future cell engineering.
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Affiliation(s)
- Kelley Heffner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.,AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | - Deniz Baycin Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Natalia I Majewska
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.,AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | - Swetha Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Venkata Gayatri Dhara
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jie Zhu
- AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | - Michael Bowen
- Allogene Therapeutics, Product and Process Development, South San Francisco, CA, USA
| | - Diane Hatton
- AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | | | | | - Robert O'Meally
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Robert Cole
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
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11
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Weinguny M, Klanert G, Eisenhut P, Jonsson A, Ivansson D, Lövgren A, Borth N. Directed evolution approach to enhance efficiency and speed of outgrowth during single cell subcloning of Chinese Hamster Ovary cells. Comput Struct Biotechnol J 2020; 18:1320-1329. [PMID: 32612755 PMCID: PMC7306589 DOI: 10.1016/j.csbj.2020.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/16/2020] [Accepted: 05/17/2020] [Indexed: 01/08/2023] Open
Abstract
Chinese Hamster Ovary (CHO) cells are the working horse of the pharmaceutical industry. To obtain high producing cell clones and to satisfy regulatory requirements single cell cloning is a necessary step in cell line development. However, it is also a tedious, labor intensive and expensive process. Here we show an easy way to enhance subclonability using subcloning by single cell sorting itself as the selection pressure, resulting in improved subcloning performance of three different host cell lines. These improvements in subclonability also lead to an enhanced cellular growth behavior during standard batch culture. RNA-seq was performed to shed light on the underlying mechanisms, showing that there is little overlap in differentially expressed genes or associated pathways between the cell lines, each finding their individual strategy for optimization. However, in all three cell lines pathways associated with the extracellular matrix were found to be enriched, indicating that cells struggle predominantly with their microenvironment and possibly lack of cell-to-cell contact. The observed small overlap may hint that there are multiple ways for a cell line to achieve a certain phenotype due to numerous genetic and subsequently metabolic redundancies.
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Key Words
- CHO
- CHO cells
- CHO, Chinese hamster ovary
- Cell line development
- Cell sorting
- Chinese Hamster Ovary Cells
- CoI, clusters of interest
- DE, directed evolved
- Directed Evolution
- ECM, extracellular matrix
- ES, enrichment score
- FACS
- FACS, fluorescent-activated cell sorting
- Fluorescent-activated cell sorting
- GSEA, gene set analysis
- Growth enhancement
- Growth improvement
- LDC, limiting dilution cloning
- NES, negative enrichment score
- PC, principal component
- PCA, principal component analysis
- POI, product of interest
- RNA Sequencing
- RNA-Seq
- RNA-Seq, RNA sequencing
- SCC, single cell cloning
- Single Cell Cloning
- Single Cell Subcloning
- Subcloning
- lfcSE, logfoldstandard error
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Affiliation(s)
- Marcus Weinguny
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Gerald Klanert
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Peter Eisenhut
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | | | | | | | - Nicole Borth
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
- Corresponding author at: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria.
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12
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Abstract
Following the success of and the high demand for recombinant protein-based therapeutics during the last 25 years, the pharmaceutical industry has invested significantly in the development of novel treatments based on biologics. Mammalian cells are the major production systems for these complex biopharmaceuticals, with Chinese hamster ovary (CHO) cell lines as the most important players. Over the years, various engineering strategies and modeling approaches have been used to improve microbial production platforms, such as bacteria and yeasts, as well as to create pre-optimized chassis host strains. However, the complexity of mammalian cells curtailed the optimization of these host cells by metabolic engineering. Most of the improvements of titer and productivity were achieved by media optimization and large-scale screening of producer clones. The advances made in recent years now open the door to again consider the potential application of systems biology approaches and metabolic engineering also to CHO. The availability of a reference genome sequence, genome-scale metabolic models and the growing number of various “omics” datasets can help overcome the complexity of CHO cells and support design strategies to boost their production performance. Modular design approaches applied to engineer industrially relevant cell lines have evolved to reduce the time and effort needed for the generation of new producer cells and to allow the achievement of desired product titers and quality. Nevertheless, important steps to enable the design of a chassis platform similar to those in use in the microbial world are still missing. In this review, we highlight the importance of mammalian cellular platforms for the production of biopharmaceuticals and compare them to microbial platforms, with an emphasis on describing novel approaches and discussing still open questions that need to be resolved to reach the objective of designing enhanced modular chassis CHO cell lines.
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13
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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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14
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Yamano-Adachi N, Ogata N, Tanaka S, Onitsuka M, Omasa T. Characterization of Chinese hamster ovary cells with disparate chromosome numbers: Reduction of the amount of mRNA relative to total protein. J Biosci Bioeng 2019; 129:121-128. [PMID: 31303495 DOI: 10.1016/j.jbiosc.2019.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/06/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
Chromosomes in Chinese hamster ovary (CHO) cells are labile. We have shown that high-chromosome-number CHO cells have greater potential to become robust producers of recombinant proteins. One explanation being the increase in transgene integration sites. However, high-chromosome-number cell clones produce more IgG3 following culture of single-cell clones, even under conditions that yield the same number of integrations as cells with normal chromosome numbers. Here, we characterized high-chromosome-number cells by transcriptome analysis. RNA standards were used to normalize transcriptomes of cells that had different chromosome numbers. Our results demonstrate that the mRNA ratio of β-actin and many other genes in high-chromosome-number cells to that in normal-chromosome-number cells per cell (normalized to RNA standards) was smaller than the equivalent genomic size and cell volume ratios. Many genes encoding membrane proteins are more highly expressed in high-chromosome-number cells, probably due to differences in cell size caused by the increase in chromosomes. In addition, genes related to histone modification and lipid metabolism are differentially expressed. The reduced transcript level required per protein produced in total and the different intracellular signal transductions might be key factors for antibody production.
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Affiliation(s)
- Noriko Yamano-Adachi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Norichika Ogata
- Nihon BioData Corporation, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan.
| | - Sho Tanaka
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, Tokushima 770-8506, Japan.
| | - Takeshi Omasa
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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15
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Bandyopadhyay AA, O’Brien SA, Zhao L, Fu HY, Vishwanathan N, Hu WS. Recurring genomic structural variation leads to clonal instability and loss of productivity. Biotechnol Bioeng 2019; 116:41-53. [PMID: 30144379 PMCID: PMC7058117 DOI: 10.1002/bit.26823] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/13/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022]
Abstract
Chinese hamster ovary cells, commonly used in the production of therapeutic proteins, are aneuploid. Their chromosomes bear structural abnormality and undergo changes in structure and number during cell proliferation. Some production cell lines are unstable and lose their productivity over time in the manufacturing process and during the product's life cycle. To better understand the link between genomic structural changes and productivity stability, an immunoglobulin G producing cell line was successively single-cell cloned to obtain subclones that retained or lost productivity, and their genomic features were compared. Although each subclone started with a single karyotype, the progeny quickly diversified to a population with a distribution of chromosome numbers that is not distinctive from the parent and among subclones. The comparative genomic hybridization (CGH) analysis showed that the extent of copy variation of gene coding regions among different subclones stayed at levels of a few percent. Genome regions that were prone to loss of copies, including one with a product transgene integration site, were identified in CGH. The loss of the transgene copy was accompanied by loss of transgene transcript level. Sequence analysis of the host cell and parental producing cell showed prominent structural variations within the regions prone to loss of copies. Taken together, we demonstrated the transient nature of clonal homogeneity in cell line development and the retention of a population distribution of chromosome numbers; we further demonstrated that structural variation in the transgene integration region caused cell line instability. Future cell line development may target the transgene into structurally stable regions.
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Affiliation(s)
| | | | | | | | | | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN 55455-0132 USA
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16
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Auer N, Hrdina A, Hiremath C, Vcelar S, Baumann M, Borth N, Jadhav V. ChromaWizard: An open source image analysis software for multicolor fluorescence in situ hybridization analysis. Cytometry A 2018; 93:749-754. [PMID: 30089195 PMCID: PMC6175483 DOI: 10.1002/cyto.a.23505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/06/2018] [Accepted: 05/16/2018] [Indexed: 02/02/2023]
Abstract
Multicolor image analysis finds its applications in a broad range of biological studies. Specifically, multiplex fluorescence in situ hybridization (M-FISH) for chromosome painting facilitates the analysis of individual chromosomes in complex metaphase spreads and is widely used to detect both numerical and structural aberrations. While this is well established for human and mouse karyotypes, for which species sophisticated software and analysis tools are available, other organisms and species are less well served. Commercially available software is proprietary and not easily adaptable to other karyotypes. Therefore, a publically available open source software that combines flexibility and customizable functionalities is needed. Here we present such a tool called "ChromaWizard" which is based on popular scientific image analysis libraries (OpenCV, scikit-image, and NumPy). We demonstrate its functionality on the example of primary Chinese hamster (Cricetulus griseus) fibroblasts metaphase spreads and on Chinese Hamster Ovary cell lines known for the large number of chromosomal rearrangements. The application can be easily adapted to any kind of available labeling kits and is independent of the used organism and instrumentation. It allows direct inspection of the original hybridization signals and enables either manual or automatic assignment of colors, making it a functional and versatile tool that can be used also for other multicolor applications.
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Affiliation(s)
- Norbert Auer
- Austrian Centre for Industrial Biotechnology GmbH, Graz, Austria
| | - Astrid Hrdina
- Austrian Centre for Industrial Biotechnology GmbH, Graz, Austria
| | - Chaitra Hiremath
- Austrian Centre for Industrial Biotechnology GmbH, Graz, Austria
| | - Sabine Vcelar
- Austrian Centre for Industrial Biotechnology GmbH, Graz, Austria
| | - Martina Baumann
- Austrian Centre for Industrial Biotechnology GmbH, Graz, Austria
| | - Nicole Borth
- Austrian Centre for Industrial Biotechnology GmbH, Graz, Austria.,University of Natural Resources and Life Sciences, Vienna, Austria
| | - Vaibhav Jadhav
- Austrian Centre for Industrial Biotechnology GmbH, Graz, Austria
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17
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Genome sequence comparison between Chinese hamster ovary (CHO) DG44 cells and mouse using end sequences of CHO BAC clones based on BAC-FISH results. Cytotechnology 2018; 70:1399-1407. [PMID: 29987698 DOI: 10.1007/s10616-018-0233-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/16/2018] [Indexed: 11/26/2022] Open
Abstract
Chinese hamster ovary (CHO) cells have frequently been used in biotechnology as a mammalian host cell platform for expressing genes of interest. Previously, we constructed a detailed physical chromosomal map of the CHO DG44 cell line by fluorescence in situ hybridization (FISH) imaging using 303 bacterial artificial chromosome (BAC) clones as hybridization probes (BAC-FISH). BAC-FISH results revealed that the two longest chromosomes were completely paired. However, other chromosomes featured partial deletions or rearrangements. In this study, we determined the end sequences of 303 BAC clones (BAC end sequences), which were used for BAC-FISH probes. Among 606 BAC-end sequences (BESs) (forward and reverse ends), 558 could be determined. We performed a comparison between all determined BESs and mouse genome sequences using NCBI BLAST. Among these 558 BESs, 465 showed high homology to mouse chromosomal sequences. We analyzed the locations of these BACs in chromosomes of the CHO DG44 cell line using a physical chromosomal map. From the obtained results, we investigated the regional similarities among CHO chromosomes (A-T) and mouse chromosomes (1-19 and sex) about 217 BESs (46.7% of 465 high homologous BESs). Twenty-three specific narrow regions in 13 chromosomes of the CHO DG44 cell line showed high homology to mouse chromosomes, but most of other regions did not show significant correlations with the mouse genome. These results contribute to accurate alignments of chromosomes of Chinese hamster and its genome sequence, analysis of chromosomal instability in CHO cells, and the development of target locations for gene and/or genome editing techniques.
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18
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Vcelar S, Jadhav V, Melcher M, Auer N, Hrdina A, Sagmeister R, Heffner K, Puklowski A, Betenbaugh M, Wenger T, Leisch F, Baumann M, Borth N. Karyotype variation of CHO host cell lines over time in culture characterized by chromosome counting and chromosome painting. Biotechnol Bioeng 2018; 115:165-173. [PMID: 28921524 DOI: 10.1002/bit.26453] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/31/2017] [Accepted: 09/14/2017] [Indexed: 12/20/2022]
Abstract
Genomic rearrangements are a common phenomenon in rapidly growing cell lines such as Chinese hamster ovary (CHO) cells, a feature that in the context of production of biologics may lead to cell line and product instability. Few methods exist to assess such genome wide instability. Here, we use the population distribution of chromosome numbers per cell as well as chromosome painting to quantify the karyotypic variation in several CHO host cell lines. CHO-S, CHO-K1 8 mM glutamine, and CHO-K1 cells adapted to grow in media containing no glutamine were analyzed over up to 6 months in culture. All three cell lines were clearly distinguishable by their chromosome number distribution and by the specific chromosome rearrangements that were present in each population. Chromosome Painting revealed a predominant karyotype for each cell line at the start of the experiment, completed by a large number of variants present in each population. Over time in culture, the predominant karyotype changed for CHO-S and CHO-K1, with the diversity increasing and new variants appearing, while CHO-K1 0 mM Gln preferred chromosome pattern increased in percent of the population over time. As control, Chinese hamster lung fibroblasts were shown to also contain an increasing number of variants over time in culture.
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Affiliation(s)
- Sabine Vcelar
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Vaibhav Jadhav
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Michael Melcher
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,University of Natural Resources and Life Sciences, Vienna, Austria
| | - Norbert Auer
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Astrid Hrdina
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | | | | | - Anja Puklowski
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Till Wenger
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Friedrich Leisch
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,University of Natural Resources and Life Sciences, Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,University of Natural Resources and Life Sciences, Vienna, Austria
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19
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Stolfa G, Smonskey MT, Boniface R, Hachmann AB, Gulde P, Joshi AD, Pierce AP, Jacobia SJ, Campbell A. CHO-Omics Review: The Impact of Current and Emerging Technologies on Chinese Hamster Ovary Based Bioproduction. Biotechnol J 2017; 13:e1700227. [PMID: 29072373 DOI: 10.1002/biot.201700227] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 01/07/2023]
Abstract
CHO cells are the most prevalent platform for modern bio-therapeutic production. Currently, there are several CHO cell lines used in bioproduction with distinct characteristics and unique genotypes and phenotypes. These differences limit advances in productivity and quality that can be achieved by the most common approaches to bioprocess optimization and cell line engineering. Incorporating omics-based approaches into current bioproduction processes will complement traditional methodologies to maximize gains from CHO engineering and bioprocess improvements. In order to highlight the utility of omics technologies in CHO bioproduction, the authors discuss current applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, lipidomics, fluxomics, glycomics, and multi-omics approaches and the potential they hold for the future of bioproduction. Multiple omics approaches are currently being used to improve CHO bioprocesses; however, the application of these technologies is still limited. As more CHO-omic datasets become available and integrated into systems models, the authors expect significant gains in product yield and quality. While individual omics technologies provide incremental improvements in bioproduction, the authors will likely see the most significant gains by applying multi-omics and systems biology approaches to individual CHO cell lines.
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Affiliation(s)
- Gino Stolfa
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Ryan Boniface
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Paul Gulde
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Atul D Joshi
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Anson P Pierce
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Scott J Jacobia
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Andrew Campbell
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
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20
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Brown AJ, Gibson S, Hatton D, James DC. Transcriptome-Based Identification of the Optimal Reference CHO Genes for Normalisation of qPCR Data. Biotechnol J 2017; 13. [PMID: 28731643 DOI: 10.1002/biot.201700259] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/06/2017] [Indexed: 12/20/2022]
Abstract
Real-time quantitative PCR (qPCR) is the standard method for determination of relative changes in mRNA transcript abundance. Analytical accuracy, precision and reliability are critically dependent on the selection of internal control reference genes. In this study, the authors have identified optimal reference genes that can be utilised universally for qPCR analysis of CHO cell mRNAs. Initially, transcriptomic datasets were analysed to identify eight endogenous genes that exhibited high expression stability across four distinct CHO cell lines sampled in different culture phases. The relative transcript abundance of each gene in 20 diverse, commonly applied experimental conditions was then determined by qPCR analysis. Utilizing GeNorm, BestKeeper and NormFinder algorithms, the authors identified four mRNAs (Gnb1, Fkbp1a, Tmed2 and Mmadhc) that exhibited a highly stable level of expression across all conditions, validating their utility as universally applicable reference genes. Whilst any combination of only two genes can be generally used for normalisation of qPCR data, the authors show that specific combinations of reference genes are particularly suited to discrete experimental conditions. In summary, the authors report the identification of fully validated universal reference genes, optimised primer sequences robust to genomic mutations and simple reference gene pair selection guidelines that enable streamlined qPCR analyses of mRNA abundance in CHO cells with maximum accuracy and precision.
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Affiliation(s)
- Adam J Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, S1 3JD, England
| | - Suzanne Gibson
- Biopharmaceutical Development, MedImmune, Cambridge, CB21 6GH, England
| | - Diane Hatton
- Biopharmaceutical Development, MedImmune, Cambridge, CB21 6GH, England
| | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, S1 3JD, England
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21
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Heffner KM, Hizal DB, Yerganian GS, Kumar A, Can Ö, O’Meally R, Cole R, Chaerkady R, Wu H, Bowen MA, Betenbaugh MJ. Lessons from the Hamster: Cricetulus griseus Tissue and CHO Cell Line Proteome Comparison. J Proteome Res 2017; 16:3672-3687. [DOI: 10.1021/acs.jproteome.7b00382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | - Amit Kumar
- Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Özge Can
- Acibadem University, Medical Biochemistry, Istanbul, Maltepe, Turkey
| | - Robert O’Meally
- Johns Hopkins Medical Institute, Baltimore, Maryland 21205, United States
| | - Robert Cole
- Johns Hopkins Medical Institute, Baltimore, Maryland 21205, United States
| | | | - Herren Wu
- MedImmune, Gaithersburg, Maryland 20878, United States
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22
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Kelly PS, Clarke C, Costello A, Monger C, Meiller J, Dhiman H, Borth N, Betenbaugh MJ, Clynes M, Barron N. Ultra-deep next generation mitochondrial genome sequencing reveals widespread heteroplasmy in Chinese hamster ovary cells. Metab Eng 2017; 41:11-22. [DOI: 10.1016/j.ymben.2017.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/31/2017] [Accepted: 02/07/2017] [Indexed: 10/20/2022]
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23
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Gowtham YK, Saski CA, Harcum SW. Low glucose concentrations within typical industrial operating conditions have minimal effect on the transcriptome of recombinant CHO cells. Biotechnol Prog 2017; 33:771-785. [PMID: 28371311 DOI: 10.1002/btpr.2462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/07/2017] [Indexed: 12/16/2022]
Abstract
Typically, mammalian cell culture medium contains high glucose concentrations that are analogous to diabetic levels in humans, suggesting that mammalian cells are cultivated in excessive glucose. Using RNA-Seq, this study characterized the Chinese hamster ovary (CHO) cell transcriptome under two glucose concentrations to assess the genetic effects associated with metabolic pathways, in addition to other global responses. The initial extracellular glucose concentrations used represented high (30 mM) and low (10 mM) glucose conditions, where at the time the transcriptomes were compared, the glucose concentrations were approximately 24 and 4.4 mM for the mid-exponential cultures, where 4.4 mM represents a common target concentration in the biopharmaceutical industry for controlled fed-batch cultures. A recombinant CHO cell line producing a monoclonal antibody was used, such that the impact on glycosylation genes could be evaluated. Relatively few genes were identified as being significantly different (FDR ≤ 0.01) between the high and low glucose conditions, for example, only 575 genes, and only 40 of these genes had 2-fold or greater differences. Gene expression differences for glycolysis, TCA cycle, and glycosylation-related reactions were minimal and unlikely to have biological significance. This transcriptome study indicates that low glucose concentrations in the culture medium are unlikely to cause any biologically significant or detrimental changes to CHO cells at the transcriptome level. Furthermore, it is well-known that maintaining low glucose concentrations in fed-batch cultures can reduce lactate production, which in turn improves process outcomes. Taken together, the transcriptome data supports the continued development of low glucose-based processes to control lactate. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:771-785, 2017.
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Affiliation(s)
| | - Christopher A Saski
- Inst. of Translational Genomics, Clemson University, Clemson, SC, 29634.,Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634
| | - Sarah W Harcum
- Dept. of Bioengineering, Clemson University, Clemson, SC, 29634
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24
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Lengthening of high-yield production levels of monoclonal antibody-producing Chinese hamster ovary cells by downregulation of breast cancer 1. J Biosci Bioeng 2017; 123:382-389. [DOI: 10.1016/j.jbiosc.2016.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 11/19/2022]
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25
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Dahodwala H, Sharfstein ST. The 'Omics Revolution in CHO Biology: Roadmap to Improved CHO Productivity. Methods Mol Biol 2017; 1603:153-168. [PMID: 28493129 DOI: 10.1007/978-1-4939-6972-2_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Increased understanding of Chinese hamster ovary (CHO) cell physiology has been ushered in upon availability of the parental CHO-K1 cell line genome. Free and openly accessible sequence information has complemented transcriptomic and proteomic studies. The previous decade has also seen an increase in sensitivity and accuracy of proteomic methods due to technology development. In this genomic era, high-throughput screening methods, sophisticated informatic tools, and models continually drive major innovations in cell line development and process engineering. This review describes the various achievements in 'omics techniques and their application to improve recombinant protein expression from CHO cell lines.
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Affiliation(s)
- Hussain Dahodwala
- Vaccine production program (VPP), VRC/NIAID/NIH, Gaithersburg, MD, 20878, USA
- SUNY Polytechnic Institute, 257 Fuller Road, Albany, NY, 12203, USA
| | - Susan T Sharfstein
- Vaccine production program (VPP), VRC/NIAID/NIH, Gaithersburg, MD, 20878, USA.
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26
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Yamano N, Takahashi M, Ali Haghparast SM, Onitsuka M, Kumamoto T, Frank J, Omasa T. Increased recombinant protein production owing to expanded opportunities for vector integration in high chromosome number Chinese hamster ovary cells. J Biosci Bioeng 2016; 122:226-31. [DOI: 10.1016/j.jbiosc.2016.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/28/2015] [Accepted: 01/05/2016] [Indexed: 10/22/2022]
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27
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Feichtinger J, Hernández I, Fischer C, Hanscho M, Auer N, Hackl M, Jadhav V, Baumann M, Krempl PM, Schmidl C, Farlik M, Schuster M, Merkel A, Sommer A, Heath S, Rico D, Bock C, Thallinger GG, Borth N. Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time. Biotechnol Bioeng 2016; 113:2241-53. [PMID: 27072894 PMCID: PMC5006888 DOI: 10.1002/bit.25990] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/15/2016] [Accepted: 04/07/2016] [Indexed: 01/03/2023]
Abstract
The most striking characteristic of CHO cells is their adaptability, which enables efficient production of proteins as well as growth under a variety of culture conditions, but also results in genomic and phenotypic instability. To investigate the relative contribution of genomic and epigenetic modifications towards phenotype evolution, comprehensive genome and epigenome data are presented for six related CHO cell lines, both in response to perturbations (different culture conditions and media as well as selection of a specific phenotype with increased transient productivity) and in steady state (prolonged time in culture under constant conditions). Clear transitions were observed in DNA‐methylation patterns upon each perturbation, while few changes occurred over time under constant conditions. Only minor DNA‐methylation changes were observed between exponential and stationary growth phase; however, throughout a batch culture the histone modification pattern underwent continuous adaptation. Variation in genome sequence between the six cell lines on the level of SNPs, InDels, and structural variants is high, both upon perturbation and under constant conditions over time. The here presented comprehensive resource may open the door to improved control and manipulation of gene expression during industrial bioprocesses based on epigenetic mechanisms. Biotechnol. Bioeng. 2016;113: 2241–2253. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Julia Feichtinger
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Inmaculada Hernández
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Christoph Fischer
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Michael Hanscho
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Norbert Auer
- University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria
| | - Matthias Hackl
- University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria
| | - Vaibhav Jadhav
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Martina Baumann
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Peter M Krempl
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Christian Schmidl
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | | | - Andreas Sommer
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Simon Heath
- Center for Genomic Regulation (CRG), Barcelona, Spain
| | - Daniel Rico
- Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Gerhard G Thallinger
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Nicole Borth
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria. .,University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria.
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28
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Moritz B, Woltering L, Becker PB, Göpfert U. High levels of histone H3 acetylation at the CMV promoter are predictive of stable expression in Chinese hamster ovary cells. Biotechnol Prog 2016; 32:776-86. [DOI: 10.1002/btpr.2271] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/11/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Benjamin Moritz
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich; Germany
- Biomedical Center and Center for Integrated Protein Science, Molecular Biology Division, Ludwig-Maximilians-University; Munich Germany
| | - Laura Woltering
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich; Germany
| | - Peter B. Becker
- Biomedical Center and Center for Integrated Protein Science, Molecular Biology Division, Ludwig-Maximilians-University; Munich Germany
| | - Ulrich Göpfert
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich; Germany
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29
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Yamano N, Kumamoto T, Takahashi M, Frank J, Onitsuka M, Omasa T. Stability difference of each chromosome in Chinese Hamster Ovary cell line. BMC Proc 2015. [PMCID: PMC4685416 DOI: 10.1186/1753-6561-9-s9-p1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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30
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Matsuyama R, Tsutsui T, Lee KH, Onitsuka M, Omasa T. Improved gene amplification by cell-cycle engineering combined with the Cre-loxP system in Chinese hamster ovary cells. J Biosci Bioeng 2015; 120:701-8. [DOI: 10.1016/j.jbiosc.2015.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/07/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
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31
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Ritter A, Voedisch B, Wienberg J, Wilms B, Geisse S, Jostock T, Laux H. Deletion of a telomeric region on chromosome 8 correlates with higher productivity and stability of CHO cell lines. Biotechnol Bioeng 2015; 113:1084-93. [DOI: 10.1002/bit.25876] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 10/01/2015] [Accepted: 10/28/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Anett Ritter
- Novartis Institutes for BioMedical Research; Basel Switzerland
- Novartis Pharma AG; Integrated Biologics Profiling Unit; Werk Klybeck Postfach CH-4002 Basel Switzerland
| | - Bernd Voedisch
- Novartis Institutes for BioMedical Research; Basel Switzerland
| | | | - Burkhard Wilms
- Novartis Pharma AG; Integrated Biologics Profiling Unit; Werk Klybeck Postfach CH-4002 Basel Switzerland
| | - Sabine Geisse
- Novartis Institutes for BioMedical Research; Basel Switzerland
| | - Thomas Jostock
- Novartis Pharma AG; Integrated Biologics Profiling Unit; Werk Klybeck Postfach CH-4002 Basel Switzerland
| | - Holger Laux
- Novartis Pharma AG; Integrated Biologics Profiling Unit; Werk Klybeck Postfach CH-4002 Basel Switzerland
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Harreither E, Hackl M, Pichler J, Shridhar S, Auer N, Łabaj PP, Scheideler M, Karbiener M, Grillari J, Kreil DP, Borth N. Microarray profiling of preselected CHO host cell subclones identifies gene expression patterns associated with increased production capacity. Biotechnol J 2015; 10:1625-38. [PMID: 26315449 DOI: 10.1002/biot.201400857] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 06/22/2015] [Accepted: 08/21/2015] [Indexed: 01/02/2023]
Abstract
Over the last three decades, product yields from CHO cells have increased dramatically, yet specific productivity (qP) remains a limiting factor. In a previous study, using repeated cell-sorting, we have established different host cell subclones that show superior transient qP over their respective parental cell lines (CHO-K1, CHO-S). The transcriptome of the resulting six cell lines in different biological states (untransfected, mock transfected, plasmid transfected) was first explored by hierarchical clustering and indicated that gene activity associated with increased qP did not stem from a certain cellular state but seemed to be inherent for a high qP host line. We then performed a novel gene regression analysis identifying drivers for an increase in qP. Genes significantly implicated were first systematically tested for enrichment of GO terms using a Bayesian approach incorporating the hierarchical structure of the GO term tree. Results indicated that specific cellular components such as nucleus, ER, and Golgi are relevant for cellular productivity. This was complemented by targeted GSA that tested functionally homogeneous, manually curated subsets of KEGG pathways known to be involved in transcription, translation, and protein processing. Significantly implicated pathways included mRNA surveillance, proteasome, protein processing in the ER and SNARE interactions in vesicular transport.
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Affiliation(s)
- Eva Harreither
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Matthias Hackl
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johannes Pichler
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Smriti Shridhar
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Paweł P Łabaj
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marcel Scheideler
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
| | - Michael Karbiener
- RNA Biology Group, Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
| | - Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - David P Kreil
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria. .,ACIB GmbH, Graz, Austria.
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Fan Y, Jimenez Del Val I, Müller C, Lund AM, Sen JW, Rasmussen SK, Kontoravdi C, Baycin-Hizal D, Betenbaugh MJ, Weilguny D, Andersen MR. A multi-pronged investigation into the effect of glucose starvation and culture duration on fed-batch CHO cell culture. Biotechnol Bioeng 2015; 112:2172-84. [DOI: 10.1002/bit.25620] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 03/01/2015] [Accepted: 04/07/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Yuzhou Fan
- Network Engineering of Eukaryotic Cell Factories; Department of Systems Biology; Technical University of Denmark; Building 223; 2800 Kgs. Lyngby Denmark
- Symphogen A/S; Pederstrupvej; 93, 2750 Ballerup Denmark
| | - Ioscani Jimenez Del Val
- Center for Process Systems Engineering; Department of Chemical Engineering; Imperial College London South Kensington Campus London SW7 2AZ UK
| | | | - Anne Mathilde Lund
- Network Engineering of Eukaryotic Cell Factories; Department of Systems Biology; Technical University of Denmark; Building 223; 2800 Kgs. Lyngby Denmark
| | | | | | - Cleo Kontoravdi
- Center for Process Systems Engineering; Department of Chemical Engineering; Imperial College London South Kensington Campus London SW7 2AZ UK
| | - Deniz Baycin-Hizal
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore Maryland 21218
| | - Michael J. Betenbaugh
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore Maryland 21218
| | | | - Mikael Rørdam Andersen
- Network Engineering of Eukaryotic Cell Factories; Department of Systems Biology; Technical University of Denmark; Building 223; 2800 Kgs. Lyngby Denmark
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Zboray K, Sommeregger W, Bogner E, Gili A, Sterovsky T, Fauland K, Grabner B, Stiedl P, Moll HP, Bauer A, Kunert R, Casanova E. Heterologous protein production using euchromatin-containing expression vectors in mammalian cells. Nucleic Acids Res 2015; 43:e102. [PMID: 25977298 PMCID: PMC4652741 DOI: 10.1093/nar/gkv475] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/29/2015] [Indexed: 01/10/2023] Open
Abstract
Upon stable cell line generation, chromosomal integration site of the vector DNA has a major impact on transgene expression. Here we apply an active gene environment, rather than specified genetic elements, in expression vectors used for random integration. We generated a set of Bacterial Artificial Chromosome (BAC) vectors with different open chromatin regions, promoters and gene regulatory elements and tested their impact on recombinant protein expression in CHO cells. We identified the Rosa26 BAC as the most efficient vector backbone showing a nine-fold increase in both polyclonal and clonal production of the human IgG-Fc. Clonal protein production was directly proportional to integrated vector copy numbers and remained stable during 10 weeks without selection pressure. Finally, we demonstrated the advantages of BAC-based vectors by producing two additional proteins, HIV-1 glycoprotein CN54gp140 and HIV-1 neutralizing PG9 antibody, in bioreactors and shake flasks reaching a production yield of 1 g/l.
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Affiliation(s)
- Katalin Zboray
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria
| | - Wolfgang Sommeregger
- Vienna Institute of BioTechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190, Austria Polymun Scientific GmbH, Klosterneuburg, 3400, Austria
| | - Edith Bogner
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria
| | - Andreas Gili
- Polymun Scientific GmbH, Klosterneuburg, 3400, Austria
| | | | | | - Beatrice Grabner
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria
| | - Patricia Stiedl
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria
| | - Herwig P Moll
- Institute of Pharmacology, Center of Physiology and Pharmacology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, 1090, Austria
| | | | - Renate Kunert
- Vienna Institute of BioTechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Emilio Casanova
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, 1090, Austria Institute of Pharmacology, Center of Physiology and Pharmacology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, 1090, Austria
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Transcriptomic variation between different Chinese hamster ovary cell lines. Biotechnol Lett 2015; 37:1737-45. [PMID: 25967036 DOI: 10.1007/s10529-015-1850-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES To identify transcription markers that uniquely determine specific Chinese hamster ovary (CHO) cell lines and can be used for the identification of cell lines in the process of biopharmaceutical cell-line development. RESULTS Five CHO cell lines with different origins were extensively characterised at the transcriptomic level and the results were compared to their karyotype characterisation. The analysed cell lines differ in their karyotype but, due to the genome instability observed during parental and recombinant cell-line establishment, karyotyping is not the preferred method for accurate identification of the various CHO cell lines. Marker genes unique to a specific cell line were identified by microarrays, and their expression was validated by reverse-transcription quantitative real-time PCR. The analysed cell lines can be differentiated by the presence/absence of detectable marker gene expression. Additionally, the similarity of the transcriptional profiles is dependent on cell-line history but independent of the manipulation steps involved in the recombinant cell-line development process. CONCLUSIONS Certain transcripts can be used as markers for the identification of a CHO cell line undergoing recombinant development and thus represent a powerful tool for ensuring the maintenance of high quality standards.
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Kremkow BG, Baik JY, MacDonald ML, Lee KH. CHOgenome.org 2.0: Genome resources and website updates. Biotechnol J 2015; 10:931-8. [DOI: 10.1002/biot.201400646] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/20/2015] [Accepted: 04/01/2015] [Indexed: 12/18/2022]
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Kaas CS, Kristensen C, Betenbaugh MJ, Andersen MR. Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy. BMC Genomics 2015; 16:160. [PMID: 25887056 PMCID: PMC4359788 DOI: 10.1186/s12864-015-1391-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
Background The DHFR negative CHO DXB11 cell line (also known as DUX-B11 and DUKX) was historically the first CHO cell line to be used for large scale production of heterologous proteins and is still used for production of a number of complex proteins. Results Here we present the genomic sequence of the CHO DXB11 genome sequenced to a depth of 33x. Overall a significant genomic drift was seen favoring GC → AT point mutations in line with the chemical mutagenesis strategy used for generation of the cell line. The sequencing depth for each gene in the genome revealed distinct peaks at sequencing depths of 0x, 16x, 33x and 49x coverage corresponding to a copy number in the genome of 0, 1, 2 and 3 copies. This indicate that 17% of the genes are haploid revealing a large number of genes which can be knocked out with relative ease. This tendency of haploidy was furthermore shown to be present in eight additional analyzed CHO genomes (15-20% haploidy) but not in the genome of the Chinese hamster. The dhfr gene is confirmed to be haploid in CHO DXB11; transcriptionally active and the remaining allele contains a G410C point mutation causing a Thr137Arg missense mutation. We find ~2.5 million single nucleotide polymorphisms (SNP’s), 44 gene deletions in the CHO DXB11 genome and 9357 SNP's, which interfere with the coding regions of 3458 genes. Copy number variations for nine CHO genomes were mapped to the chromosomes of the Chinese hamster showing unique signatures for each chromosome. The data indicate that chromosome one and four appear to be more stable over the course of the CHO evolution compared to the other chromosomes thus might presenting the most attractive landing platforms for knock-ins of heterologous genes. Conclusions Our studies reveal an unexpected degree of haploidy in CHO DXB11 and CHO cells in general and highlight the chromosomal changes that have occurred among the CHO cell lines sequenced to date. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1391-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christian Schrøder Kaas
- Mammalian Cell Technology, Global Research Unit, Novo Nordisk A/S, A9.2.36, Novo Nordisk Park, 2760, Måløv, Denmark. .,Network Engineering of Eukaryotic Cell Factories, Technical University of Denmark, Kgs Lyngby, Denmark. .,Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Claus Kristensen
- Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Michael J Betenbaugh
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Mikael Rørdam Andersen
- Network Engineering of Eukaryotic Cell Factories, Technical University of Denmark, Kgs Lyngby, Denmark.
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38
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Toward product attribute control: developments from genome sequencing. Curr Opin Biotechnol 2014; 30:40-4. [DOI: 10.1016/j.copbio.2014.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 05/02/2014] [Indexed: 01/16/2023]
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39
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Toward genome-scale models of the Chinese hamster ovary cells: incentives, status and perspectives. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.54] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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40
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Statistical methods for mining Chinese hamster ovary cell ‘omics data: from differential expression to integrated multilevel analysis of the biological system. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.50] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Accurate comparison of antibody expression levels by reproducible transgene targeting in engineered recombination-competent CHO cells. Appl Microbiol Biotechnol 2014; 98:9723-33. [PMID: 25158835 PMCID: PMC4231286 DOI: 10.1007/s00253-014-6011-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/30/2014] [Accepted: 08/01/2014] [Indexed: 11/23/2022]
Abstract
Over the years, Chinese hamster ovary (CHO) cells have emerged as the major host for expressing biotherapeutic proteins. Traditional methods to generate high-producer cell lines rely on random integration(s) of the gene of interest but have thereby left the identification of bottlenecks as a challenging task. For comparison of different producer cell lines derived from various transfections, a system that provides control over transgene expression behavior is highly needed. This motivated us to develop a novel “DUKX-B11 F3/F” cell line to target different single-chain antibody fragments into the same chromosomal target site by recombinase-mediated cassette exchange (RMCE) using the flippase (FLP)/FLP recognition target (FRT) system. The RMCE-competent cell line contains a gfp reporter fused to a positive/negative selection system flanked by heterospecific FRT (F) variants under control of an external CMV promoter, constructed as “promoter trap”. The expression stability and FLP accessibility of the tagged locus was demonstrated by successive rounds of RMCE. As a proof of concept, we performed RMCE using cassettes encoding two different anti-HIV single-chain Fc fragments, 3D6scFv-Fc and 2F5scFv-Fc. Both targeted integrations yielded homogenous cell populations with comparable intracellular product contents and messenger RNA (mRNA) levels but product related differences in specific productivities. These studies confirm the potential of the newly available “DUKX-B11 F3/F” cell line to guide different transgenes into identical transcriptional control regions by RMCE and thereby generate clones with comparable amounts of transgene mRNA. This new host is a prerequisite for cell biology studies of independent transfections and transgenes.
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42
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43
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Kildegaard HF, Baycin-Hizal D, Lewis NE, Betenbaugh MJ. The emerging CHO systems biology era: harnessing the ‘omics revolution for biotechnology. Curr Opin Biotechnol 2013; 24:1102-7. [DOI: 10.1016/j.copbio.2013.02.007] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/17/2013] [Accepted: 02/09/2013] [Indexed: 11/29/2022]
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44
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Next-generation sequencing technologies and their potential impact on CHO cell-based biomanufacturing. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.52] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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45
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Lee KH, Tsutsui T, Honda K, Asano R, Kumagai I, Ohtake H, Omasa T. Generation of high-producing cell lines by overexpression of cell division cycle 25 homolog A in Chinese hamster ovary cells. J Biosci Bioeng 2013; 116:754-60. [DOI: 10.1016/j.jbiosc.2013.05.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/21/2013] [Accepted: 05/24/2013] [Indexed: 01/25/2023]
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46
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Overexpression of mutant cell division cycle 25 homolog B (CDC25B) enhances the efficiency of selection in Chinese hamster ovary cells. Cytotechnology 2013; 65:1017-26. [PMID: 24248275 DOI: 10.1007/s10616-013-9662-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/18/2013] [Indexed: 10/26/2022] Open
Abstract
The effects of mutant cell division cycle 25 homolog B (CDC25B) overexpression on the generation of cells producing a monoclonal antibody were investigated in Chinese hamster ovary (CHO) cells. Mutant CDC25B (m-CDC25B) expression plasmids were transfected into CHO DG44-derived cells producing a monoclonal antibody, and the frequency of highly producing cells was assessed following gene amplification in the presence of 250 nM methotrexate. Most of the clones obtained from the m-CDC25B-overexpressing cells had higher antibody titers than did mock-transfected control cells. This arose from either higher transgene copy numbers or higher mRNA expression levels for the antibody. However, the high mRNA expression levels were not always accompanied by increases in transgene copy numbers. Our results suggest that cells producing high levels of a monoclonal antibody can be selected efficiently using m-CDC25B overexpression.
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47
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Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Palsson BO. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol 2013; 31:759-65. [PMID: 23873082 DOI: 10.1038/nbt.2624] [Citation(s) in RCA: 283] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 06/03/2013] [Indexed: 12/19/2022]
Abstract
Chinese hamster ovary (CHO) cells, first isolated in 1957, are the preferred production host for many therapeutic proteins. Although genetic heterogeneity among CHO cell lines has been well documented, a systematic, nucleotide-resolution characterization of their genotypic differences has been stymied by the lack of a unifying genomic resource for CHO cells. Here we report a 2.4-Gb draft genome sequence of a female Chinese hamster, Cricetulus griseus, harboring 24,044 genes. We also resequenced and analyzed the genomes of six CHO cell lines from the CHO-K1, DG44 and CHO-S lineages. This analysis identified hamster genes missing in different CHO cell lines, and detected >3.7 million single-nucleotide polymorphisms (SNPs), 551,240 indels and 7,063 copy number variations. Many mutations are located in genes with functions relevant to bioprocessing, such as apoptosis. The details of this genetic diversity highlight the value of the hamster genome as the reference upon which CHO cells can be studied and engineered for protein production.
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48
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Maccani A, Ernst W, Grabherr R. Whole genome sequencing improves estimation of nuclear DNA content of Chinese hamster ovary cells. Cytometry A 2013; 83:893-5. [PMID: 23843198 DOI: 10.1002/cyto.a.22331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/14/2013] [Accepted: 06/07/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Andreas Maccani
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
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49
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Lee KH, Onitsuka M, Honda K, Ohtake H, Omasa T. Rapid construction of transgene-amplified CHO cell lines by cell cycle checkpoint engineering. Appl Microbiol Biotechnol 2013; 97:5731-41. [DOI: 10.1007/s00253-013-4923-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/07/2013] [Accepted: 04/10/2013] [Indexed: 01/02/2023]
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50
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Datta P, Linhardt RJ, Sharfstein ST. An 'omics approach towards CHO cell engineering. Biotechnol Bioeng 2013; 110:1255-71. [DOI: 10.1002/bit.24841] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 12/19/2012] [Accepted: 01/02/2013] [Indexed: 12/15/2022]
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