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Pastor-López EJ, Escolà M, Kisielius V, Arias CA, Carvalho PN, Gorito AM, Ramos S, Freitas V, Guimarães L, Almeida CMR, Müller JA, Küster E, Kilian RM, Diawara A, Ba S, Matamoros V. Potential of nature-based solutions to reduce antibiotics, antimicrobial resistance, and pathogens in aquatic ecosystems. a critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174273. [PMID: 38925380 DOI: 10.1016/j.scitotenv.2024.174273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/03/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
This comprehensive scientific review evaluates the effectiveness of nature-based solutions (NBS) in reducing antibiotics (ABs), combating antimicrobial resistance (AMR), and controlling pathogens in various aquatic environments at different river catchment levels. It covers conventional and innovative treatment wetland configurations for wastewater treatment to reduce pollutant discharge into the aquatic ecosystems as well as exploring how river restoration and saltmarshes can enhance pollutant removal. Through the analysis of experimental studies and case examples, the review shows NBS's potential for providing sustainable and cost-effective solutions to improve the health of aquatic ecosystems. It also evaluates the use of diagnostic indicators to predict NBS effectiveness in removing specific pollutants such as ABs and AMR. The review concludes that NBS are feasible for addressing the new challenges stemming from human activities such as the presence of ABs, AMR and pathogens, contributing to a better understanding of NBS, highlighting success stories, addressing knowledge gaps, and providing recommendations for future research and implementation.
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Affiliation(s)
- Edward J Pastor-López
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain
| | - Mònica Escolà
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain
| | - Vaidotas Kisielius
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Carlos A Arias
- Department of Biology, Aarhus University, Aarhus, Denmark; WATEC - Centre for Water Technology, Aarhus University, Aarhus, Denmark
| | - Pedro N Carvalho
- Department of Environmental Science, Aarhus University, Roskilde, Denmark; WATEC - Centre for Water Technology, Aarhus University, Aarhus, Denmark
| | - Ana M Gorito
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal
| | - Sandra Ramos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal; Faculty of Sciences, University of Porto, Porto, Portugal
| | - Vânia Freitas
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal
| | - Laura Guimarães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal; Faculty of Sciences, University of Porto, Porto, Portugal
| | - Jochen A Müller
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Eberhard Küster
- Helmholtz Centre for Environmental Research - UFZ, Dept. Bioanalytical Ecotoxicology, Leipzig, Germany
| | - R M Kilian
- Kilian Water Ltd., Torupvej 4, 8654 Bryrup, Denmark
| | - Abdoulaye Diawara
- Department of Geology and Mines, École Nationale d'Ingénieurs - Abderhamane Baba Touré (ENI-ABT), Bamako, Mali
| | - Sidy Ba
- Department of Geology and Mines, École Nationale d'Ingénieurs - Abderhamane Baba Touré (ENI-ABT), Bamako, Mali
| | - Víctor Matamoros
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain.
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2
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Lee Z, Wan J, Shen A, Barnard G. Gene copy number, gene configuration and LC/HC mRNA ratio impact on antibody productivity and product quality in targeted integration CHO cell lines. Biotechnol Prog 2024; 40:e3433. [PMID: 38321634 DOI: 10.1002/btpr.3433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/01/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
The augmentation of transgene copy numbers is a prevalent approach presumed to enhance transcriptional activity and product yield. CHO cell lines engineered via targeted integration (TI) offer an advantageous platform for investigating the interplay between gene copy number, mRNA abundance, product yield, and product quality. Our investigation revealed that incrementally elevating the gene copy numbers of both IgG heavy chain (HC) and light chain (LC) concurrently resulted in the attainment of plateaus in mRNA levels and product titers, notably occurring beyond four to five gene copies integrated at the same TI site. Furthermore, maintaining a fixed gene copy number while varying the position of genes within the vector influenced the LC/HC mRNA ratio, which subsequently exerted a substantial impact on product titer. Moreover, manipulation of the LC/HC gene ratio through the introduction of surplus LC gene copies led to heightened LC mRNA expression and a reduction in the levels of high molecular weight species. It is noteworthy that the effects of excess LC on product titer were dependent on the specific molecule under consideration. The strategic utilization of PCR tags enabled precise quantification of transcription from each expression slot within the vector, facilitating the identification of highly expressive and less expressive slots. Collectively, these findings significantly enhance our understanding of stable antibody production in TI CHO cell lines.
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Affiliation(s)
- Zion Lee
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
| | - Jun Wan
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
| | - Amy Shen
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
| | - Gavin Barnard
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
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3
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Engineering of Chinese hamster ovary cells for co-overexpressing MYC and XBP1s increased cell proliferation and recombinant EPO production. Sci Rep 2023; 13:1482. [PMID: 36707606 PMCID: PMC9883479 DOI: 10.1038/s41598-023-28622-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/20/2023] [Indexed: 01/29/2023] Open
Abstract
Improving the cellular capacity of Chinese hamster ovary (CHO) cells to produce large amounts of therapeutic proteins remains a major challenge for the biopharmaceutical industry. In previous studies, we observed strong correlations between the performance of CHO cells and expression of two transcription factors (TFs), MYC and XBP1s. Here, we have evaluated the effective of overexpression of these two TFs on CHO cell productivity. To address this goal, we generated an EPO-producing cell line (CHOEPO) using a targeted integration approach, and subsequently engineered it to co-overexpress MYC and XBP1s (a cell line referred to as CHOCXEPO). Cells overexpressing MYC and XBP1s increased simultaneously viable cell densities and EPO production, leading to an enhanced overall performance in cultures. These improvements resulted from the individual effect of each TF in the cell behaviour (i.e., MYC-growth and XBP1s-productivity). An evaluation of the CHOCXEPO cells under different environmental conditions (temperature and media glucose concentration) indicated that CHOCXEPO cells increased cell productivity in high glucose concentration. This study showed the potential of combining TF-based cell engineering and process optimisation for increasing CHO cell productivity.
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4
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Use of ubiquitous chromatin opening elements (UCOE) as tools to maintain transgene expression in biotechnology. Comput Struct Biotechnol J 2022; 21:275-283. [PMID: 36582439 PMCID: PMC9764128 DOI: 10.1016/j.csbj.2022.11.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Amongst the most important outputs of the biopharmaceutical industry are recombinant proteins, many of which are produced by integrating transgenes into the genomes of mammalian cells. However, expression is highly variable and can be unstable during prolonged culture. This is often due to epigenetic mechanisms silencing the transgenes. To combat this problem, vectors have been engineered to include ubiquitous chromatin opening elements (UCOEs) that protect against silencing. Here, we recount the evidence that UCOEs can modify chromatin environments and benefit biomanufacturing.
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5
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Screening of CHO-K1 endogenous promoters for expressing recombinant proteins in mammalian cell cultures. Plasmid 2022; 119-120:102620. [DOI: 10.1016/j.plasmid.2022.102620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 12/28/2022]
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Chang M, Kumar A, Kumar S, Huhn S, Timp W, Betenbaugh M, Du Z. Epigenetic Comparison of CHO Hosts and Clones Reveals Divergent Methylation and Transcription Patterns Across Lineages. Biotechnol Bioeng 2022; 119:1062-1076. [PMID: 35028935 DOI: 10.1002/bit.28036] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/08/2021] [Accepted: 12/26/2021] [Indexed: 11/11/2022]
Abstract
In this study, we examined DNA methylation and transcription profiles of recombinant clones derived from two different Chinese hamster ovary hosts. We found striking epigenetic differences between the clones, with global hypomethylation in the host 1 clones that produce bispecific antibody with higher productivity and complex assembly efficiency. Whereas the methylation patterns were found mostly inherited from the host, the host 1 clones exhibited continued demethylation reflected by the hypomethylation of newly emerged differential methylation regions (DMRs) even at the clone development stage. Several interconnected biological functions and pathways including cell adhesion, regulation of ion transport, and cholesterol biosynthesis were significantly altered between the clones at the RNA expression level and contained DMR in the promoter and/or gene-body of the transcripts, suggesting epigenetic regulation. Indeed, expression changes of epigenetic regulators were observed including writers (Dnmt1, Setdb1), readers (Mecp2), and erasers (Tet3, Kdm3a, Kdm1b/5c) involved in CpG methylation, histone methylation and heterochromatin maintenance. In addition, we identified putative transcription factors that may be readers or effectors of the epigenetic regulation in these clones. By combining transcriptomics with DNA methylation data, we identified potential processes and factors that may contribute to the variability in cell physiology between different production hosts. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Meiping Chang
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Amit Kumar
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Swetha Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
| | - Steven Huhn
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
| | - Zhimei Du
- Process Cell Sciences, Biologics Process R&D, Merck & Co., Inc., Kenilworth, NJ, USA
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Marx N, Dhiman H, Schmieder V, Freire CM, Nguyen LN, Klanert G, Borth N. Enhanced targeted DNA methylation of the CMV and endogenous promoters with dCas9-DNMT3A3L entails distinct subsequent histone modification changes in CHO cells. Metab Eng 2021; 66:268-282. [PMID: 33965614 DOI: 10.1016/j.ymben.2021.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/02/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023]
Abstract
With the emergence of new CRISPR/dCas9 tools that enable site specific modulation of DNA methylation and histone modifications, more detailed investigations of the contribution of epigenetic regulation to the precise phenotype of cells in culture, including recombinant production subclones, is now possible. These also allow a wide range of applications in metabolic engineering once the impact of such epigenetic modifications on the chromatin state is available. In this study, enhanced DNA methylation tools were targeted to a recombinant viral promoter (CMV), an endogenous promoter that is silenced in its native state in CHO cells, but had been reactivated previously (β-galactoside α-2,6-sialyltransferase 1) and an active endogenous promoter (α-1,6-fucosyltransferase), respectively. Comparative ChIP-analysis of histone modifications revealed a general loss of active promoter histone marks and the acquisition of distinct repressive heterochromatin marks after targeted methylation. On the other hand, targeted demethylation resulted in autologous acquisition of active promoter histone marks and loss of repressive heterochromatin marks. These data suggest that DNA methylation directs the removal or deposition of specific histone marks associated with either active, poised or silenced chromatin. Moreover, we show that de novo methylation of the CMV promoter results in reduced transgene expression in CHO cells. Although targeted DNA methylation is not efficient, the transgene is repressed, thus offering an explanation for seemingly conflicting reports about the source of CMV promoter instability in CHO cells. Importantly, modulation of epigenetic marks enables to nudge the cell into a specific gene expression pattern or phenotype, which is stabilized in the cell by autologous addition of further epigenetic marks. Such engineering strategies have the added advantage of being reversible and potentially tunable to not only turn on or off a targeted gene, but also to achieve the setting of a desirable expression level.
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Affiliation(s)
- Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Heena Dhiman
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Valerie Schmieder
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | | | - Ly Ngoc Nguyen
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Gerald Klanert
- Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Nicole Borth
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria.
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Gödecke N, Herrmann S, Hauser H, Mayer-Bartschmid A, Trautwein M, Wirth D. Rational Design of Single Copy Expression Cassettes in Defined Chromosomal Sites Overcomes Intraclonal Cell-to-Cell Expression Heterogeneity and Ensures Robust Antibody Production. ACS Synth Biol 2021; 10:145-157. [PMID: 33382574 DOI: 10.1021/acssynbio.0c00519] [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: 11/30/2022]
Abstract
The expression of endogenous genes as well as transgenes depends on regulatory elements within and surrounding genes as well as their epigenetic modifications. Members of a cloned cell population often show pronounced cell-to-cell heterogeneity with respect to the expression of a certain gene. To investigate the heterogeneity of recombinant protein expression we targeted cassettes into two preselected chromosomal hot-spots in Chinese hamster ovary (CHO) cells. Depending on the gene of interest and the design of the expression cassette, we found strong expression variability that could be reduced by epigenetic modifiers, but not by site-specific recruitment of the modulator dCas9-VPR. In particular, the implementation of ubiquitous chromatin opening elements (UCOEs) reduced cell-to-cell heterogeneity and concomitantly increased expression. The application of this method to recombinant antibody expression confirmed that rational design of cell lines for production of transgenes with predictable and high titers is a promising approach.
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Affiliation(s)
- Natascha Gödecke
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Sabrina Herrmann
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Hansjörg Hauser
- Staff Unit Scientific Strategy, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | | | | | - Dagmar Wirth
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
- Institute of Experimental Hematology, Medical University Hannover, Hannover 30625, Germany
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9
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Puente-Massaguer E, Grau-Garcia P, Strobl F, Grabherr R, Striedner G, Lecina M, Gòdia F. Accelerating HIV-1 VLP production using stable High Five insect cell pools. Biotechnol J 2020; 16:e2000391. [PMID: 33247883 DOI: 10.1002/biot.202000391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/21/2020] [Indexed: 12/25/2022]
Abstract
Stable cell pools are receiving a renewed interest as a potential alternative system to clonal cell lines. The shorter development timelines and the capacity to achieve high product yields make them an interesting approach for recombinant protein production. In this study, stable High Five cell pools are assessed for the production of a simple protein, mCherry, and the more complex HIV-1 Gag-eGFP virus-like particles (VLPs). Random integration coupled to fluorescence-activated cell sorting (FACS) in suspension conditions is applied to accelerate the stable cell pool generation process and enrich it with high producer cells. This methodology is successfully transferred to a bioreactor for VLP production, resulting in a 2-fold increase in VLP yields with respect to shake flask cultures. In these conditions, maximum viable cell concentration improves by 1.5-fold, and by-product formation is significantly reduced. Remarkably, a global increase in the uptake of amino acids in the Gag-eGFP stable cell pool is observed when compared with parental High Five cells, reflecting the additional metabolic burden associated with VLP production. These results suggest that stable High Five cell pools are a robust and powerful approach to produce VLPs and other recombinant proteins, and put the basis for future studies aiming to scale up this system.
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Affiliation(s)
- Eduard Puente-Massaguer
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain
| | - Paula Grau-Garcia
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain
| | - Florian Strobl
- Austrian Centre of Industrial Biotechnology (acib GmbH), Vienna, 1010, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Reingard Grabherr
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Martí Lecina
- IQS School of Engineering, Universitat Ramón Llull, Barcelona, 08017, Spain
| | - Francesc Gòdia
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain
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10
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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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Qin Y, Tang T, Li W, Liu Z, Yang X, Shi X, Sun G, Liu X, Wang M, Liang X, Cong P, Mo D, Liu X, Chen Y, He Z. Bone Morphogenetic Protein 15 Knockdown Inhibits Porcine Ovarian Follicular Development and Ovulation. Front Cell Dev Biol 2019; 7:286. [PMID: 31803742 PMCID: PMC6877722 DOI: 10.3389/fcell.2019.00286] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/04/2019] [Indexed: 12/21/2022] Open
Abstract
Bone morphogenetic protein 15 (BMP15) is strongly associated with animal reproduction and woman reproductive disease. As a multifunctional oocyte-specific secret factor, BMP15 controls female fertility and follicular development in both species-specific and dosage-sensitive manners. Previous studies found that BMP15 played a critical role in follicular development and ovulation rate in mono-ovulatory mammalian species, especially in sheep and human, but study on knockout mouse model implied that BMP15 possibly has minimal impact on female fertility of poly-ovulatory species. However, this needs to be validated in other poly-ovulatory species. To investigate the regulatory role of BMP15 on porcine female fertility, we generated a BMP15-knockdown pig model through somatic nuclear transfer technology. The BMP15-knockdown gilts showed markedly reduced fertility accompanied by phenotype of dysplastic ovaries containing significantly declined number of follicles, increased number of abnormal follicles, and abnormally enlarged antral follicles resulting in disordered ovulation, which is remarkably different from the unchanged fertility observed in BMP15 knockout mice. Molecular and transcriptome analysis revealed that the knockdown of BMP15 significantly affected both granulosa cells (GCs) and oocytes development, including suppression of cell proliferation, differentiation, and follicle stimulating hormone receptor (Fshr) expression, leading to premature luteinization and reduced estradiol (E2) production in GCs, and simultaneously decreased quality and meiotic maturation of oocyte. Our results provide in vivo evidence of the essential role of BMP15 in porcine ovarian and follicular development, and new insight into the complicated regulatory function of BMP15 in female fertility of poly-ovulatory species.
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Affiliation(s)
- Yufeng Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhiguo Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaoliang Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Guanjie Sun
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Min Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinyu Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiqing Cong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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12
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Coronel J, Heinrich C, Klausing S, Noll T, Figueredo‐Cardero A, Castilho LR. Perfusion process combining low temperature and valeric acid for enhanced recombinant factor VIII production. Biotechnol Prog 2019; 36:e2915. [DOI: 10.1002/btpr.2915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/09/2019] [Accepted: 09/17/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Juliana Coronel
- Federal University of Rio de Janeiro (UFRJ), COPPECell Culture Engineering Laboratory Rio de Janeiro RJ Brazil
| | | | | | - Thomas Noll
- Bielefeld UniversityInstitute of Cell Culture Technology, Universitätsstraße 25 Bielefeld Germany
| | | | - Leda R. Castilho
- Federal University of Rio de Janeiro (UFRJ), COPPECell Culture Engineering Laboratory Rio de Janeiro RJ Brazil
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13
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Tharmalingam T, Barkhordarian H, Tejeda N, Daris K, Yaghmour S, Yam P, Lu F, Goudar C, Munro T, Stevens J. Characterization of phenotypic and genotypic diversity in subclones derived from a clonal cell line. Biotechnol Prog 2019; 34:613-623. [PMID: 29882350 PMCID: PMC6099272 DOI: 10.1002/btpr.2666] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/09/2018] [Indexed: 12/19/2022]
Abstract
Regulatory guidelines require the sponsors to provide assurance of clonality of the production cell line, and when such evidence is not available, additional studies are typically required to further ensure consistent long‐term manufacturing of the product. One potential approach to provide such assurance of clonal derivation of a production cell line is to characterize subclones generated from the original cell line and assess their phenotypic and genotypic similarity with the hypothesis that cell lines derived from a clonal bank will share performance, productivity and product quality characteristics. In this study, a production cell line that was cloned by a validated FACS approach coupled with day 0 imaging for verification of single‐cell deposition was subcloned using validated FACS and imaging methods. A total of 46 subclones were analyzed for growth, productivity, product quality, copy number, and integration site analysis. Significant diversity in cell growth, protein productivity, product quality attributes, and copy number was observed between the subclones, despite stability of the parent clone over time. The diversity in protein productivity and quality of the subclones were reproduced across time and production scales, suggesting that the resulting population post sub‐cloning originating from a single cell is stable but with unique properties. Overall, this work demonstrates that the characteristics of isolated subclones are not predictive of a clonally derived parental clone. Consequently, the analysis of subclones may not be an effective approach to demonstrate clonal origin of a cell bank. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:613–623, 2018
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Affiliation(s)
- Tharmala Tharmalingam
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Hedieh Barkhordarian
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Nicole Tejeda
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Kristi Daris
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Sam Yaghmour
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Pheng Yam
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Fang Lu
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Chetan Goudar
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Trent Munro
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
| | - Jennitte Stevens
- Drug Substance Technologies, Process Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320
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14
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Rodríguez MC, Ceaglio N, Antuña S, Tardivo MB, Etcheverrigaray M, Prieto C. Production of Therapeutic Enzymes by Lentivirus Transgenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1148:25-54. [PMID: 31482493 DOI: 10.1007/978-981-13-7709-9_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Since ERT for several LSDs treatment has emerged at the beginning of the 1980s with Orphan Drug approval, patients' expectancy and life quality have been improved. Most LSDs treatment are based on the replaced of mutated or deficient protein with the natural or recombinant protein.One of the main ERT drawback is the high drug prices. Therefore, different strategies trying to optimize the global ERT biotherapeutic production have been proposed. LVs, a gene delivery tool, can be proposed as an alternative method to generate stable cell lines in manufacturing of recombinant proteins. Since LVs have been used in human gene therapy, clinical trials, safety testing assays and procedures have been developed. Moreover, one of the main advantages of LVs strategy to obtain manufacturing cell line is the short period required as well as the high protein levels achieved.In this chapter, we will focus on LVs as a recombinant protein production platform and we will present a case study that employs LVs to express in a manufacturing cell line, alpha-Galactosidase A (rhαGAL), which is used as ERT for Fabry disease treatment.
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Affiliation(s)
| | - Natalia Ceaglio
- Cell Culture Laboratory, UNL, CONICET, FBCB, Santa Fe, Argentina
| | | | | | | | - Claudio Prieto
- Cell Culture Laboratory, UNL, FBCB, Santa Fe, Argentina.
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15
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Patel NA, Anderson CR, Terkildsen SE, Davis RC, Pack LD, Bhargava S, Clarke HR. Antibody expression stability in CHO clonally derived cell lines and their subclones: Role of methylation in phenotypic and epigenetic heterogeneity. Biotechnol Prog 2018; 34:635-649. [DOI: 10.1002/btpr.2655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/24/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Neha A. Patel
- Dept. of Bioprocess Development; Seattle Genetics; Bothell WA 98021
| | | | | | - Ray C. Davis
- Dept. of Bioprocess Development; Seattle Genetics; Bothell WA 98021
| | - Laura D. Pack
- Dept. of CMC Statistics; Seattle Genetics; Bothell WA 98021
| | - Swapnil Bhargava
- Dept. of Bioprocess Development; Seattle Genetics; Bothell WA 98021
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16
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Marx N, Grünwald-Gruber C, Bydlinski N, Dhiman H, Ngoc Nguyen L, Klanert G, Borth N. CRISPR-Based Targeted Epigenetic Editing Enables Gene Expression Modulation of the Silenced Beta-Galactoside Alpha-2,6-Sialyltransferase 1 in CHO Cells. Biotechnol J 2018; 13:e1700217. [DOI: 10.1002/biot.201700217] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/01/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Nicolas Marx
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
| | - Clemens Grünwald-Gruber
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
| | - Nina Bydlinski
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
| | - Heena Dhiman
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
| | - Ly Ngoc Nguyen
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
| | - Gerald Klanert
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
| | - Nicole Borth
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
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17
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Soo BPC, Tay J, Ng S, Ho SCL, Yang Y, Chao SH. Correlation Between Expression of Recombinant Proteins and Abundance of H3K4Me3 on the Enhancer of Human Cytomegalovirus Major Immediate-Early Promoter. Mol Biotechnol 2017; 59:315-322. [DOI: 10.1007/s12033-017-0019-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Chen K, Li D, Li H, Li B, Li J, Huang L, Li R, Xu X, Jiang L, Jiang C, Gu H, Fang J. Genetic analysis of heterogeneous sub-clones in recombinant Chinese hamster ovary cells. Appl Microbiol Biotechnol 2017; 101:5785-5797. [DOI: 10.1007/s00253-017-8331-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 05/03/2017] [Accepted: 05/06/2017] [Indexed: 01/11/2023]
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19
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Bandyopadhyay AA, Khetan A, Malmberg LH, Zhou W, Hu WS. Advancement in bioprocess technology: parallels between microbial natural products and cell culture biologics. J Ind Microbiol Biotechnol 2017; 44:785-797. [PMID: 28185098 DOI: 10.1007/s10295-017-1913-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/29/2017] [Indexed: 10/20/2022]
Abstract
The emergence of natural products and industrial microbiology nearly eight decades ago propelled an era of bioprocess innovation. Half a century later, recombinant protein technology spurred the tremendous growth of biologics and added mammalian cells to the forefront of industrial producing cells in terms of the value of products generated. This review highlights the process technology of natural products and protein biologics. Despite the separation in time, there is a remarkable similarity in their progression. As the new generation of therapeutics for gene and cell therapy emerges, its process technology development can take inspiration from that of natural products and biologics.
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Affiliation(s)
- Arpan A Bandyopadhyay
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN, 55455-0132, USA
| | - Anurag Khetan
- Biological Process Development, Bristol Myers Squibb, 521 NJ-173, Bloomsbury, NJ, 08804, USA
| | - Li-Hong Malmberg
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA, 01605, USA
| | | | - 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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20
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Ho SCL, Koh EYC, Soo BPC, Mariati, Chao SH, Yang Y. Evaluating the use of a CpG free promoter for long-term recombinant protein expression stability in Chinese hamster ovary cells. BMC Biotechnol 2016; 16:71. [PMID: 27756290 PMCID: PMC5070371 DOI: 10.1186/s12896-016-0300-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/13/2016] [Indexed: 12/04/2022] Open
Abstract
Background Methylated CpG dinucleotides in promoters are associated with the loss of gene expression in recombinant Chinese hamster ovary (CHO) cells during large-scale commercial manufacturing. We evaluated a promoter devoid of CpG dinucleotides, CpGfree, in parallel with a similar CpG containing promoter, CpGrich, for their ability to maintain the expression of recombinant enhanced green fluorescent protein (EGFP) after 8 weeks of culturing. Results While the promoters gave similar transient expression levels, CpGfree clones had significantly higher average stable expression possibly due to increased resistance to early silencing during integration into the chromosome. A greater proportion of cells in clones generated using the CpGfree promoter were still expressing detectable levels of EGFP after 8 weeks but the relative expression levels measured at week 8 to those measured at week 0 did not improve compared to clones generated using the CpGrich promoter. Chromatin immunoprecipitation assays indicated that the repression of the CpGfree promoter was likely linked to histone deacetylation and methylation. Use of histone deacetylase inhibitors also managed to recover some of the lost expression. Conclusion Using a promoter without CpG dinucleotides could mitigate the early gene silencing but did not improve longer-term expression stability as silencing due to histone modifications could still take place. The results presented here would aid in promoter selection and design for improved protein production in CHO and other mammalian cells.
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Affiliation(s)
- Steven C L Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Esther Y C Koh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Benjamin P C Soo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Mariati
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Sheng-Hao Chao
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore.,Department of Microbiology, National University of Singapore, Block MD4, 5 Science Drive 2, Singapore, 117597, Singapore
| | - Yuansheng Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore.
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21
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Recombinant protein production from stable mammalian cell lines and pools. Curr Opin Struct Biol 2016; 38:129-36. [DOI: 10.1016/j.sbi.2016.06.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/06/2016] [Accepted: 06/06/2016] [Indexed: 11/23/2022]
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22
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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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23
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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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24
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Industry view on the relative importance of “clonality” of biopharmaceutical-producing cell lines. Biologicals 2016; 44:117-22. [DOI: 10.1016/j.biologicals.2016.01.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/05/2016] [Accepted: 01/09/2016] [Indexed: 12/16/2022] Open
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