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Novak N, Baumann M, Friss A, Cairns V, DeMaria C, Borth N. LncRNA analysis of mAb producing CHO clones reveals marker and engineering potential. Metab Eng 2023; 78:26-40. [PMID: 37196898 DOI: 10.1016/j.ymben.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 05/19/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a potential new cell line engineering tool for improvement of yield and stability of CHO cells. In this study, we performed RNA sequencing of mAb producer CHO clones to study the lncRNA and protein coding transcriptome in relation to productivity. First, a robust linear model was used to identify genes correlating to productivity. To unravel specific patterns in expression of these genes, we employed weighted gene coexpression analysis (WGCNA) to find coexpressed modules, looking both for lncRNAs and coding genes. There was little overlap in the genes associated with productivity between the two products studied, possibly due to the difference in absolute range of productivity between the two mAbs. Therefore, we focused on the product with higher productivity and stronger candidate lncRNAs. To evaluate their potential as engineering targets, these candidate lncRNAs were transiently overexpressed or deleted by stable CRISPR Cas9 knock out both in a high and a low productivity subclone. We found that the thus achieved expression level of the identified lncRNAs, as confirmed by qPCR, does correlate well to productivity, so that they represent good markers that may be used for early clone selection. Additionally, we found that the deletion of one tested lncRNA region decreased viable cell density (VCD), prolonged culture time and increased cell size, final titer and specific productivity per cell. These results demonstrate the feasibility and usefulness of engineering lncRNA expression in production cell lines.
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Affiliation(s)
- Neža Novak
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; ACIB, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Martina Baumann
- ACIB, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Amy Friss
- Sanofi Biopharmaceutics Development, Framingham, MA, USA
| | - Victor Cairns
- Sanofi Biopharmaceutics Development, Framingham, MA, USA
| | | | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; ACIB, Austrian Centre of Industrial Biotechnology, Graz, Austria.
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2
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Skrika-Alexopoulos E, Mark Smales C. Isolation and characterisation of exosomes from Chinese hamster ovary (CHO) cells. Biotechnol Lett 2023; 45:425-437. [PMID: 36708458 PMCID: PMC10038950 DOI: 10.1007/s10529-023-03353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/29/2022] [Accepted: 01/12/2023] [Indexed: 01/29/2023]
Abstract
Exosomes have previously been isolated from Chinese hamster ovary (CHO) cells and their anti-apoptotic properties reported. However, to further facilitate the study of CHO cell derived exosomes and allow their comparison across studies, it is necessary to characterise and define such exosomes using at least three criteria that can act as a reference for the generation of CHO cell produced exosomes. Here we report on the isolation of exosomes from CHO cells, an industrially relevant and widely used cell host for biopharmaceutical protein production, during the exponential and stationary phase of growth during batch culture using a Total Exosome Isolation (TEI) method. The resulting vesicles were characterized and visualized using a diverse range of techniques including Dynamic Light Scattering (DLS), Zeta potential, Electron Microscopy and immunoblotting, and their protein and RNA content determined. We also generated the lipid fingerprint of isolated exosomes using MALDI-ToF mass spectroscopy. We confirmed the presence of nano sized extracellular vesicles from CHO cells and their subsequent characterization revealed details of their size, homogeneity, surface charge, protein and RNA content. The lipid content of exosomes was also found to differ between exosomes isolated on different days of batch culture. This analysis provides a profile and characterisation of CHO cell exosomes to aid future studies on exosomes from CHO cells and improving the manufacturing of exosomes for biotherapeutic application.
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Affiliation(s)
| | - C Mark Smales
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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3
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Recent developments in miRNA based recombinant protein expression in CHO. Biotechnol Lett 2022; 44:671-681. [PMID: 35507207 DOI: 10.1007/s10529-022-03250-1] [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: 09/25/2021] [Accepted: 03/30/2022] [Indexed: 11/02/2022]
Abstract
It is widely accepted that the growing demand for recombinant therapeutic proteins has led to the expansion of the biopharmaceutical industry and the development of strategies to increase recombinant protein production in mammalian cell lines such as SP2/0 HEK and particularly Chinese hamster ovary cells. For a long time now, most investigations have been focused on increasing host cell productivity using genetic manipulating of cellular processes like cell cycle, apoptosis, cell growth, protein secretory and other pathways. In recent decades MicroRNAs beside different genetic engineering tools (e.g., TALEN, ZFN, and Crisper/Cas) have attracted further attention as a tool in the genetic engineering of host cells to increase protein expression levels. Their ability to simultaneously target multiple mRNAs involved in one or more cellular processes made them a favorable tool in this field. Accordingly, this study aimed to review the methods of selecting target miRNA for cell line engineering, miRNA gain- or loss-of-function strategies, examples of laboratory and pilot studies in this field and discussed advantages and disadvantages of this technology.
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4
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The potential of emerging sub-omics technologies for CHO cell engineering. Biotechnol Adv 2022; 59:107978. [DOI: 10.1016/j.biotechadv.2022.107978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/25/2022] [Accepted: 05/07/2022] [Indexed: 11/23/2022]
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5
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Marx N, Eisenhut P, Weinguny M, Klanert G, Borth N. How to train your cell - Towards controlling phenotypes by harnessing the epigenome of Chinese hamster ovary production cell lines. Biotechnol Adv 2022; 56:107924. [PMID: 35149147 DOI: 10.1016/j.biotechadv.2022.107924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in omics technologies and the broad availability of big datasets have revolutionized our understanding of Chinese hamster ovary cells in their role as the most prevalent host for production of complex biopharmaceuticals. In consequence, our perception of this "workhorse of the biopharmaceutical industry" has successively shifted from that of a nicely working, but unknown recombinant protein producing black box to a biological system governed by multiple complex regulatory layers that might possibly be harnessed and manipulated at will. Despite the tremendous progress that has been made to characterize CHO cells on various omics levels, our understanding is still far from complete. The well-known inherent genetic plasticity of any immortalized and rapidly dividing cell line also characterizes CHO cells and can lead to problematic instability of recombinant protein production. While the high mutational frequency has been a focus of CHO cell research for decades, the impact of epigenetics and its role in differential gene expression has only recently been addressed. In this review we provide an overview about the current understanding of epigenetic regulation in CHO cells and discuss its significance for shaping the cell's phenotype. We also look into current state-of-the-art technology that can be applied to harness and manipulate the epigenetic network so as to nudge CHO cells towards a specific phenotype. Here, we revise current strategies on site-directed integration and random as well as targeted epigenome modifications. Finally, we address open questions that need to be investigated to exploit the full repertoire of fine-tuned control of multiplexed gene expression using epigenetic and systems biology tools.
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Affiliation(s)
- Nicolas Marx
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Eisenhut
- Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Marcus Weinguny
- University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Gerald Klanert
- Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Nicole Borth
- University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria.
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6
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Schmieder V, Novak N, Dhiman H, Nguyen LN, Serafimova E, Klanert G, Baumann M, Kildegaard HF, Borth N. A pooled CRISPR/AsCpf1 screen using paired gRNAs to induce genomic deletions in Chinese hamster ovary cells. ACTA ACUST UNITED AC 2021; 31:e00649. [PMID: 34277363 PMCID: PMC8261548 DOI: 10.1016/j.btre.2021.e00649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 06/06/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022]
Abstract
• Development of a small-scale CRISPR/AsCpf1 screen in CHO. • Usage of paired gRNAs enables full deletion of coding or noncoding genomic regions. • Growth perturbing paired gRNAs identified. • Key points for considerations in future screens identified.
Chinese hamster ovary (CHO) cells are the most widely used host for the expression of therapeutic proteins. Recently, significant progress has been made due to advances in genome sequence and annotation quality to unravel the black box CHO. Nevertheless, in many cases the link between genotype and phenotype in the context of suspension cultivated production cell lines is still not fully understood. While frameshift approaches targeting coding genes are frequently used, the non-coding regions of the genome have received less attention with respect to such functional annotation. Importantly, for non-coding regions frameshift knock-out strategies are not feasible. In this study, we developed a CRISPR-mediated screening approach that performs full deletions of genomic regions to enable the functional study of both the translated and untranslated genome. An in silico pipeline for the computational high-throughput design of paired guide RNAs (pgRNAs) directing CRISPR/AsCpf1 was established and used to generate a library tackling process-related genes and long non-coding RNAs. Next generation sequencing analysis of the plasmid library revealed a sufficient, but highly variable pgRNA composition. Recombinase-mediated cassette exchange was applied for pgRNA library integration rather than viral transduction to ensure single copy representation of pgRNAs per cell. After transient AsCpf1 expression, cells were cultivated over two sequential batches to identify pgRNAs which massively affected growth and survival. By comparing pgRNA abundance, depleted candidates were identified and individually validated to verify their effect.
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Key Words
- AsCpf1, Cpf1 from Acidaminococcus sp BV3L6
- CHO, Chinese hamster ovary
- CPM, counts per million reads mapped
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- CRISPR/AsCpf1
- Cas9, CRISPR-associated protein 9
- Chinese hamster ovary cells
- Cpf1, CRISPR-associated protein in Prevotella and Francisella
- DE, differentially expressed
- DOWN-TTS, downstream transcription termination site
- DR, differentially represented
- EV, empty vector
- EpoFc, Erythropoietin Fc fusion protein
- FACS, fluorescence activated cell sorting
- FC, fold change
- FDR, false discovery rate
- GS, glutamine synthetase
- Genetic screen
- NGS, next generation sequencing
- NTC, no template control
- PAM, protospacer adjacent motif
- PCA, principal component analysis
- Qp, specific productivity
- RMCE, recombinase-mediated cassette exchange
- TMM, trimmed mean of M values
- UP-TSS, upstream transcription start site
- VCD, viable cell density
- dCas9, deactivated Cas9
- gRNA, guide RNA
- genomic deletion
- lncRNA, long non-coding RNA
- ncGene, non-coding gene
- oligo, oligonucleotide
- paired gRNAs
- pgRNA, paired gRNA
- sgRNA, single guide RNA
- µ, growth rate
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Affiliation(s)
- Valerie Schmieder
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Neža Novak
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Heena Dhiman
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Ly Ngoc Nguyen
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Evgenija Serafimova
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Gerald Klanert
- acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Martina Baumann
- acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Kgs. Lyngby, Denmark
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
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7
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Motheramgari K, Valdés‐Bango Curell R, Tzani I, Gallagher C, Castro‐Rivadeneyra M, Zhang L, Barron N, Clarke C. Expanding the Chinese hamster ovary cell long noncoding RNA transcriptome using RNASeq. Biotechnol Bioeng 2020; 117:3224-3231. [DOI: 10.1002/bit.27467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 06/02/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Krishna Motheramgari
- National Institute for Bioprocessing Research and Training Fosters Avenue, Blackrock Co. Dublin Ireland
- National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin Ireland
| | | | - Ioanna Tzani
- National Institute for Bioprocessing Research and Training Fosters Avenue, Blackrock Co. Dublin Ireland
| | - Clair Gallagher
- National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin Ireland
| | - Marina Castro‐Rivadeneyra
- National Institute for Bioprocessing Research and Training Fosters Avenue, Blackrock Co. Dublin Ireland
- School of Chemical and Bioprocess Engineering University College Dublin, Belfield Dublin Ireland
| | - Lin Zhang
- Bioprocess R&D, Pfizer Inc. Andover Massachusetts
| | - Niall Barron
- National Institute for Bioprocessing Research and Training Fosters Avenue, Blackrock Co. Dublin Ireland
- School of Chemical and Bioprocess Engineering University College Dublin, Belfield Dublin Ireland
| | - Colin Clarke
- National Institute for Bioprocessing Research and Training Fosters Avenue, Blackrock Co. Dublin Ireland
- School of Chemical and Bioprocess Engineering University College Dublin, Belfield Dublin Ireland
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8
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Vito D, Eriksen JC, Skjødt C, Weilguny D, Rasmussen SK, Smales CM. Defining lncRNAs Correlated with CHO Cell Growth and IgG Productivity by RNA-Seq. iScience 2019; 23:100785. [PMID: 31962234 PMCID: PMC6971398 DOI: 10.1016/j.isci.2019.100785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 10/05/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
How the long non-coding RNA (lncRNA) genome in recombinant protein producing Chinese hamster ovary (CHO) cell lines relates to phenotype is not well described. We therefore defined the CHO cell lncRNA transcriptome from cells grown in controlled miniature bioreactors under fed-batch conditions using RNA-Seq to identify lncRNAs and how the expression of these changes throughout growth and between IgG producers. We identify lncRNAs including Adapt15, linked to ER stress, GAS5, linked to mTOR signaling/growth arrest, and PVT1, linked to Myc expression, which are differentially regulated during fed-batch culture and whose expression correlates to productivity and growth. Changes in (non)-coding RNA expression between the seed train and the equivalent day of fed-batch culture are also reported and compared with existing datasets. Collectively, we present a comprehensive lncRNA CHO cell profiling and identify targets for engineering growth and productivity characteristics of CHO cells. The CHO cell lncRNA transcriptome is defined using RNA-Seq Correlations between lncRNA expression and CHO cell growth and IgG productivity found Expression of lncRNAs involved in ER stress correlates to productivity Expression of lncRNAs involved in mTOR signaling/growth arrest correlates to growth
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Affiliation(s)
- Davide Vito
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Jens Christian Eriksen
- Symphogen A/S, Pederstrupvej 93, DK-2750 Ballerup, Denmark; AGC Biologics, Vandtårnsvej 83, DK-2860 Søborg, Denmark
| | | | - Dietmar Weilguny
- Symphogen A/S, Pederstrupvej 93, DK-2750 Ballerup, Denmark; Alligator Bioscience AB, Medicon Village, Scheelevägen 2, 223 63 Lund, Sweden
| | | | - C Mark Smales
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
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9
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Vito D, Smales CM. Engineering of the cellular translational machinery and non-coding RNAs to enhance CHO cell growth, recombinant product yields and quality. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Borth N, Hu WS. Enhancing CHO by Systems Biotechnology. Biotechnol J 2018; 13:e1800488. [PMID: 30270533 DOI: 10.1002/biot.201800488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nicole Borth
- Department of Biotechnology, Universität für Bodenkultur, Vienna, Austria
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Saint Paul, MN, USA
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11
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Pan X, Alsayyari AA, Dalm C, Hageman JA, Wijffels RH, Martens DE. Transcriptome Analysis of CHO Cell Size Increase During a Fed-Batch Process. Biotechnol J 2018; 14:e1800156. [PMID: 30024106 DOI: 10.1002/biot.201800156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/11/2018] [Indexed: 12/14/2022]
Abstract
In a Chinese Hamster Ovary (CHO) cell fed-batch process, arrest of cell proliferation and an almost threefold increase in cell size occurred, which is associated with an increase in cell-specific productivity. In this study, transcriptome analysis is performed to identify the molecular mechanisms associated with this. Cell cycle analysis reveals that the cells are arrested mainly in the G0 /G1 phase. The cell cycle arrest is associated with significant up-regulation of cyclin-dependent kinases inhibitors (CDKNs) and down-regulation of cyclin-dependent kinases (CDKs) and cyclins. During the cell size increase phase, the gene expression of the upstream pathways of mechanistic target of rapamycin (mTOR), which is related to the extracellular growth factor, cytokine, and amino acid conditions, shows a strongly synchronized pattern to promote the mTOR activity. The downstream genes of mTOR also show a synchronized pattern to stimulate protein translation and lipid synthesis. The results demonstrate that cell cycle inhibition and stimulated mTOR activity at the transcriptome level are related to CHO cell size increase. The cell size increase is related to the extracellular nutrient conditions through a number of cascade pathways, indicating that by rational design of media and feeds, CHO cell size can be manipulated during culture processes, which may further improve cell growth and specific productivity.
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Affiliation(s)
- Xiao Pan
- Bioprocess Engineering, Wageningen University and Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Abdulaziz A Alsayyari
- Bioprocess Engineering, Wageningen University and Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Ciska Dalm
- Upstream Process Development, Synthon Biopharmaceuticals BV, PO Box 7071, 6503 GN, Nijmegen, The Netherlands
| | - Jos A Hageman
- Biometris, Wageningen University and Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, Wageningen University and Research, PO Box 16, 6700 AA, Wageningen, The Netherlands.,Faculty of Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway
| | - Dirk E Martens
- Bioprocess Engineering, Wageningen University and Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
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