1
|
Belliveau J, Papoutsakis ET. The microRNomes of Chinese hamster ovary (CHO) cells and their extracellular vesicles, and how they respond to osmotic and ammonia stress. Biotechnol Bioeng 2023; 120:2700-2716. [PMID: 36788116 DOI: 10.1002/bit.28356] [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: 12/12/2022] [Revised: 01/23/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
A new area of focus in Chinese hamster ovary (CHO) biotechnology is the role of small (exosomes) and large (microvesicles or microparticles) extracellular vesicles (EVs). CHO cells in culture exchange large quantities of proteins and RNA through these EVs, yet the content and role of these EVs remain elusive. MicroRNAs (miRs or miRNA) are central to adaptive responses to stress and more broadly to changes in culture conditions. Given that EVs are highly enriched in miRs, and that EVs release large quantities of miRs both in vivo and in vitro, EVs and their miR content likely play an important role in adaptive responses. Here we report the miRNA landscape of CHO cells and their EVs under normal culture conditions and under ammonia and osmotic stress. We show that both cells and EVs are highly enriched in five miRs (among over 600 miRs) that make up about half of their total miR content, and that these highly enriched miRs differ significantly between normal and stress culture conditions. Notable is the high enrichment in miR-92a and miR-23a under normal culture conditions, in contrast to the high enrichment in let-7 family miRs (let-7c, let-7b, and let-7a) under both stress conditions. The latter suggests a preserved stress-responsive function of the let-7 miR family, one of the most highly preserved miR families across species, where among other functions, let-7 miRs regulate core oncogenes, which, depending on the biological context, may tip the balance between cell cycle arrest and apoptosis. While the expected-based on their profound enrichment-important role of these highly enriched miRs remains to be dissected, our data and analysis constitute an important resource for exploring the role of miRs in cell adaptation as well as for synthetic applications.
Collapse
Affiliation(s)
- Jessica Belliveau
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| |
Collapse
|
2
|
Characterization of dynamic regulation in Chinese hamster ovary (CHO) cell cultures in the late exponential phase. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
3
|
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
Collapse
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.
| |
Collapse
|
4
|
Combating viral contaminants in CHO cells by engineering innate immunity. Sci Rep 2019; 9:8827. [PMID: 31222165 PMCID: PMC6586939 DOI: 10.1038/s41598-019-45126-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/31/2019] [Indexed: 12/19/2022] Open
Abstract
Viral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo-3) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited activation of cellular immune responses and increased resistance to the RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production among many other biomedical applications.
Collapse
|
5
|
Li S, Cha SW, Heffner K, Hizal DB, Bowen MA, Chaerkady R, Cole RN, Tejwani V, Kaushik P, Henry M, Meleady P, Sharfstein ST, Betenbaugh MJ, Bafna V, Lewis NE. Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements. J Proteome Res 2019; 18:2433-2445. [PMID: 31020842 DOI: 10.1021/acs.jproteome.8b00935] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A high-quality genome annotation greatly facilitates successful cell line engineering. Standard draft genome annotation pipelines are based largely on de novo gene prediction, homology, and RNA-Seq data. However, draft annotations can suffer from incorrect predictions of translated sequence, inaccurate splice isoforms, and missing genes. Here, we generated a draft annotation for the newly assembled Chinese hamster genome and used RNA-Seq, proteomics, and Ribo-Seq to experimentally annotate the genome. We identified 3529 new proteins compared to the hamster RefSeq protein annotation and 2256 novel translational events (e.g., alternative splices, mutations, and novel splices). Finally, we used this pipeline to identify the source of translated retroviruses contaminating recombinant products from Chinese hamster ovary (CHO) cell lines, including 119 type-C retroviruses, thus enabling future efforts to eliminate retroviruses to reduce the costs incurred with retroviral particle clearance. In summary, the improved annotation provides a more accurate resource for CHO cell line engineering, by facilitating the interpretation of omics data, defining of cellular pathways, and engineering of complex phenotypes.
Collapse
Affiliation(s)
| | | | | | - Deniz Baycin Hizal
- Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , Maryland , United States
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , Maryland , United States
| | - Raghothama Chaerkady
- Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , Maryland , United States
| | | | - Vijay Tejwani
- Colleges of Nanoscale Science and Engineering , SUNY Polytechnic Institute , Albany , New York 12203 , United States
| | - Prashant Kaushik
- National Institute for Cellular Biotechnology , Dublin City University , Dublin 9, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology , Dublin City University , Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology , Dublin City University , Dublin 9, Ireland
| | - Susan T Sharfstein
- Colleges of Nanoscale Science and Engineering , SUNY Polytechnic Institute , Albany , New York 12203 , United States
| | | | | | | |
Collapse
|
6
|
Geoghegan D, Arnall C, Hatton D, Noble-Longster J, Sellick C, Senussi T, James DC. Control of amino acid transport into Chinese hamster ovary cells. Biotechnol Bioeng 2018; 115:2908-2929. [PMID: 29987891 DOI: 10.1002/bit.26794] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/06/2018] [Accepted: 07/04/2018] [Indexed: 12/21/2022]
Abstract
Amino acid transporters (AATs) represent a key interface between the cell and its environment, critical for all cellular processes: Energy generation, redox control, and synthesis of cell and product biomass. However, very little is known about the activity of different functional classes of AATs in Chinese hamster ovary (CHO) cells, how they support cell growth and productivity, and the potential for engineering their activity and/or the composition of amino acids in growth media to improve CHO cell performance in vitro. In this study, we have comparatively characterized AAT expression in untransfected and monoclonal antibody (MAb)-producing CHO cells using transcriptome analysis by RNA-seq, and mechanistically dissected AAT function using a variety of transporter-specific chemical inhibitors, comparing their effect on cell proliferation, recombinant protein production, and amino acid transport. Of a possible 56 mammalian plasma membrane AATs, 16 AAT messenger RNAs (mRNAs) were relatively abundant across all CHO cell populations. Of these, a subset of nine AAT mRNAs were more abundant in CHO cells engineered to produce a recombinant MAb. Together, upregulated AATs provide additional supply of specific amino acids overrepresented in MAb biomass compared to CHO host cell biomass, enable transport of synthetic substrates for glutathione synthesis, facilitate transport of essential amino acids to maintain active protein synthesis, and provide amino acid substrates for coordinated antiport systems to maintain supplies of proteinogenic and essential amino acids.
Collapse
Affiliation(s)
- Darren Geoghegan
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Claire Arnall
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | - Joanne Noble-Longster
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | | | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| |
Collapse
|
7
|
Singh A, Kildegaard HF, Andersen MR. An Online Compendium of CHO RNA-Seq Data Allows Identification of CHO Cell Line-Specific Transcriptomic Signatures. Biotechnol J 2018; 13:e1800070. [DOI: 10.1002/biot.201800070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/16/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Ankita Singh
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; 2800 Kgs. Lyngby Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark; 2800 Kgs. Lyngby Denmark
| | - Helene F. Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; 2800 Kgs. Lyngby Denmark
| | - Mikael R. Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark; 2800 Kgs. Lyngby Denmark
| |
Collapse
|
8
|
He L, Desai JX, Gao J, Hazeltine LB, Lian Z, Calley JN, Frye CC. Elucidating the Impact of CHO Cell Culture Media on Tryptophan Oxidation of a Monoclonal Antibody Through Gene Expression Analyses. Biotechnol J 2018. [DOI: 10.1002/biot.201700254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Luhong He
- Bioprocess Research and Development, Eli Lilly and Company; Indianapolis 46285 IN USA
| | - Jairav X. Desai
- Informatics Capabilities − Research IT, Eli Lilly and Company; Indianapolis 46285 IN USA
| | - Jinxin Gao
- Statistics- Discovery/Development, Eli Lilly and Company; Indianapolis 46285 IN USA
| | - Laurie B. Hazeltine
- Bioprocess Research and Development, Eli Lilly and Company; Indianapolis 46285 IN USA
| | - Zhirui Lian
- Bioprocess Research and Development, Eli Lilly and Company; Indianapolis 46285 IN USA
| | - John N. Calley
- Tailored Therapeutics Bioinformatics, Eli Lilly and Company; Indianapolis 46285 IN USA
| | - Christopher C. Frye
- Bioprocess Research and Development, Eli Lilly and Company; Indianapolis 46285 IN USA
| |
Collapse
|