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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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Maraux M, Gaillardet A, Gally A, Saas P, Cherrier T. Human primary neutrophil mRNA does not contaminate human resolving macrophage mRNA after efferocytosis. J Immunol Methods 2020; 483:112810. [PMID: 32592772 DOI: 10.1016/j.jim.2020.112810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/20/2020] [Accepted: 06/15/2020] [Indexed: 02/07/2023]
Abstract
The ingestion of apoptotic corpses by macrophages, a process called efferocytosis, is a crucial step in inflammation resolution, since it alters macrophage phenotype toward a pro-resolving profile to foil inflammation and to favor tissue repair. Up to now, the resolving macrophages remain poorly characterized, especially in humans. Global investigations, like RNA sequencing, would be very helpful to unravel some features of these elusive cells. Nonetheless, these inquiries may be challenging in a single-species model, since the fate of ingested mRNA remains unknown and may hinder any subsequent mRNA investigations in the phagocyte. A full human model consisting of primary human neutrophil and primary human monocyte-derived macrophage co-culture was set up several decades ago to mimic in vitro the efferocytosis process. However, to our knowledge, this model has not been characterized as a suitable model to perform global mRNA investigations. Indeed, the extent of ingested neutrophil mRNA contamination has not been assessed in resolving macrophages. This work answers to this crucial question. Indeed, based on the protocols presented in this article, we demonstrate that neutrophil mRNA is severely degraded and is not able to cross-contaminate resolving macrophage mRNA, contrary to apoptotic human peripheral blood derived mononuclear cell (PBMC) or apoptotic leukemic Jurkat cell mRNA. Moreover, this allogenic co-culture system does not favor neither neutrophil activation nor macrophage pro-inflammatory cytokine release. Collectively, we highlight that this model of primary human neutrophil and primary human monocyte-derived macrophage co-culture is the best model for mRNA investigations in human resolving macrophages to help improving our knowledge on these crucial cells.
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Affiliation(s)
- M Maraux
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Fédération Hospitalo-Universitaire INCREASE, LabEx LipSTIC, F-25000 Besançon, France
| | - A Gaillardet
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Fédération Hospitalo-Universitaire INCREASE, LabEx LipSTIC, F-25000 Besançon, France
| | - A Gally
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Fédération Hospitalo-Universitaire INCREASE, LabEx LipSTIC, F-25000 Besançon, France
| | - P Saas
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Fédération Hospitalo-Universitaire INCREASE, LabEx LipSTIC, F-25000 Besançon, France
| | - T Cherrier
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Fédération Hospitalo-Universitaire INCREASE, LabEx LipSTIC, F-25000 Besançon, France.
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Sha S, Bhatia H, Yoon S. An RNA-seq based transcriptomic investigation into the productivity and growth variants with Chinese hamster ovary cells. J Biotechnol 2018; 271:37-46. [DOI: 10.1016/j.jbiotec.2018.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 01/26/2018] [Accepted: 02/19/2018] [Indexed: 02/06/2023]
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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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Chen C, Le H, Goudar CT. Evaluation of two public genome references for chinese hamster ovary cells in the context of rna-seq based gene expression analysis. Biotechnol Bioeng 2017; 114:1603-1613. [PMID: 28295162 DOI: 10.1002/bit.26290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/21/2017] [Accepted: 03/10/2017] [Indexed: 11/08/2022]
Abstract
RNA-Seq is a powerful transcriptomics tool for mammalian cell culture process development. Successful RNA-Seq data analysis requires a high quality reference for read mapping and gene expression quantification. Currently, there are two public genome references for Chinese hamster ovary (CHO) cells, the predominant mammalian cell line in the biopharmaceutical industry. In this study, we compared these two references by analyzing 60 RNA-Seq samples from a variety of CHO cell culture conditions. Among the 20,891 common genes in both references, we observed that 31.5% have more than 7.1% quantification differences, implying gene definition differences in the two references. We propose a framework to quantify this difference using two metrics, Consistency and Stringency, which account for the average quantification difference between the two references over all samples, and the sample-specific effect on the quantification result, respectively. These two metrics can be used to identify potential genes for future gene model improvement and to understand the reliability of differentially expressed genes identified by RNA-Seq data analysis. Before a more comprehensive genome reference for CHO cells emerges, the strategy proposed in this study can enable more robust transcriptome analysis from CHO cell RNA-Seq data. Biotechnol. Bioeng. 2017;114: 1603-1613. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Chun Chen
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, California, 91320
| | - Huong Le
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, California, 91320
| | - Chetan T Goudar
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, California, 91320
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Muluhngwi P, Richardson K, Napier J, Rouchka EC, Mott JL, Klinge CM. Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells. Mol Cell Endocrinol 2017; 444:38-47. [PMID: 28137615 PMCID: PMC5316361 DOI: 10.1016/j.mce.2017.01.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 01/28/2023]
Abstract
miR-29b and miR-29a transcript levels were reported to increase in exponentially growing CHO-K1 cells. Here, we examine the regulation of miR-29b-1/a in CHO-K1 cells. We observed that 4-hydroxytamoxifen (4-OHT) increased pri-miR-29b-1 and pri-miR-29a transcription in CHO-K1 cells by activating endogenous estrogen receptor α (ERα). DICER, an established, bona fide target of miR-29b-1/a, was shown to be regulated by 4-OHT in CHO-K1 cells. We showed that miR-29b-1 and miR-29a serve a repressive role in cell proliferation, migration, invasion, and colony formation in CHO-K1 cells. To identify other targets of miR-29b-1 and miR-29a, RNA sequencing was performed by transfecting cells with anti-miR-29a, which inhibits both miR-29a and miR-29b-1, pre-miR-29b-1, and/or pre-miR-29a. In silico network analysis in MetaCore™ identified common and unique putative gene targets of miR-29b-1 and miR-29a. Pathway analysis of identified putative miR-29 targets were related to cell adhesion, cytoskeletal remodeling, and development. Further inquiry revealed regulation of pathways mediating responses to growth factor stimulus and cell cycle regulation.
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Affiliation(s)
- Penn Muluhngwi
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Kirsten Richardson
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Joshua Napier
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA
| | - Justin L Mott
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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Lund AM, Kaas CS, Brandl J, Pedersen LE, Kildegaard HF, Kristensen C, Andersen MR. Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data. BMC SYSTEMS BIOLOGY 2017; 11:37. [PMID: 28298216 PMCID: PMC5353859 DOI: 10.1186/s12918-017-0414-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 02/27/2017] [Indexed: 11/21/2022]
Abstract
Background Protein secretion is one of the most important processes in eukaryotes. It is based on a highly complex machinery involving numerous proteins in several cellular compartments. The elucidation of the cell biology of the secretory machinery is of great importance, as it drives protein expression for biopharmaceutical industry, a 140 billion USD global market. However, the complexity of secretory process is difficult to describe using a simple reductionist approach, and therefore a promising avenue is to employ the tools of systems biology. Results On the basis of manual curation of the literature on the yeast, human, and mouse secretory pathway, we have compiled a comprehensive catalogue of characterized proteins with functional annotation and their interconnectivity. Thus we have established the most elaborate reconstruction (RECON) of the functional secretion pathway network to date, counting 801 different components in mouse. By employing our mouse RECON to the CHO-K1 genome in a comparative genomic approach, we could reconstruct the protein secretory pathway of CHO cells counting 764 CHO components. This RECON furthermore facilitated the development of three alternative methods to study protein secretion through graphical visualizations of omics data. We have demonstrated the use of these methods to identify potential new and known targets for engineering improved growth and IgG production, as well as the general observation that CHO cells seem to have less strict transcriptional regulation of protein secretion than healthy mouse cells. Conclusions The RECON of the secretory pathway represents a strong tool for interpretation of data related to protein secretion as illustrated with transcriptomic data of Chinese Hamster Ovary (CHO) cells, the main platform for mammalian protein production. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0414-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne Mathilde Lund
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kgs. Lyngby, Denmark
| | - Christian Schrøder Kaas
- Recombinant Expression Technologies, Global Research Unit, Novo Nordisk A/S, Novo Nordisk Park, DK-2760, Måløv, Denmark
| | - Julian Brandl
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kgs. Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Claus Kristensen
- Faculty of Health and Medical Sciences, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, DK-2200, København N, Denmark
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kgs. Lyngby, Denmark.
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Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion. Sci Rep 2017; 7:40388. [PMID: 28091612 PMCID: PMC5238448 DOI: 10.1038/srep40388] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 12/05/2016] [Indexed: 12/22/2022] Open
Abstract
Recombinant protein production coopts the host cell machinery to provide high protein yields of industrial enzymes or biotherapeutics. However, since protein translation is energetically expensive and tightly controlled, it is unclear if highly expressed recombinant genes are translated as efficiently as host genes. Furthermore, it is unclear how the high expression impacts global translation. Here, we present the first genome-wide view of protein translation in an IgG-producing CHO cell line, measured with ribosome profiling. Through this we found that our recombinant mRNAs were translated as efficiently as the host cell transcriptome, and sequestered up to 15% of the total ribosome occupancy. During cell culture, changes in recombinant mRNA translation were consistent with changes in transcription, demonstrating that transcript levels influence specific productivity. Using this information, we identified the unnecessary resistance marker NeoR to be a highly transcribed and translated gene. Through siRNA knock-down of NeoR, we improved the production- and growth capacity of the host cell. Thus, ribosomal profiling provides valuable insights into translation in CHO cells and can guide efforts to enhance protein production.
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Chen C, Le H, Goudar CT. Integration of systems biology in cell line and process development for biopharmaceutical manufacturing. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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