1
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Rives D, Peak C, Blenner MA. RNASeq highlights ATF6 pathway regulators for CHO cell engineering with different impacts of ATF6β and WFS1 knockdown on fed-batch production of IgG 1. Sci Rep 2024; 14:14141. [PMID: 38898154 PMCID: PMC11187196 DOI: 10.1038/s41598-024-64767-1] [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: 01/05/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024] Open
Abstract
Secretion levels required of industrial Chinese hamster ovary (CHO) cell lines can challenge endoplasmic reticulum (ER) homeostasis, and ER stress caused by accumulation of misfolded proteins can be a bottleneck in biomanufacturing. The unfolded protein response (UPR) is initiated to restore homeostasis in response to ER stress, and optimization of the UPR can improve CHO cell production of therapeutic proteins. We compared the fed-batch growth, production characteristics, and transcriptomic response of an immunoglobulin G1 (IgG1) producer to its parental, non-producing host cell line. We conducted differential gene expression analysis using high throughput RNA sequencing (RNASeq) and quantitative polymerase chain reaction (qPCR) to study the ER stress response of each cell line during fed-batch culture. The UPR was activated in the IgG1 producer compared to the host cell line and our analysis of differential expression profiles indicated transient upregulation of ATF6α target mRNAs in the IgG1 producer, suggesting two upstream regulators of the ATF6 arm of the UPR, ATF6β and WFS1, are rational engineering targets. Although both ATF6β and WFS1 have been reported to negatively regulate ATF6α, this study shows knockdown of either target elicits different effects in an IgG1-producing CHO cell line. Stable knockdown of ATF6β decreased cell growth without decreasing titer; however, knockdown of WFS1 decreased titer without affecting growth. Relative expression measured by qPCR indicated no direct relationship between ATF6β and WFS1 expression, but upregulation of WFS1 in one pool was correlated with decreased growth and upregulation of ER chaperone mRNAs. While knockdown of WFS1 had negative impacts on UPR activation and product mRNA expression, knockdown of ATF6β improved the UPR specifically later in fed-batch leading to increased overall productivity.
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Affiliation(s)
- Dyllan Rives
- Department of Chemical & Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634-0909, USA
| | - Caroline Peak
- Department of Chemical & Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634-0909, USA
| | - Mark A Blenner
- Department of Chemical & Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634-0909, USA.
- Department of Chemical & Biomolecular Engineering, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
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2
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Wolnick NQ, Dickson MR, Webster TA, Connolly RP, Fernandes N, Encheva V, Crittenden H, Hodgkins J, Hadley BC, Palermo G, Hendrick SJ, Newell RA, Gray G, Siltanen C, Armstrong J, Downey BJ, Mason C. Impact of fed-batch process intensification on the productivity and product quality of two CHO cell lines expressing unique novel molecular format proteins. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-02997-3. [PMID: 38653840 DOI: 10.1007/s00449-024-02997-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/10/2024] [Indexed: 04/25/2024]
Abstract
While monospecific antibodies have long been the foundational offering of protein therapeutics, recent advancements in antibody engineering have allowed for the development of far more complex antibody structures. Novel molecular format (NMF) proteins, such as bispecific antibodies (BsAbs), are structures capable of multispecific binding, allowing for expanded therapeutic functionality. As demand for NMF proteins continues to rise, biomanufacturers face the challenge of increasing bioreactor process productivity while simultaneously maintaining consistent product quality. This challenge is exacerbated when producing structurally complex proteins with asymmetric modalities, as seen in NMFs. In this study, the impact of a high inoculation density (HID) fed-batch process on the productivity and product quality attributes of two CHO cell lines expressing unique NMFs, a monospecific antibody with an Fc-fusion protein and a bispecific antibody, compared to low inoculation density (LID) platform fed-batch processes was evaluated. It was observed that an intensified platform fed-batch process increased product concentrations by 33 and 109% for the two uniquely structured complex proteins in a shorter culture duration while maintaining similar product quality attributes to traditional fed-batch processes.
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Affiliation(s)
| | | | | | | | - Nancy Fernandes
- Research and Development, Lonza Biologics, Portsmouth, NH, USA
| | | | | | | | - Brian C Hadley
- Research and Development, Lonza Biologics, Portsmouth, NH, USA
| | | | | | - Roy A Newell
- Research and Development, Lonza Biologics, Portsmouth, NH, USA
| | - Genevieve Gray
- Research and Development, Lonza Biologics, Portsmouth, NH, USA
| | | | | | | | - Carrie Mason
- Research and Development, Lonza Biologics, Portsmouth, NH, USA
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3
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Guadarrama-Pérez V, Aguilar C, Porras-Sanjuanico A, Merino E, Ramírez OT, Barona-Gómez F, Palomares LA. Expression in CHO cells of a bacterial biosynthetic pathway producing a small non-ribosomal peptide aldehyde prevents proteolysis of recombinant proteins. Metab Eng 2024; 82:79-88. [PMID: 38290598 DOI: 10.1016/j.ymben.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/19/2023] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
A significant problem during recombinant protein production is proteolysis. One of the most common preventive strategies is the addition of protease inhibitors, which has drawbacks, such as their short half-life and high cost, and their limited prevention of extracellular proteolysis. Actinomycetes produce the most commonly used inhibitors, which are non-ribosomal small aldehydic peptides. Previously, an unprecedented biosynthetic route involving a condensation-minus non-ribosomal peptide synthetase (NRPSs) and a tRNA utilizing enzyme (tRUE) was shown to direct the synthesis of one of these inhibitor peptides, livipeptin. Here, we show that expression of the livipeptin biosynthetic pathway encoded by the lvp genes in CHO cells resulted in the production of this metabolite with cysteine protease inhibitory activity, implying that mammalian tRNAs were recruited by the lvp system. CHO cells transiently expressing the biosynthetic pathway produced livipeptin without affecting cell growth or viability. Expression of the lvp system in CHO cells producing two model proteins, secreted alkaline phosphatase (hSeAP) and a monoclonal antibody, resulted in higher specific productivity with reduced proteolysis. We show for the first time that the expression of a bacterial biosynthetic pathway is functional in CHO cells, resulting in the efficient, low-cost synthesis of a protease inhibitor without adverse effects on CHO cells. This expands the field of metabolic engineering of mammalian cells by expressing the overwhelming diversity of actinomycetes biosynthetic pathways and opens a new option for proteolysis inhibition in bioprocess engineering.
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Affiliation(s)
- Violeta Guadarrama-Pérez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología. Universidad Nacional Autónoma de México. Cuernavaca, Mor, 62210, México.
| | - César Aguilar
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (LANGEBIO), Cinvestav-IPN, Irapuato, Guanajuato, Mexico; Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
| | - Alberto Porras-Sanjuanico
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología. Universidad Nacional Autónoma de México. Cuernavaca, Mor, 62210, México.
| | - Enrique Merino
- Departamento de Microbiología Molecular. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, 62210, Mexico.
| | - Octavio T Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología. Universidad Nacional Autónoma de México. Cuernavaca, Mor, 62210, México.
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (LANGEBIO), Cinvestav-IPN, Irapuato, Guanajuato, Mexico; Institute of Biology, Leiden University, Leiden, 2333, BE, the Netherlands.
| | - Laura A Palomares
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología. Universidad Nacional Autónoma de México. Cuernavaca, Mor, 62210, México.
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4
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Sebastião MJ, Hoffman M, Escandell J, Tousi F, Zhang J, Figueroa B, DeMaria C, Gomes-Alves P. Identification of Mispairing Omic Signatures in Chinese Hamster Ovary (CHO) Cells Producing a Tri-Specific Antibody. Biomedicines 2023; 11:2890. [PMID: 38001891 PMCID: PMC10669571 DOI: 10.3390/biomedicines11112890] [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: 09/15/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Monoclonal antibody-based therapy has shown efficacy against cancer, autoimmune, infectious, and inflammatory diseases. Multispecific antibodies (MsAbs), including trispecifics (tsAbs), offer enhanced therapeutic potential by targeting different epitopes. However, when co-expressed from three or more different polypeptide chains, MsAb production can lead to incorrect chain assembly and co-production of mispaired species with impaired biological activity. Moreover, mispairing carries significant challenges for downstream purification, decreasing yields and increasing the cost of bioprocess development. In this study, quantitative transcriptomics and proteomics analyses were employed to investigate which signaling pathways correlated with low and high mispairing clone signatures. Gene and protein expression profiles of Chinese hamster ovary (CHO) clones producing an tsAb were analyzed in the exponential growth and stationary (tsAb production) phase of fed-batch culture. Functional analysis revealed activated endoplasmic reticulum stress in high mispairing clones in both culture phases, while low mispairing clones exhibited expression profiles indicative of activated protein translation, as well as higher endocytosis and target protein degradation, suggesting the clearance of unfolded proteins through ubiquitin-mediated mechanisms. In addition, through transcriptomic profiling, we identified a group of genes that have the potential to be used as a biomarker panel tool for identifying high mispairing levels in the early stages of bioprocess development.
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Affiliation(s)
- Maria João Sebastião
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal; (M.J.S.)
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Michael Hoffman
- Sanofi Cell Line and Cell Bank Development, Mammalian Platform, Global CMC Development, Framingham, MA 01701, USA (B.F.)
| | - José Escandell
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal; (M.J.S.)
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Fatemeh Tousi
- Sanofi Bioanalytics Development, Global CMC Development, Framingham, MA 01701, USA
| | - Jin Zhang
- Sanofi Cell Line and Cell Bank Development, Mammalian Platform, Global CMC Development, Framingham, MA 01701, USA (B.F.)
| | - Bruno Figueroa
- Sanofi Cell Line and Cell Bank Development, Mammalian Platform, Global CMC Development, Framingham, MA 01701, USA (B.F.)
| | - Christine DeMaria
- Sanofi Cell Line and Cell Bank Development, Mammalian Platform, Global CMC Development, Framingham, MA 01701, USA (B.F.)
| | - Patrícia Gomes-Alves
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal; (M.J.S.)
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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5
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Nguyen M, Zimmer A. A reflection on the improvement of Chinese Hamster ovary cell-based bioprocesses through advances in proteomic techniques. Biotechnol Adv 2023; 65:108141. [PMID: 37001570 DOI: 10.1016/j.biotechadv.2023.108141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 03/05/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
Chinese hamster ovary (CHO) cells are the preferred mammalian host for the large-scale production of recombinant proteins in the biopharmaceutical industry. Research endeavors have been directed to the optimization of CHO-based bioprocesses to increase protein quantity and quality, often in an empirical manner. To provide a rationale for those achievements, a myriad of CHO proteomic studies has arisen in recent decades. This review gives an overview of significant advances in LC-MS-based proteomics and sheds light on CHO proteomic studies, with a particular focus on CHO cells with superior bioprocessing phenotypes (growth, viability, titer, productivity and cQA), that have exploited novel proteomic or sub-omic techniques. These proteomic findings expand the current knowledge and understanding about the underlying protein clusters, protein regulatory networks and biological pathways governing such phenotypic changes. The proteomic studies, highlighted herein, will help in the targeted modulation of these cell factories to the desired needs.
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6
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Knight TJ, Povey JF, Vito D, Mohindra A, Jaques CM, Smales CM. Manipulation of mRNA translation elongation influences the fragmentation of a biotherapeutic Fc-fusion protein produced in CHO cells. Biotechnol Bioeng 2022; 119:3408-3420. [PMID: 36082414 PMCID: PMC9826484 DOI: 10.1002/bit.28230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/05/2022] [Accepted: 09/01/2022] [Indexed: 01/11/2023]
Abstract
Mammalian cells, particularly Chinese hamster ovary cells, are the dominant system for the production of protein-based biotherapeutics, however, product degradation, particularly of Fc-fusion proteins, is sometimes observed that impacts the quality of the protein generated. Here, we identify the site of fragmentation of a model immunoglobulin G1 Fc-fusion protein, show that the observed clipping and aggregation are decreased by reduced temperature culturing, that the fragmentation/clipping is intracellular, and that reduced clipping at a lower temperature (<37°C) relates to mesenger RNA (mRNA) translation elongation. We subsequently show that reduced fragmentation can be achieved at 37°C by addition of chemical reagents that slow translation elongation. We then modified mRNA translation elongation speeds by designing different transcript sequences for the Fc-fusion protein based on alternative codon usage and improved the product yield at 37°C, and the ratio of intact to a fragmented product. Our data suggest that rapid elongation results in misfolding that decreases product fidelity, generating a region susceptible to degradation/proteolysis, whilst the slowing of mRNA translation improves the folding, reducing susceptibility to fragmentation. Manipulation of mRNA translation and/or the target Fc-fusion transcript is, therefore, an approach that can be applied to potentially reduce fragmentation of clipping-prone Fc-fusion proteins.
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Affiliation(s)
- Tanya J. Knight
- School of Biosciences, Industrial Biotechnology CentreUniversity of KentCanterbury, KentUK
| | - Jane F. Povey
- School of Biosciences, Industrial Biotechnology CentreUniversity of KentCanterbury, KentUK
| | - Davide Vito
- School of Biosciences, Industrial Biotechnology CentreUniversity of KentCanterbury, KentUK
| | | | | | - C. Mark Smales
- School of Biosciences, Industrial Biotechnology CentreUniversity of KentCanterbury, KentUK,National Institute for Bioprocessing Research and TrainingBlackrock Co.DublinIreland
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7
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Apley KD, Laflin AD, Johnson SN, Batrash N, Griffin JD, Berkland CJ, DeKosky BJ. Optimized Production of Fc Fusion Proteins by Sortase Enzymatic Ligation. Ind Eng Chem Res 2021; 60:16839-16853. [PMID: 38646185 PMCID: PMC11031256 DOI: 10.1021/acs.iecr.1c02842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fc fusions are a growing class of drugs comprising an antibody Fc domain covalently linked to a protein or peptide and can pose manufacturing challenges. In this study we evaluated three synthetic approaches to generate Fc fusions, using Fc-insulin as a model drug candidate. Engineered human IgG1 was digested with HRV3C to produce an Fc fragment with a C-terminal sortase tag (Fc-LPETGGH6). The synthesis of Fc-insulin2 from Fc-LPETGGH6 was evaluated with direct sortase-mediated ligation (SML) and two chemoenzymatic strategies. Direct SML was performed with triglycine-insulin, and chemoenzymatic strategies used to SML fuse either triglycine-azide or triglycine-DBCO prior to linking insulin with copper-catalyzed or strain-promoted azidealkyne cycloaddition. Reaction conditions were optimized by evaluating reagent concentrations, relative equivalents, temperature, and time. Direct SML provided the most effective reaction yields, converting 60-70% of Fc-LPETGGH6 to Fc-insulin2, whereas our optimized chemoenzymatic synthesis converted 30-40% of Fc-LPETGGH6 to Fc-insulin2. Here we show that SML is a practical and efficient method to synthesize Fc fusions and provide an optimized pathway for fusion drug synthesis.
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Affiliation(s)
- Kyle D Apley
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Amy D Laflin
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Stephanie N Johnson
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Noora Batrash
- Department of Chemical and Petroleum Engineering, University of Kansas, Lawrence, Kansas 66045, United States
| | - J Daniel Griffin
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Cory J Berkland
- Department of Pharmaceutical Chemistry, Department of Chemical and Petroleum Engineering, and Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045, United States
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, Department of Chemical and Petroleum Engineering, and Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045, United States; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States; The Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
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8
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Bagal D, Gibson BW. Identification of Proteolysis Products in Protein Therapeutics through TMPP N-Terminal Tagging and Electron Transfer Dissociation Product Triggered Collisional Induced Dissociation Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1936-1944. [PMID: 33534996 DOI: 10.1021/jasms.0c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Thorough characterization of protein therapeutics is often challenging due to the heterogeneity arising from primary sequence variants, post-translational modifications, proteolytic clipping, or incomplete processing of the signal peptide. Modern mass spectrometry (MS) techniques are now routinely used to characterize such heterogeneous protein populations. Here, we present an LC-MS/MS method using (N-succinimidyloxycarbonylmethyl)-tris (2,4,6-trimethoxyphenyl) phosphonium bromide (TMPP-Ac-OSu) to label any free N-terminal α-amines to rapidly and selectively identify proteolytic clipping events. Electron transfer dissociation (ETD) fragmentation of these chemically tagged peptides generates two unique TMPP product ions, TMPP+ and TMPP-Ac-NH2/c0. The presence of these signature ions following ETD is used to trigger subsequent collisional induced dissociation (CID) fragmentation of the precursor ion. This results in a small subset of CID tandem MS spectra that are used in a customized database search. Using a purified fusion monoclonal antibody (mAb) as an example, we demonstrate how TMPP labeling followed by ETD product ion triggered CID fragmentation is used to accurately identify two undesired clipping sites.
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Affiliation(s)
- Dhanashri Bagal
- Amgen Discovery Research, Discovery Attribute Sciences, South San Francisco, California 94080, United States
| | - Bradford W Gibson
- Amgen Discovery Research, Discovery Attribute Sciences, South San Francisco, California 94080, United States
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9
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Bryan L, Henry M, Kelly RM, Frye CC, Osborne MD, Clynes M, Meleady P. Mapping the molecular basis for growth related phenotypes in industrial producer CHO cell lines using differential proteomic analysis. BMC Biotechnol 2021; 21:43. [PMID: 34301236 PMCID: PMC8305936 DOI: 10.1186/s12896-021-00704-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background The ability to achieve high peak viable cell density earlier in CHO cell culture and maintain an extended cell viability throughout the production process is highly desirable to increase recombinant protein yields, reduce host cell impurities for downstream processing and reduce the cost of goods. In this study we implemented label-free LC-MS/MS proteomic profiling of IgG4 producing CHO cell lines throughout the duration of the cell culture to identify differentially expressed (DE) proteins and intracellular pathways associated with the high peak viable cell density (VCD) and extended culture VCD phenotypes. Results We identified key pathways in DNA replication, mitotic cell cycle and evasion of p53 mediated apoptosis in high peak VCD clonally derived cell lines (CDCLs). ER to Golgi vesicle mediated transport was found to be highly expressed in extended culture VCD CDCLs while networks involving endocytosis and oxidative stress response were significantly downregulated. Conclusion This investigation highlights key pathways for targeted engineering to generate desirable CHO cell phenotypes for biotherapeutic production. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00704-8.
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Affiliation(s)
- Laura Bryan
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ronan M Kelly
- Eli Lilly and Company, LTC-North, 1200 Kentucky Avenue, Indianapolis, IN, 46225, USA
| | - Christopher C Frye
- Eli Lilly and Company, LTC-North, 1200 Kentucky Avenue, Indianapolis, IN, 46225, USA
| | | | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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10
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Pérez-Rodriguez S, Wulff T, Voldborg BG, Altamirano C, Trujillo-Roldán MA, Valdez-Cruz NA. Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. ACS OMEGA 2021; 6:12439-12458. [PMID: 34056395 PMCID: PMC8154153 DOI: 10.1021/acsomega.0c06030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 05/11/2023]
Abstract
Different cellular processes that contribute to protein production in Chinese hamster ovary (CHO) cells have been previously investigated by proteomics. However, although the classical secretory pathway (CSP) has been well documented as a bottleneck during recombinant protein (RP) production, it has not been well represented in previous proteomic studies. Hence, the significance of this pathway for production of RP was assessed by identifying its own proteins that were associated to changes in RP production, through subcellular fractionation coupled to shot-gun proteomics. Two CHO cell lines producing a monoclonal antibody with different specific productivities were used as cellular models, from which 4952 protein groups were identified, which represent a coverage of 59% of the Chinese hamster proteome. Data are available via ProteomeXchange with identifier PXD021014. By using SAM and ROTS algorithms, 493 proteins were classified as differentially expressed, of which about 80% was proposed as novel targets and one-third were assigned to the CSP. Endoplasmic reticulum (ER) stress, unfolded protein response, calcium homeostasis, vesicle traffic, glycosylation, autophagy, proteasomal activity, protein synthesis and translocation into ER lumen, and secretion of extracellular matrix components were some of the affected processes that occurred in the secretory pathway. Processes from other cellular compartments, such as DNA replication, transcription, cytoskeleton organization, signaling, and metabolism, were also modified. This study gives new insights into the molecular traits of higher producer cells and provides novel targets for development of new sub-lines with improved phenotypes for RP production.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Tune Wulff
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Bjørn G. Voldborg
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Claudia Altamirano
- Laboratorio
de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085 Valparaíso, Chile
| | - Mauricio A. Trujillo-Roldán
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Norma A. Valdez-Cruz
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
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11
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Clarke C, Gallagher C, Kelly RM, Henry M, Meleady P, Frye CC, Osborne MD, Brady CP, Barron N, Clynes M. Transcriptomic analysis of IgG4 Fc‐fusion protein degradation in a panel of clonally‐derived CHO cell lines using RNASeq. Biotechnol Bioeng 2019; 116:1556-1562. [DOI: 10.1002/bit.26958] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/22/2019] [Accepted: 02/21/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Colin Clarke
- National Institute for Bioprocessing Research and TrainingBlackrock, Co. Dublin Ireland
| | - Clair Gallagher
- National Institute for Cellular BiotechnologyDublin City UniversityGlasnevin Dublin Ireland
| | - Ronan M. Kelly
- Bioprocess Research & Development, Bioprocess Research and DevelopmentEli Lilly and Company, LTC‐North Indianapolis
| | - Michael Henry
- National Institute for Cellular BiotechnologyDublin City UniversityGlasnevin Dublin Ireland
| | - Paula Meleady
- National Institute for Cellular BiotechnologyDublin City UniversityGlasnevin Dublin Ireland
| | - Christopher C. Frye
- Bioprocess Research & Development, Bioprocess Research and DevelopmentEli Lilly and Company, LTC‐North Indianapolis
| | - Matthew D. Osborne
- Biotech Technical Services/ Manufacturing SciencesEli Lilly S. A. Irish BranchKinsale Cork Ireland
| | - Ciaran P Brady
- Bioprocess Research & Development, Bioprocess Research and DevelopmentEli Lilly and Company, LTC‐North Indianapolis
| | - Niall Barron
- National Institute for Bioprocessing Research and TrainingBlackrock, Co. Dublin Ireland
- National Institute for Cellular BiotechnologyDublin City UniversityGlasnevin Dublin Ireland
- UCD School of Chemical and Bioprocess Engineering, UCD Engineering and Materials Science CentreUniversity College DublinBelfield Dublin Ireland
| | - Martin Clynes
- National Institute for Cellular BiotechnologyDublin City UniversityGlasnevin Dublin Ireland
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12
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Depletion of endogenous miRNA-378-3p increases peak cell density of CHO DP12 cells and is correlated with elevated levels of ubiquitin carboxyl-terminal hydrolase 14. J Biotechnol 2018; 288:30-40. [DOI: 10.1016/j.jbiotec.2018.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/27/2018] [Accepted: 10/28/2018] [Indexed: 01/01/2023]
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