1
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Ito T, Lutz H, Tan L, Wang B, Tan J, Patel M, Chen L, Tsunakawa Y, Park B, Banerjee S. Host cell proteins in monoclonal antibody processing: Control, detection, and removal. Biotechnol Prog 2024:e3448. [PMID: 38477405 DOI: 10.1002/btpr.3448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Host cell proteins (HCPs) are process-related impurities in a therapeutic protein expressed using cell culture technology. This review presents biopharmaceutical industry trends in terms of both HCPs in the bioprocessing of monoclonal antibodies (mAbs) and the capabilities for HCP clearance by downstream unit operations. A comprehensive assessment of currently implemented and emerging technologies in the manufacturing processes with extensive references was performed. Meta-analyses of published downstream data were conducted to identify trends. Improved analytical methods and understanding of "high-risk" HCPs lead to more robust manufacturing processes and higher-quality therapeutics. The trend of higher cell density cultures leads to both higher mAb expression and higher HCP levels. However, HCP levels can be significantly reduced with improvements in operations, resulting in similar concentrations of approx. 10 ppm HCPs. There are no differences in the performance of HCP clearance between recent enhanced downstream operations and traditional batch processing. This review includes best practices for developing improved processes.
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Affiliation(s)
- Takao Ito
- Life Science, Process Solutions, Merck Ltd. (An Affiliate of Merck KGaA, Darmstadt, Germany), Tokyo, Japan
| | - Herb Lutz
- Independent Consultant, Sudbury, Massachusetts, USA
| | - Lihan Tan
- Life Science Services, Sigma-Aldrich Pte Ltd, Singapore, Singapore
| | - Bin Wang
- Life Science, Process Solutions, Merck Chemicals (Shanghai) Co. Ltd. (An Affiliate of Merck KGaA Darmstadt, Germany), Shanghai, China
| | - Janice Tan
- Life Science, Process Solutions, Merck Pte Ltd. (An Affiliate of Merck KGaA, Darmstadt, Germany), Singapore
| | - Masum Patel
- Life Science, Process Solutions, Merck Life Sciences Pvt. Ltd. (An Affiliate of Merck KGaA, Darmstadt, Germany), Bangalore, India
| | - Lance Chen
- Life Science, Process Solutions, Merck Pte Ltd. (An Affiliate of Merck KGaA, Darmstadt, Germany), Singapore
| | - Yuki Tsunakawa
- Life Science, Process Solutions, Merck Ltd. (An Affiliate of Merck KGaA, Darmstadt, Germany), Tokyo, Japan
| | - Byunghyun Park
- Life Science, Process Solutions, Merck Ltd. (An Affiliate of Merck KGaA, Darmstadt, Germany), Seoul, South Korea
| | - Subhasis Banerjee
- Life Science, Process Solutions, Merck Life Sciences Pvt. Ltd. (An Affiliate of Merck KGaA, Darmstadt, Germany), Bangalore, India
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2
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Haltaufderhyde K, Roberts BJ, Khan S, Terry F, Boyle CM, McAllister M, Martin W, Rosenberg A, De Groot AS. Immunoinformatic Risk Assessment of Host Cell Proteins During Process Development for Biologic Therapeutics. AAPS J 2023; 25:87. [PMID: 37697150 DOI: 10.1208/s12248-023-00852-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023] Open
Abstract
The identification and removal of host cell proteins (HCPs) from biologic products is a critical step in drug development. Despite recent improvements to purification processes, biologics such as monoclonal antibodies, enzyme replacement therapies, and vaccines that are manufactured in a range of cell lines and purified using diverse processes may contain HCP impurities, making it necessary for developers to identify and quantify impurities during process development for each drug product. HCPs that contain sequences that are less conserved with human homologs may be more immunogenic than those that are more conserved. We have developed a computational tool, ISPRI-HCP, that estimates the immunogenic potential of HCP sequences by evaluating and quantifying T cell epitope density and relative conservation with similar T cell epitopes in the human proteome. Here we describe several case studies that support the use of this method for classifying candidate HCP impurities according to their immunogenicity risk.
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Affiliation(s)
| | - Brian J Roberts
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | - Sundos Khan
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | - Frances Terry
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | | | | | - William Martin
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | - Amy Rosenberg
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | - Anne S De Groot
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA.
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, USA.
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3
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Glinšek K, Bozovičar K, Bratkovič T. CRISPR Technologies in Chinese Hamster Ovary Cell Line Engineering. Int J Mol Sci 2023; 24:ijms24098144. [PMID: 37175850 PMCID: PMC10179654 DOI: 10.3390/ijms24098144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The Chinese hamster ovary (CHO) cell line is a well-established platform for the production of biopharmaceuticals due to its ability to express complex therapeutic proteins with human-like glycopatterns in high amounts. The advent of CRISPR technology has opened up new avenues for the engineering of CHO cell lines for improved protein production and enhanced product quality. This review summarizes recent advances in the application of CRISPR technology for CHO cell line engineering with a particular focus on glycosylation modulation, productivity enhancement, tackling adventitious agents, elimination of problematic host cell proteins, development of antibiotic-free selection systems, site-specific transgene integration, and CRISPR-mediated gene activation and repression. The review highlights the potential of CRISPR technology in CHO cell line genome editing and epigenetic engineering for the more efficient and cost-effective development of biopharmaceuticals while ensuring the safety and quality of the final product.
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Affiliation(s)
- Katja Glinšek
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Krištof Bozovičar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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4
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Pedroso A, Herrera Belén L, Beltrán JF, Castillo RL, Pessoa A, Pedroso E, Farías JG. In Silico Design of a Chimeric Humanized L-asparaginase. Int J Mol Sci 2023; 24:ijms24087550. [PMID: 37108713 PMCID: PMC10144303 DOI: 10.3390/ijms24087550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/13/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer among children worldwide, characterized by an overproduction of undifferentiated lymphoblasts in the bone marrow. The treatment of choice for this disease is the enzyme L-asparaginase (ASNase) from bacterial sources. ASNase hydrolyzes circulating L-asparagine in plasma, leading to starvation of leukemic cells. The ASNase formulations of E. coli and E. chrysanthemi present notorious adverse effects, especially the immunogenicity they generate, which undermine both their effectiveness as drugs and patient safety. In this study, we developed a humanized chimeric enzyme from E. coli L-asparaginase which would reduce the immunological problems associated with current L-asparaginase therapy. For these, the immunogenic epitopes of E. coli L-asparaginase (PDB: 3ECA) were determined and replaced with those of the less immunogenic Homo sapiens asparaginase (PDB:4O0H). The structures were modeled using the Pymol software and the chimeric enzyme was modeled using the SWISS-MODEL service. A humanized chimeric enzyme with four subunits similar to the template structure was obtained, and the presence of asparaginase enzymatic activity was predicted by protein-ligand docking.
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Affiliation(s)
- Alejandro Pedroso
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Lisandra Herrera Belén
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomas, Avenida Carlos Schorr 255, Talca 3460000, Chile
| | - Jorge F Beltrán
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
| | - Rodrigo L Castillo
- Department of Internal Medicine, East Division, Faculty of Medicine, University of Chile, Santiago 7500922, Chile
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Enrique Pedroso
- Department of Family Medicine, Faculty of Medicine, University of Medical Sciences Matanzas, Matanzas 42300, Cuba
| | - Jorge G Farías
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco 4811230, Chile
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5
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Lu Y, Lin J, Bian T, Chen J, Liu D, Ma M, Gao Z, Chen J, Ju D, Wang X. Risk control of host cell proteins in one therapeutic antibody produced by concentrated fed-batch (CFB) mode. Eng Life Sci 2023; 23:e2200060. [PMID: 36874608 PMCID: PMC9978904 DOI: 10.1002/elsc.202200060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/26/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
Multiple control strategies, including a downstream purification process with well-controlled parameters and a comprehensive release or characterization for intermediates or drug substances, were implemented to mitigate the potential risk of host cell proteins (HCPs) in one concentrated fed-batch (CFB) mode manufactured product. A host cell process specific enzyme-linked immunosorbent assay (ELISA) method was developed for the quantitation of HCPs. The method was fully validated and showed good performance including high antibody coverage. This was confirmed by 2D Gel-Western Blot analysis. Furthermore, a LC-MS/MS method with non-denaturing digestion and a long gradient chromatographic separation coupled with data dependent acquisition (DDA) on a Thermo/QE-HF-X mass spectrometer was developed as an orthogonal method to help identify the specific types of HCPs in this CFB product. Because of the high sensitivity, selectivity and adaptability of the new developed LC-MS/MS method, significantly more species of HCP contaminants were able to be identified. Even though high levels of HCPs were observed in the harvest bulk of this CFB product, the development of multiple processes and analytical control strategies may greatly mitigate potential risks and reduce HCPs contaminants to a very low level. No high-risk HCP was identified and the total amount of HCPs was very low in the CFB final product.
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Affiliation(s)
- Yiling Lu
- Department of Analytical ScienceFormulation & Quality Control, Genor Biopharma Co., Ltd.ShanghaiChina
| | - Jun Lin
- Department of Biological Medicines & Shanghai Engineering Research Center of ImmunotherapeuticsFudan University School of PharmacyShanghaiChina
- Department of Analytical ScienceFormulation & Quality Control, Genor Biopharma Co., Ltd.ShanghaiChina
| | - Tianze Bian
- Department of Analytical ScienceFormulation & Quality Control, Genor Biopharma Co., Ltd.ShanghaiChina
| | - Jin Chen
- Department of Analytical ScienceFormulation & Quality Control, Genor Biopharma Co., Ltd.ShanghaiChina
| | - Dan Liu
- Department of Analytical ScienceFormulation & Quality Control, Genor Biopharma Co., Ltd.ShanghaiChina
| | - Mingjun Ma
- Department of Analytical ScienceFormulation & Quality Control, Genor Biopharma Co., Ltd.ShanghaiChina
| | - Zhen Gao
- Department of Analytical ScienceFormulation & Quality Control, Genor Biopharma Co., Ltd.ShanghaiChina
| | - Jiemin Chen
- Department of Analytical ScienceFormulation & Quality Control, Genor Biopharma Co., Ltd.ShanghaiChina
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of ImmunotherapeuticsFudan University School of PharmacyShanghaiChina
| | - Xing Wang
- Array Bridge Inc.St. LouisMissouriUSA
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6
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Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system, particularly in the separation of intact proteins. A modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups. Both these methods have distinct advantages in the separation and identification of thousands of individual protein species including protein isoforms and post-translational modifications. This chapter discusses the principles of 2D-PAGE and 2D-DIGE including limitations to the methods. 2D-PAGE and 2D-DIGE continue to be popular methods in bioprocessing-related research, particularly on recombinant Chinese hamster ovary cells, which are also discussed in this chapter.
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Affiliation(s)
- Paula Meleady
- School of Biotechnology, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland.
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7
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Hamaker NK, Min L, Lee KH. Comprehensive Assessment of Host Cell Protein Expression after Extended Culture and Bioreactor Production of CHO Cell Lines. Biotechnol Bioeng 2022; 119:2221-2238. [PMID: 35508759 DOI: 10.1002/bit.28128] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/12/2022]
Abstract
The biomanufacturing industry is advancing toward continuous processes that will involve longer culture durations and older cell ages. These upstream trends may bring unforeseen challenges for downstream purification due to fluctuations in host cell protein (HCP) levels. To understand the extent of HCP expression instability exhibited by Chinese hamster ovary (CHO) cells over these time scales, an industry-wide consortium collaborated to develop a study to characterize age-dependent changes in HCP levels across 30, 60, and 90 cell doublings, representing a period of approximately 60 days. A monoclonal antibody (mAb)-producing cell line with bulk productivity up to 3 g/L in a bioreactor was aged in parallel with its parental CHO-K1 host. Subsequently, both cell types at each age were cultivated in an automated bioreactor system to generate harvested cell culture fluid (HCCF) for HCP analysis. More than 1,500 HCPs were quantified using complementary proteomic techniques, two-dimensional electrophoresis (2DE) and liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). While up to 13% of proteins showed variable expression with age, more changes were observed when comparing between the two cell lines with up to 47% of HCPs differentially expressed. A small subset (50 HCPs) with age-dependent expression were previously reported to be problematic as high-risk and/or difficult-to-remove impurities; however, the vast majority of these were down-regulated with age. Our findings suggest that HCP expression changes over this time scale may not be as dramatic and pose as great of a challenge to downstream processing as originally expected but that monitoring of variably expressed problematic HCPs remains critical. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nathaniel K Hamaker
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware
| | - Lie Min
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware
| | - Kelvin H Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware
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8
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Wang F, Li X, Swanson M, Guetschow E, Winston M, Smith JP, Hoyt E, Liu Z, Richardson D, Bu X, Jawa V, Variankaval N. Holistic Analytical Characterization and Risk Assessment of Residual Host Cell Protein Impurities in an Active Pharmaceutical Ingredient (API) Synthesized by Biocatalysts. Biotechnol Bioeng 2022; 119:2088-2104. [PMID: 35437754 DOI: 10.1002/bit.28112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/04/2022] [Accepted: 04/13/2022] [Indexed: 11/10/2022]
Abstract
Host cell proteins (HCPs) are a significant class of process-related impurities commonly associated with the manufacturing of biopharmaceuticals. However, due to the increased use of crude enzymes as biocatalysts for modern organic synthesis, HCPs can also be introduced as a new class of impurities in chemical drugs. In both cases, residual HCPs need to be adequately controlled to ensure product purity, quality, and patient safety. Although a lot of attentions have been focused on defining a universally acceptable limit for such impurities, the risks associated with residual HCPs on product quality, safety, and efficacy often need to be determined on a case-by-case basis taking into consideration the residual HCP profile in the product, the dose, dosage form, and administration route etc. Here we describe the unique challenges for residual HCP control presented by the biocatalytic synthesis of a Merck investigational stimulator of interferon genes protein (STING) agonist, MK-1454, which is a cyclic dinucleotide synthesized using E. coli cell lysate overexpressing cyclic GMP-AMP synthase (cGAS) as a biocatalyst. In this study, a holistic characterization of residual protein impurities using a variety of analytical tools including nano-LC-MS/MS, together with in silico immunogenicity prediction of identified proteins, facilitated risk assessment and guided process development to achieve adequate removal of residual protein impurities in MK-1454 API. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fengqiang Wang
- Small Molecular Analytical Research & Development, Rahway, NJ.,Biologics Analytical Research & Development, Kenilworth, NJ
| | - Xuanwen Li
- Analytical Enabling Technologies, Analytical Research & Development, Kenilworth, NJ
| | - Michael Swanson
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), West Point, PA
| | - Erik Guetschow
- Small Molecular Analytical Research & Development, Rahway, NJ
| | | | - Joseph P Smith
- Analytical Enabling Technologies, Analytical Research & Development, Kenilworth, NJ
| | - Erik Hoyt
- Small Molecular Analytical Research & Development, Rahway, NJ
| | - Zhijian Liu
- Small Molecular Process Research & Development, Rahway, NJ
| | - Douglas Richardson
- Analytical Enabling Technologies, Analytical Research & Development, Kenilworth, NJ
| | - Xiaodong Bu
- Small Molecular Analytical Research & Development, Rahway, NJ
| | - Vibha Jawa
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), West Point, PA
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9
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Wilson LJ, Lewis W, Kucia-Tran R, Bracewell DG. Identification and classification of host cell proteins during biopharmaceutical process development. Biotechnol Prog 2021; 38:e3224. [PMID: 34751518 DOI: 10.1002/btpr.3224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 11/10/2022]
Abstract
As significant improvements in volumetric antibody productivity have been achieved by advances in upstream processing over the last decade, and harvest material has become progressively more difficult to recover with these intensified upstream operations, the segregation of upstream and downstream processing has remained largely unchanged. By integrating upstream and downstream process development, product purification issues are given consideration during the optimization of upstream operating conditions, which mitigates the need for extensive and expensive clearance strategies downstream. To investigate the impact of cell culture duration on critical quality attributes, CHO-expressed IgG1 was cultivated in two 2 L bioreactors with samples taken on days 8, 10, 13, 15, and 17. The material was centrifuged, filtered and protein A purified on a 1 ml HiTrap column. Host cell protein (HCP) identification by mass spectrometry (MS) was applied to this system to provide insights into cellular behavior and HCP carryover during protein A purification. It was shown that as cultivation progressed from day 8 to 17 and antibody titer increased, product quality declined due to an increase in post-protein A HCPs (from 72 to 475 peptides detected by MS) and a decrease in product monomer percentage (from 98% to 95.5%). Additionally, the MS data revealed an increase in the abundance of several classes of post-protein A HCPs (e.g., stress response proteins and indicators of cell age), particularly on days 15 and 17 of culture, which were associated with significant increases in total overall HCP levels. This provides new insight into the specific types of HCPs that are retained during mAb purification and may be used to aid process development strategies.
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Affiliation(s)
- Louisa J Wilson
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London, UK.,GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Will Lewis
- GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | | | - Daniel G Bracewell
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London, UK
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10
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Waldera-Lupa DM, Jasper Y, Köhne P, Schwichtenhövel R, Falkenberg H, Flad T, Happersberger P, Reisinger B, Dehghani A, Moussa R, Waerner T. Host cell protein detection gap risk mitigation: quantitative IAC-MS for ELISA antibody reagent coverage determination. MAbs 2021; 13:1955432. [PMID: 34347561 PMCID: PMC8344763 DOI: 10.1080/19420862.2021.1955432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Host cell proteins (HCPs) must be sufficiently cleared from recombinant biopharmaceuticals during the downstream process (DSP) to ensure product quality, purity, and patient safety. For monitoring of HCP clearance, the typical method chosen is an enzyme-linked immunosorbent assay (ELISA) using polyclonal anti-HCP antibodies obtained from an immunization campaign. This polyclonal reagent is a critical factor for functionality and confidence of the ELISA. Therefore, it is important to ensure that the pool of ELISA antibodies covers a broad spectrum of the HCPs that potentially could persist in the final drug substance. Typically, coverage is determined by gel-based approaches. Here, we present a quantitative proteomics approach combined with purification of HCPs by immunoaffinity chromatography (qIAC-MS) for assessment of ELISA coverage. The cell culture fluid (CCF) of a mock fermentation and a recombinant monoclonal antibody product were characterized in detail to investigate whether the HCPs used for immunization of animals accurately represent HCPs that are relevant to the process. Using the qIAC-MS approach, the ELISA antibody coverage was determined for mock fermentation and product CCF, as well as several different DSP intermediates. Here, the use of different controls facilitated the identification and quantification of HCPs present in the polyclonal reagent and those that nonspecifically bound to IAC material. This study successfully demonstrates that the described qIAC-MS approach is not only a suitable orthogonal method to commonly used 2D SDS-PAGE-based analysis for evaluating ELISA antibody coverage, but that it further identifies HCPs covered as well as missed by the ELISA, enabling an improved risk assessment of HCP ELISA.
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Affiliation(s)
| | - Yvonne Jasper
- Bioanalytics, Protagen Protein Services GmbH, Dortmund, Germany
| | - Pia Köhne
- Bioanalytics, Protagen Protein Services GmbH, Dortmund, Germany
| | | | | | - Thomas Flad
- Bioanalytics, Protagen Protein Services GmbH, Dortmund, Germany
| | - Peter Happersberger
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Bernd Reisinger
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Alireza Dehghani
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Roland Moussa
- Bioanalytics, Protagen Protein Services GmbH, Dortmund, Germany
| | - Thomas Waerner
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
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11
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Jones M, Palackal N, Wang F, Gaza-Bulseco G, Hurkmans K, Zhao Y, Chitikila C, Clavier S, Liu S, Menesale E, Schonenbach NS, Sharma S, Valax P, Waerner T, Zhang L, Connolly T. "High-risk" host cell proteins (HCPs): A multi-company collaborative view. Biotechnol Bioeng 2021; 118:2870-2885. [PMID: 33930190 DOI: 10.1002/bit.27808] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 12/14/2022]
Abstract
Host cell proteins (HCPs) are process-related impurities that may copurify with biopharmaceutical drug products. Within this class of impurities there are some that are more problematic. These problematic HCPs can be considered high-risk and can include those that are immunogenic, biologically active, or enzymatically active with the potential to degrade either product molecules or excipients used in formulation. Some have been shown to be difficult to remove by purification. Why should the biopharmaceutical industry worry about these high-risk HCPs? What approach could be taken to understand the origin of its copurification and address these high-risk HCPs? To answer these questions, the BioPhorum Development Group HCP Workstream initiated a collaboration among its 26-company team with the goal of industry alignment around high-risk HCPs. The information gathered through literature searches, company experiences, and surveys were used to compile a list of frequently seen problematic/high-risk HCPs. These high-risk HCPs were further classified based on their potential impact into different risk categories. A step-by-step recommendation is provided for establishing a comprehensive control strategy based on risk assessments for monitoring and/or eliminating the known impurity from the process that would be beneficial to the biopharmaceutical industry.
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Affiliation(s)
- Marisa Jones
- GlaxoSmithKline, CMC Analytical, Structure & Function Characterization, Collegeville, Pennsylvania, USA
| | - Nisha Palackal
- Regeneron Pharmaceuticals Inc., Protein Biochemistry, Tarrytown, New York, USA
| | - Fengqiang Wang
- Merck & Co. Inc., Analytical Research & Development, Kenilworth, New Jersey, USA
| | | | - Karen Hurkmans
- AbbVie Bioresearch Center, Protein Analytics, Worcester, Massachusetts, USA
| | - Yiwei Zhao
- Takeda Pharmaceuticals, Pharmaceutical science, Cambridge, Massachusetts, USA
| | - Carmelata Chitikila
- Janssen R&D LLC, BioTherapeutics Development and Supply, Analytical Development, Bioassay Methods Development, Malvern, Pennsylvania, USA
| | - Severine Clavier
- Sanofi R&D, BioAnalytics, Biologics Development, Vitry-sur-seine, France
| | - Suli Liu
- Biogen, Analytical Development, Cambridge, Massachusetts, USA
| | - Emily Menesale
- Biogen, Analytical Development, Cambridge, Massachusetts, USA
| | - Nicole S Schonenbach
- Pfizer, Downstream Process Development, Bioprocess R&D, Chesterfield, Missouri, USA
| | - Satish Sharma
- Bristol Meyers Squibb, Analytical Development, New York, New York, USA
| | - Pascal Valax
- Merck KGaA, Global Healthcare Operations, Development and Launch, Biotech Process Sciences, Merck BioDevelopment, Martillac, France
| | - Thomas Waerner
- Boehringer Ingelheim Pharma, GmbH & Co. KG, Analytical Development, Biologicals, Biberach, Germany
| | - Lei Zhang
- Bristol Meyers Squibb, Analytical Development, New York, New York, USA
| | - Trish Connolly
- Development Group Phorum, BioPhorum, The Gridiron building, One Pancras Square, London, UK
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12
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Nie S, Greer T, O'Brien Johnson R, Zheng X, Torri A, Li N. Simple and Sensitive Method for Deep Profiling of Host Cell Proteins in Therapeutic Antibodies by Combining Ultra-Low Trypsin Concentration Digestion, Long Chromatographic Gradients, and BoxCar Mass Spectrometry Acquisition. Anal Chem 2021; 93:4383-4390. [PMID: 33656852 DOI: 10.1021/acs.analchem.0c03931] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Liquid chromatography coupled to mass spectrometry (LC-MS) is a powerful tool for the analysis of host cell proteins (HCP) during antibody drug process development due to its sensitivity, selectivity, and adaptability. However, the enormous dynamic range between the therapeutic antibody and accompanying HCPs poses a significant challenge for LC-MS based detection of these low abundance impurities. To address this challenge, enrichment of HCPs via immunoaffinity, protein A, 2D-LC, or other strategies is typically performed. However, these enrichments are time-consuming and sometimes require a large quantity of sample. Here, we report a simple and sensitive strategy to analyze HCPs in therapeutic antibody samples without cumbersome enrichment by combining an ultra-low trypsin concentration during digestion under nondenaturing conditions, a long chromatographic gradient, and BoxCar acquisition (ULTLB) on a quadrupole-Orbitrap mass spectrometer. Application of this strategy to the NIST monoclonal antibody standard (NISTmAb) resulted in the identification of 453 mouse HCPs, which is a significant increase in the number of identified HCPs without enrichment compared to previous reports. Known amounts of HCPs were spiked into the purified antibody drug substance, demonstrating that the method sensitivity is as low as 0.5 ppm. Thus, the ULTLB method represents a sensitive and simple platform for deep profiling of HCPs in antibodies.
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Affiliation(s)
- Song Nie
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Tyler Greer
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Reid O'Brien Johnson
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Xiaojing Zheng
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Albert Torri
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
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13
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Molden R, Hu M, Yen E S, Saggese D, Reilly J, Mattila J, Qiu H, Chen G, Bak H, Li N. Host cell protein profiling of commercial therapeutic protein drugs as a benchmark for monoclonal antibody-based therapeutic protein development. MAbs 2021; 13:1955811. [PMID: 34365906 PMCID: PMC8354607 DOI: 10.1080/19420862.2021.1955811] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 01/20/2023] Open
Abstract
Therapeutic proteins including monoclonal antibodies (mAbs) are usually produced in engineered host cell lines that also produce thousands of endogenous proteins at varying levels. A critical aspect of the development of biotherapeutics manufacturing processes is the removal of these host cell proteins (HCP) to appropriate levels in order to minimize risk to patient safety and drug efficacy. During the development process and associated analytical characterization, mass spectrometry (MS) has become an increasingly popular tool for HCP analysis due to its ability to provide both relative abundance and identity of individual HCP and because the method does not rely on polyclonal antibodies, which are used in enzyme-linked immunosorbent assays. In this study, HCP from 29 commercially marketed mAb and mAb-based therapeutics were profiled using liquid chromatography (LC)-MS/MS with the identification and relative quantification of 79 individual HCP in total. Excluding an outlier drug, the relative levels of individual HCP determined in the approved therapeutics were generally low, with an average of 20 ppm (µmol HCP/mol drug) measured by LC-MS/MS, and only a few (<7 in average) HCP were identified in each drug analyzed. From this analysis, we also gained knowledge about which HCP are frequently identified in mAb-based products and their typical levels relative to the drugs for the identified individual HCP. In addition, we examined HCP composition from antibodies produced in house and found our current development process brings HCP to levels that are consistent with marketed drugs. Finally, we described a specific case to demonstrate how the HCP information from commercially marketed drugs could inform future HCP analyses.
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Affiliation(s)
- Rosalynn Molden
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Mengqi Hu
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Sook Yen E
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Diana Saggese
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - James Reilly
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - John Mattila
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Haibo Qiu
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Gang Chen
- Protein Expression Sciences, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Hanne Bak
- Preclinical Manufacturing and Process Development, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
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14
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Clavier S, Fougeron D, Petrovic S, Elmaleh H, Fourneaux C, Bugnazet D, Duffieux F, Masiero A, Mitra-Kaushik S, Genet B, Fromentin Y, Kreiss P, Laborderie B, Brault D, Menet JM. Improving the analytical toolbox to investigate copurifying host cell proteins presence: N-(4)-(β-acetylglucosaminyl)- l-asparaginase case study. Biotechnol Bioeng 2020; 117:3368-3378. [PMID: 32706388 PMCID: PMC7689792 DOI: 10.1002/bit.27514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/01/2020] [Accepted: 07/13/2020] [Indexed: 11/16/2022]
Abstract
Levels of host cell proteins (HCPs) in purification intermediates and drug substances (DS) of monoclonal antibodies (mAbs) must be carefully monitored for the production of safe and efficacious biotherapeutics. During the development of mAb1, an immunoglobulin G1 product, unexpected results generated with HCP Enzyme‐Linked Immunosorbent Assay (ELISA) kit triggered an investigation which led to the identification of a copurifying HCP called N‐(4)‐(β‐acetylglucosaminyl)‐l‐asparaginase (AGA, EC3.5.1.26) by liquid chromatography–tandem mass spectrometry (LC‐MS/MS). The risk assessment performed indicated a low immunogenicity risk for the copurifying HCP and an ad hoc stability study demonstrated no mAb glycan cleavage and thus no impact on product quality. Fractionation studies performed on polishing steps revealed that AGA was coeluted with the mAb. Very interestingly, the native digestion protocol implemented to go deeper in the MS–HCP profiling was found to be incompatible with correct AGA detection in last purification intermediate and DS, further suggesting a hitchhiking behavior of AGA. In silico surface characterization of AGA also supports this hypothesis. Finally, the combined support of HCP ELISA results and MS allowed process optimization and removal of this copurifying HCP.
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Affiliation(s)
- Séverine Clavier
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | - Delphine Fougeron
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | - Suzana Petrovic
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | - Hagit Elmaleh
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | - Céline Fourneaux
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | - Dawid Bugnazet
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | - Francis Duffieux
- Protein Science and Technology, Biologics Research, Sanofi R&D, Vitry-Sur-Seine, France
| | | | | | - Bruno Genet
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | - Yann Fromentin
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | - Patrick Kreiss
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | | | - Dominique Brault
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
| | - Jean-Michel Menet
- BioAnalytics, Biologics Development, Sanofi R&D, Vitry-Sur-Seine, France
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15
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Chamberlain P, Rup B. Immunogenicity Risk Assessment for an Engineered Human Cytokine Analogue Expressed in Different Cell Substrates. AAPS J 2020; 22:65. [PMID: 32291556 DOI: 10.1208/s12248-020-00443-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/02/2020] [Indexed: 11/30/2022]
Abstract
The purpose of this article is to illustrate how performance of an immunogenicity risk assessment at the earliest stage of product development can be instructive for critical early decision-making such as choice of host system for expression of a recombinant therapeutic protein and determining the extent of analytical characterization and control of heterogeneity in co- and post-translational modifications. Application of a risk-based approach for a hypothetical recombinant DNA analogue of a human endogenous cytokine with immunomodulatory functions is described. The manner in which both intrinsic and extrinsic factors could interact to influence the relative scale of risk associated with expression in alternative hosts, namely Chinese hamster ovary (CHO) cells, Pichia pastoris, Escherichia coli, or Nicotinia tabacum is considered in relation to the development of the investigational product to treat an autoimmune condition. The article discusses how particular product-related variants (primary amino acid sequence modifications and post-translational glycosylation or other modifications) and process-derived impurities (host cell proteins, endotoxins, beta-glucans) associated with the different expression systems might influence the impact of immunogenicity on overall clinical benefit versus risk for a therapeutic protein candidate that has intrinsic MHC Class II binding potential. The implications of the choice of expression system for relative risk are discussed in relation to specific actions for evaluation and measures for risk mitigation, including use of in silico and in vitro methods to understand intrinsic immunogenic potential relative to incremental risk associated with non-human glycan and protein impurities. Finally, practical guidance on presentation of this information in regulatory submissions to support clinical development is provided.
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Affiliation(s)
- Paul Chamberlain
- NDA Advisory Board, NDA Regulatory Science Ltd, Grove House, Guildford Road, Leatherhead, Surrey, KT22 9DF, UK.
| | - Bonita Rup
- Bonnie Rup Consulting, LLC, Reading, Massachusetts, USA
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16
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Dahodwala H, Lee KH. The fickle CHO: a review of the causes, implications, and potential alleviation of the CHO cell line instability problem. Curr Opin Biotechnol 2019; 60:128-137. [DOI: 10.1016/j.copbio.2019.01.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/04/2018] [Accepted: 01/21/2019] [Indexed: 02/08/2023]
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17
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Lavoie RA, Fazio A, Williams TI, Carbonell R, Menegatti S. Targeted capture of Chinese hamster ovary host cell proteins: Peptide ligand binding by proteomic analysis. Biotechnol Bioeng 2019; 117:438-452. [DOI: 10.1002/bit.27213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/04/2019] [Accepted: 10/21/2019] [Indexed: 01/06/2023]
Affiliation(s)
- R. Ashton Lavoie
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh North Carolina
| | - Alice Fazio
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh North Carolina
| | - Taufika Islam Williams
- Molecular Education, Technology, and Research Innovation Center (METRIC)North Carolina State UniversityRaleigh North Carolina
| | - Ruben Carbonell
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh North Carolina
- Biomanufacturing Training and Education Center (BTEC)North Carolina State UniversityRaleigh North Carolina
- The National Institute for Innovation in Manufacturing Biopharmaceuticals (NIIMBL)Newark Delaware
| | - Stefano Menegatti
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh North Carolina
- Biomanufacturing Training and Education Center (BTEC)North Carolina State UniversityRaleigh North Carolina
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18
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Gilgunn S, El-Sabbahy H, Albrecht S, Gaikwad M, Corrigan K, Deakin L, Jellum G, Bones J. Identification and tracking of problematic host cell proteins removed by a synthetic, highly functionalized nonwoven media in downstream bioprocessing of monoclonal antibodies. J Chromatogr A 2019; 1595:28-38. [DOI: 10.1016/j.chroma.2019.02.056] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/15/2019] [Accepted: 02/24/2019] [Indexed: 01/15/2023]
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19
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Belén LH, Lissabet JB, de Oliveira Rangel-Yagui C, Effer B, Monteiro G, Pessoa A, Farías Avendaño JG. A structural in silico analysis of the immunogenicity of l-asparaginase from Escherichia coli and Erwinia carotovora. Biologicals 2019; 59:47-55. [DOI: 10.1016/j.biologicals.2019.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 12/20/2022] Open
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20
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Fukuda N, Senga Y, Honda S. Anxa2
‐ and
Ctsd
‐knockout CHO cell lines to diminish the risk of contamination with host cell proteins. Biotechnol Prog 2019; 35:e2820. [DOI: 10.1002/btpr.2820] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/08/2019] [Accepted: 04/09/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Nobuo Fukuda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Ibaraki Japan
| | - Yukako Senga
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Ibaraki Japan
| | - Shinya Honda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Ibaraki Japan
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21
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Wilson LJ, Lewis W, Kucia-Tran R, Bracewell DG. Identification of upstream culture conditions and harvest time parameters that affect host cell protein clearance. Biotechnol Prog 2019; 35:e2805. [PMID: 30868763 DOI: 10.1002/btpr.2805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 02/01/2023]
Abstract
During early stage bioprocess development, characterizing interactions between unit operations is a key challenge. Such interactions include the release of host cell enzymes early in the process causing losses in product quality downstream. Using a CHO-expressed IgG1 system, the impact of cell culture duration was investigated using a 50 L bioreactor and performing scale-down protein A purification. While antibody titer doubled during the last week of culture, the post-protein A host cell protein (HCP) levels increased from 243 to 740 ppm. Effects of pH and temperature were then explored using fed-batch ambr250 bioreactors, and parameters enabling higher titers were linked to a decrease in post-protein A product purity. These trade-offs between titer and product quality were visualized using a window of operation. The downstream space was explored further by exposing shake flask material to shear representative of disc stack centrifugation, prior to purification, and by adding polishing chromatography. While product quality decreased with progressing cultivation, cells became more shear resistant. Polishing chromatography resulted in product fragmentation which increased fourfold from Day 10 to 24, adding constraint to achieving both efficient HCP clearance as well as high monomer purities. These examples highlight the importance of adopting integrated approaches to upstream and downstream development strategies to enable whole process optimization.
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Affiliation(s)
- Louisa J Wilson
- Department of Biochemical Engineering, University College London, London, UK.,Department of Biopharm Process Research, GlaxoSmithKline, Stevenage, Herts, UK
| | - Will Lewis
- Department of Biopharm Process Research, GlaxoSmithKline, Stevenage, Herts, UK
| | - Richard Kucia-Tran
- Department of Biopharm Process Research, GlaxoSmithKline, Stevenage, Herts, UK
| | - Daniel G Bracewell
- Department of Biochemical Engineering, University College London, London, UK
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22
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Falkenberg H, Waldera-Lupa DM, Vanderlaan M, Schwab T, Krapfenbauer K, Studts JM, Flad T, Waerner T. Mass spectrometric evaluation of upstream and downstream process influences on host cell protein patterns in biopharmaceutical products. Biotechnol Prog 2019; 35:e2788. [DOI: 10.1002/btpr.2788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/03/2019] [Accepted: 02/10/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Heiner Falkenberg
- Protagen Protein Services GmbH; Biotherapeutical Analytics; Dortmund Germany
| | | | | | - Thomas Schwab
- Department of Analytical Development Biologicals; Boehringer Ingelheim Pharma GmbH & Co. KG, Analytical Development Biologicals; Biberach Germany
| | - Kurt Krapfenbauer
- Department of European Affairs; European Association for Predictive, Preventive and Personalised Medicine; Vienna Austria
| | - Joey Michael Studts
- Department of Bioprocess Development Biologicals; Boehringer Ingelheim Pharma GmbH & Co. KG, Bioprocess Development Biologicals; Biberach Germany
| | - Thomas Flad
- Protagen Protein Services GmbH; Biotherapeutical Analytics; Dortmund Germany
| | - Thomas Waerner
- Department of Analytical Development Biologicals; Boehringer Ingelheim Pharma GmbH & Co. KG, Analytical Development Biologicals; Biberach Germany
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23
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Gilgunn S, Bones J. Challenges to industrial mAb bioprocessing—removal of host cell proteins in CHO cell bioprocesses. Curr Opin Chem Eng 2018; 22:98-106. [DOI: 10.1016/j.coche.2018.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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24
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Abstract
Complete, accurate genome assemblies are necessary to design targets for genetic engineering strategies. Successful gene knockdowns and knockouts in Chinese hamster ovary (CHO) cells may prevent the expression of difficult-to-remove host cell proteins (HCPs). HCPs, if not removed, can cause problems in stability, safety, and efficacy of the biotherapeutic. A significantly improved Chinese hamster (CH) reference genome was used to identify new knockout targets with similar predicted functions and characteristics as the difficult-to-remove host cell lipases, LPL, PLBL2, and LPLA2. The CHO-K1 gene and protein sequences of several of these lipases were corrected using the updated CH genome. Sequence alignments were then used to identify conserved regions that may serve as possible targets for multiple simultaneous gene knockouts. Finally, comparison of the CHO-K1 lipase protein sequences to their human orthologs provided insight into which lipases, if persistent in the drug product, could possibly cause immunogenic responses in patients.
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Affiliation(s)
- Madolyn L. MacDonald
- Delaware Biotechnology Institute University of Delaware Newark DE, 19711
- Center for Bioinformatics and Computational Biology University of Delaware Newark DE, 19711
- Dept. of Computer and Information Sciences University of Delaware Newark DE, 19716
| | - Nathaniel K. Hamaker
- Delaware Biotechnology Institute University of Delaware Newark DE, 19711
- Dept. of Chemical and Biomolecular Engineering University of Delaware Newark DE, 19716
| | - Kelvin H. Lee
- Delaware Biotechnology Institute University of Delaware Newark DE, 19711
- Dept. of Chemical and Biomolecular Engineering University of Delaware Newark DE, 19716
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25
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Valente KN, Levy NE, Lee KH, Lenhoff AM. Applications of proteomic methods for CHO host cell protein characterization in biopharmaceutical manufacturing. Curr Opin Biotechnol 2018; 53:144-50. [DOI: 10.1016/j.copbio.2018.01.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/27/2017] [Accepted: 01/04/2018] [Indexed: 12/17/2022]
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26
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Goey CH, Alhuthali S, Kontoravdi C. Host cell protein removal from biopharmaceutical preparations: Towards the implementation of quality by design. Biotechnol Adv 2018; 36:1223-1237. [DOI: 10.1016/j.biotechadv.2018.03.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/12/2018] [Accepted: 03/29/2018] [Indexed: 01/05/2023]
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27
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Vanderlaan M, Zhu-Shimoni J, Lin S, Gunawan F, Waerner T, Van Cott KE. Experience with host cell protein impurities in biopharmaceuticals. Biotechnol Prog 2018; 34:828-837. [PMID: 29693803 DOI: 10.1002/btpr.2640] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/09/2018] [Indexed: 12/29/2022]
Abstract
In the 40-year history of biopharmaceuticals, there have been a few cases where the final products contained residual host cell protein (HCP) impurities at levels high enough to be of concern. This article summarizes the industry experience in these cases where HCP impurities have been presented in public forums and/or published. Regulatory guidance on HCP impurities is limited to advising that products be as pure as practical, with no specified numerical limit because the risk associated with HCP exposure often depends on the clinical setting (route of administration, dose, indication, patient population) and the particular impurity. While the overall safety and purity track record of the industry is excellent, these examples illustrate several important lessons learned about the kinds of HCPs that co-purify with products (e.g., product homologs, and HCPs that react with product), and the kinds of clinical consequences of HCP impurities (e.g., direct biological activity, immunogenicity, adjuvant). The literature on industry experience with HCP impurities is scattered, and this review draws in to one reference documented examples where the data have been presented in meetings, patents, product inserts, or press releases, in addition to peer-reviewed journal articles. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:828-837, 2018.
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Affiliation(s)
- Martin Vanderlaan
- Department of Analytical Development and Quality Control, Genentech, 1 DNA Way, South San Francisco, CA, 94080
| | - Judith Zhu-Shimoni
- Department of Analytical Development and Quality Control, Genentech, 1 DNA Way, South San Francisco, CA, 94080
| | - Sansan Lin
- Department of Analytical Development and Quality Control, Genentech, 1 DNA Way, South San Francisco, CA, 94080
| | - Feny Gunawan
- Department of Analytical Development and Quality Control, Genentech, 1 DNA Way, South San Francisco, CA, 94080
| | - Thomas Waerner
- Department of Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Kevin E Van Cott
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588
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28
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29
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Abstract
Host cell proteins (HCPs) are endogenous impurities, and their proteolytic and binding properties can compromise the integrity, and, hence, the stability and efficacy of recombinant therapeutic proteins such as monoclonal antibodies (mAbs). Nonetheless, purification of mAbs currently presents a challenge because they often co-elute with certain HCP species during the capture step of protein A affinity chromatography. A Quality-by-Design (QbD) strategy to overcome this challenge involves identifying residual HCPs and tracing their source to the harvested cell culture fluid (HCCF) and the corresponding cell culture operating parameters. Then, problematic HCPs in HCCF may be reduced by cell engineering or culture process optimization. Here, we present experimental results linking cell culture temperature and post-protein A residual HCP profile. We had previously reported that Chinese hamster ovary cell cultures conducted at standard physiological temperature and with a shift to mild hypothermia on day 5 produced HCCF of comparable product titer and HCP concentration, but with considerably different HCP composition. In this study, we show that differences in HCP variety at harvest cascaded to downstream purification where different residual HCPs were present in the two sets of samples post-protein A purification. To detect low-abundant residual HCPs, we designed a looping liquid chromatography-mass spectrometry method with continuous expansion of a preferred, exclude, and targeted peptide list. Mild hypothermic cultures produced 20% more residual HCP species, especially cell membrane proteins, distinct from the control. Critically, we identified that half of the potentially immunogenic residual HCP species were different between the two sets of samples.
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Affiliation(s)
- Cher Hui Goey
- a Department of Chemical Engineering , Centre for Process Systems Engineering, Imperial College London , London , U.K
| | - David Bell
- b Department of Medicine , Imperial College London , London , U.K
| | - Cleo Kontoravdi
- a Department of Chemical Engineering , Centre for Process Systems Engineering, Imperial College London , London , U.K
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30
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Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system. In particular, a modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups. Both these methods have distinct advantages in the separation and identification of thousands of individual proteins species including protein isoforms and post-translational modifications. This review will discuss the principles of 2D-PAGE and 2D-DIGE including limitations to the methods. 2D-PAGE and 2D-DIGE continue to be popular methods in bioprocessing-related research (particularly on recombinant Chinese hamster ovary cells), which will also be discussed in the review chapter.
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Affiliation(s)
- Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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31
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Hogwood CEM, Chiverton LM, Mark Smales C. Characterization of Host Cell Proteins (HCPs) in CHO Cell Bioprocesses. Methods Mol Biol 2017; 1603:243-50. [PMID: 28493135 DOI: 10.1007/978-1-4939-6972-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Host cell protein content during bioprocessing of biotherapeutic proteins generated from cultured Chinese hamster ovary (CHO) cells is typically measured using immunological and gel-based methods. Estimation of HCP concentration is usually undertaken using Enzyme-Linked ImmunoSorbent Assays (ELISA), while estimation of HCP clearance/presence can be achieved by comparing 2D-PAGE images of samples and by undertaking western blotting of 2D-PAGE analyzed samples. Here, we describe the analyses of HCP content using these methodologies.
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Mufarrege EF, Giorgetti S, Etcheverrigaray M, Terry F, Martin W, De Groot AS. De-immunized and Functional Therapeutic (DeFT) versions of a long lasting recombinant alpha interferon for antiviral therapy. Clin Immunol 2017; 176:31-41. [PMID: 28089609 DOI: 10.1016/j.clim.2017.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/05/2017] [Accepted: 01/07/2017] [Indexed: 11/18/2022]
Abstract
Interferon α (IFN-α) exerts potent antiviral, immunomodulatory, and antiproliferative activity and have proven clinical utility in chronic hepatitis B and C virus infections. However, repeated IFN-α administration induces neutralizing antibodies (NAb) against the therapeutic in a significant number of patients. Associations between IFN-α immunogenicity and loss of efficacy have been described. So as to improve the in vivo biological efficacy of IFN-α, a long lasting hyperglycosylated protein (4N-IFN) derived from IFN-α2b wild type (WT-IFN) was developed. However, in silico analysis performed using established in silico methods revealed that 4N-IFN had more T cell epitopes than WT-IFN. In order to develop a safer and more efficient IFN therapy, we applied the DeFT (De-immunization of Functional Therapeutics) approach to producing functional, de-immunized versions of 4N-IFN. Using the OptiMatrix in silico tool in ISPRI, the 4N-IFN sequence was modified to reduce HLA binding potential of specific T cell epitopes. Following verification of predictions by HLA binding assays, eight modifications were selected and integrated in three variants: 4N-IFN(VAR1), (VAR2) and (VAR3). Two of the three variants (VAR1 and VAR3) retained anti-viral function and demonstrated reduced T-cell immunogenicity in terms of T-cell proliferation and Th1 and Th2 cytokine levels, when compared to controls (commercial NG-IFN (non-glycosylated), PEG-IFN, WT-IFN and 4N-IFN). It was previously demonstrated that N-glycosylation improved IFN-α pharmacokinetic properties. Here, we further reduce immunogenicity as measured in vitro using T cell assays and cytokine profiling by modifying the T cell epitope content of a protein (de-immunizing). Taking into consideration the present results and previously reported immunogenicity data for commercial IFN-α2b variants, 4N-IFN(VAR1) and 4N-IFN-4N(VAR3) appear to be promising candidates for improved IFN-α therapy of HCV and HBV.
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Affiliation(s)
- Eduardo F Mufarrege
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Cultivos Celulares, FBCB, UNL, Santa Fe, Argentina.
| | - Sofía Giorgetti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Cultivos Celulares, FBCB, UNL, Santa Fe, Argentina
| | - Marina Etcheverrigaray
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Cultivos Celulares, FBCB, UNL, Santa Fe, Argentina
| | | | | | - Anne S De Groot
- EpiVax, Inc., Providence, RI, USA; Institute for Immunology and Informatics, University of Rhode Island, RI, USA
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Agarabi CD, Chavez BK, Lute SC, Read EK, Rogstad S, Awotwe-Otoo D, Brown MR, Boyne MT, Brorson KA. Exploring the linkage between cell culture process parameters and downstream processing utilizing a plackett-burman design for a model monoclonal antibody. Biotechnol Prog 2016; 33:163-170. [DOI: 10.1002/btpr.2402] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/16/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Cyrus D. Agarabi
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Brittany K. Chavez
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Scott C. Lute
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Erik K. Read
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Sarah Rogstad
- Div. of Pharmaceutical Analysis; Office of Testing and Research, OPQ, CDER, FDA; Silver Spring MD
| | - David Awotwe-Otoo
- Div. of Post Marketing Activities II; OPQ, CDER, FDA; Silver Spring MD
| | - Matthew R. Brown
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
| | - Michael T. Boyne
- Div. of Pharmaceutical Analysis; Office of Testing and Research, OPQ, CDER, FDA; Silver Spring MD
| | - Kurt A. Brorson
- Div. II, Office of Biotechnology Products, Office of Pharmaceutical Quality, CDER; FDA; Silver Spring MD
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Jawa V, Joubert MK, Zhang Q, Deshpande M, Hapuarachchi S, Hall MP, Flynn GC. Evaluating Immunogenicity Risk Due to Host Cell Protein Impurities in Antibody-Based Biotherapeutics. AAPS J 2016; 18:1439-1452. [DOI: 10.1208/s12248-016-9948-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/11/2016] [Indexed: 11/30/2022]
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Chiverton LM, Evans C, Pandhal J, Landels AR, Rees BJ, Levison PR, Wright PC, Smales CM. Quantitative definition and monitoring of the host cell protein proteome using iTRAQ - a study of an industrial mAb producing CHO-S cell line. Biotechnol J 2016; 11:1014-24. [PMID: 27214759 PMCID: PMC5031201 DOI: 10.1002/biot.201500550] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/28/2016] [Accepted: 05/12/2016] [Indexed: 11/14/2022]
Abstract
There are few studies defining CHO host cell proteins (HCPs) and the flux of these throughout a downstream purification process. Here we have applied quantitative iTRAQ proteomics to follow the HCP profile of an antibody (mAb) producing CHO‐S cell line throughout a standard downstream purification procedure consisting of a Protein A, cation and anion exchange process. We used both 6 sample iTRAQ experiment to analyze technical replicates of three samples, which were culture harvest (HCCF), Protein A flow through and Protein A eluate and an 8 sample format to analyze technical replicates of four sample types; HCCF compared to Protein A eluate and subsequent cation and anion exchange purification. In the 6 sample iTRAQ experiment, 8781 spectra were confidently matched to peptides from 819 proteins (including the mAb chains). Across both the 6 and 8 sample experiments 936 proteins were identified. In the 8 sample comparison, 4187 spectra were confidently matched to peptides from 219 proteins. We then used the iTRAQ data to enable estimation of the relative change of individual proteins across the purification steps. These data provide the basis for application of iTRAQ for process development based upon knowledge of critical HCPs.
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Affiliation(s)
- Lesley M Chiverton
- Centre for Molecular Processing and School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Caroline Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Jagroop Pandhal
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Andrew R Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | | | - Phillip C Wright
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.
| | - C Mark Smales
- Centre for Molecular Processing and School of Biosciences, University of Kent, Canterbury, Kent, UK.
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Tran B, Grosskopf V, Wang X, Yang J, Walker D, Yu C, McDonald P. Investigating interactions between phospholipase B-Like 2 and antibodies during Protein A chromatography. J Chromatogr A 2016; 1438:31-8. [PMID: 26896920 DOI: 10.1016/j.chroma.2016.01.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/22/2015] [Accepted: 01/19/2016] [Indexed: 11/27/2022]
Abstract
Purification processes for therapeutic antibodies typically exploit multiple and orthogonal chromatography steps in order to remove impurities, such as host-cell proteins. While the majority of host-cell proteins are cleared through purification processes, individual host-cell proteins such as Phospholipase B-like 2 (PLBL2) are more challenging to remove and can persist into the final purification pool even after multiple chromatography steps. With packed-bed chromatography runs using host-cell protein ELISAs and mass spectrometry analysis, we demonstrated that different therapeutic antibodies interact to varying degrees with host-cell proteins in general, and PLBL2 specifically. We then used a high-throughput Protein A chromatography method to further examine the interaction between our antibodies and PLBL2. Our results showed that the co-elution of PLBL2 during Protein A chromatography is highly dependent on the individual antibody and PLBL2 concentration in the chromatographic load. Process parameters such as antibody resin load density and pre-elution wash conditions also influence the levels of PLBL2 in the Protein A eluate. Furthermore, using surface plasmon resonance, we demonstrated that there is a preference for PLBL2 to interact with IgG4 subclass antibodies compared to IgG1 antibodies.
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Affiliation(s)
- Benjamin Tran
- Benjamin Tran, Purification Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, United States; Pharma Technical Development, Genentech, Inc., United States.
| | | | - Xiangdan Wang
- Development Sciences, Genentech, Inc., United States
| | - Jihong Yang
- Development Sciences, Genentech, Inc., United States
| | - Don Walker
- Pharma Technical Development, Genentech, Inc., United States
| | - Christopher Yu
- Pharma Technical Development, Genentech, Inc., United States
| | - Paul McDonald
- Pharma Technical Development, Genentech, Inc., United States
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Mihara K, Ito Y, Hatano Y, Komurasaki Y, Sugimura A, Jones M, Liu H, Mai S, Lara-Velasco O, Bai L, Ketkar A, Adams M, Hirato T, Ionescu R. Host Cell Proteins: The Hidden Side of Biosimilarity Assessment. J Pharm Sci 2015; 104:3991-3996. [DOI: 10.1002/jps.24642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 07/29/2015] [Accepted: 08/21/2015] [Indexed: 11/05/2022]
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Kumar A, Baycin-Hizal D, Wolozny D, Pedersen LE, Lewis NE, Heffner K, Chaerkady R, Cole RN, Shiloach J, Zhang H, Bowen MA, Betenbaugh MJ. Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics. J Proteome Res 2015; 14:4687-703. [PMID: 26418914 DOI: 10.1021/acs.jproteome.5b00588] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chinese hamster ovary (CHO) cells are the preferred host cell line for manufacturing a variety of complex biotherapeutic drugs including monoclonal antibodies. We performed a proteomics and bioinformatics analysis on the spent medium from adherent CHO cells. Supernatant from CHO-K1 culture was collected and subjected to in-solution digestion followed by LC/LC-MS/MS analysis, which allowed the identification of 3281 different host cell proteins (HCPs). To functionally categorize them, we applied multiple bioinformatics tools to the proteins identified in our study including SignalP, TargetP, SecretomeP, TMHMM, WoLF PSORT, and Phobius. This analysis provided information on the presence of signal peptides, transmembrane domains, and cellular localization and showed that both secreted and intracellular proteins were constituents of the supernatant. Identified proteins were shown to be localized to the secretory pathway including ones playing roles in cell growth, proliferation, and folding as well as those involved in protein degradation and removal. After combining proteins predicted to be secreted or having a signal peptide, we identified 1015 proteins, which we termed as CHO supernatant-ome (CHO-SO), or superome. As a part of this effort, we created a publically accessible web-based tool called GO-CHO to functionally categorize proteins found in CHO-SO and identify enriched molecular functions, biological processes, and cellular components. We also used a tool to evaluate the immunogenicity potential of high-abundance HCPs. Among enriched functions were catalytic activity and structural constituents of the cytoskeleton. Various transport related biological processes, such as vesicle mediated transport, were found to be highly enriched. Extracellular space and vesicular exosome associated proteins were found to be the most enriched cellular components. The superome also contained proteins secreted from both classical and nonclassical secretory pathways. The work and database described in our study will enable the CHO community to rapidly identify high-abundance HCPs in their cultures and therefore help assess process and purification methods used in the production of biologic drugs.
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Affiliation(s)
- Amit Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.,Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases , National Institute of Health, Building 14A, Bethesda, Maryland 20892, United States
| | - Deniz Baycin-Hizal
- Antibody Discovery and Protein Engineering, MedImmune LLC , 1 MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Daniel Wolozny
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2970 Hørsholm, Denmark
| | - Nathan E Lewis
- Department of Biology, Brigham Young University , Provo, Utah 84602, United States.,Department of Pediatrics, University of California , San Diego, California 92093, United States
| | - Kelley Heffner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Raghothama Chaerkady
- Institute of Basic Biomedical Sciences, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine , 733 North Broadway Street, Baltimore, Maryland 21205, United States
| | - Robert N Cole
- Institute of Basic Biomedical Sciences, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine , 733 North Broadway Street, Baltimore, Maryland 21205, United States
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases , National Institute of Health, Building 14A, Bethesda, Maryland 20892, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins School of Medicine , 400 North Broadway Street, Baltimore, Maryland 21287, United States
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering, MedImmune LLC , 1 MedImmune Way, Gaithersburg, Maryland 20878, United States
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
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Farrell A, Mittermayr S, Morrissey B, Mc Loughlin N, Navas Iglesias N, Marison IW, Bones J. Quantitative host cell protein analysis using two dimensional data independent LC-MS(E). Anal Chem 2015; 87:9186-93. [PMID: 26280711 DOI: 10.1021/acs.analchem.5b01377] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Host cell proteins (HCPs) are bioprocess-related impurities arising from cell-death or secretion from nonhuman cells used for recombinant protein production. Clearance of HCPs through downstream purification (DSP) is required to produce safe and efficacious therapeutic proteins. While traditionally measured using anti-HCP ELISA, more in-depth approaches for HCP characterization may ensure that risks to patients from HCPs are adequately assessed. Mass spectrometry methods provide rationale for targeted removal strategies through the provision of both qualitative and quantitative HCP information. A high pH, low pH, reversed-phase data independent 2D-LC-MS(E) proteomic platform was applied to determine HCP repertoires in the Protein A purified monoclonal antibody (mAb) samples as a function of culture harvest time, elution buffer used for DSP and also following inclusion of additional DSP steps. Critical quality attributes (CQAs) were examined for mAbs purified with different Protein A elution buffers to ensure that the selected buffers not only minimized the HCP profile but also exhibited no adverse effect on product quality. Results indicated that an arginine based Protein A elution buffer minimized the levels of HCPs identified and quantified in a purified mAb sample and also demonstrated no impact on product CQAs. It was also observed that mAbs harvested at later stages of cell culture contained higher concentrations of HCPs but that these were successfully removed by the addition of DSP steps complementary to Protein A purification. Taken together, our results showed how mass spectrometry based methods for HCP determination in conjunction with careful consideration of processing parameters such as harvest time, Protein A elution buffers, and subsequent DSP steps can reduce the HCP repertoire of therapeutic mAbs.
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Affiliation(s)
- Amy Farrell
- Characterisation and Comparability Laboratory, NIBRT-The National Institute for Bioprocessing Research and Training , Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland.,School of Biotechnology, Dublin City University , Glasnevin, Dublin 9, Ireland
| | - Stefan Mittermayr
- Characterisation and Comparability Laboratory, NIBRT-The National Institute for Bioprocessing Research and Training , Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
| | - Brian Morrissey
- Characterisation and Comparability Laboratory, NIBRT-The National Institute for Bioprocessing Research and Training , Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
| | - Niaobh Mc Loughlin
- Characterisation and Comparability Laboratory, NIBRT-The National Institute for Bioprocessing Research and Training , Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
| | - Natalia Navas Iglesias
- Department of Analytical Chemistry, University of Granada , Avenue Fuentenueva S/N, 18071 Granada, Spain
| | - Ian W Marison
- School of Biotechnology, Dublin City University , Glasnevin, Dublin 9, Ireland
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, NIBRT-The National Institute for Bioprocessing Research and Training , Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
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Madsen JA, Farutin V, Carbeau T, Wudyka S, Yin Y, Smith S, Anderson J, Capila I. Toward the complete characterization of host cell proteins in biotherapeutics via affinity depletions, LC-MS/MS, and multivariate analysis. MAbs 2015; 7:1128-37. [PMID: 26291024 DOI: 10.1080/19420862.2015.1082017] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Host cell protein (HCP) impurities are generated by the host organism during the production of therapeutic recombinant proteins, and are difficult to remove completely. Though commonly present in small quantities, if levels are not controlled, HCPs can potentially reduce drug efficacy and cause adverse patient reactions. A high resolution approach for thorough HCP characterization of therapeutic monoclonal antibodies is presented herein. In this method, antibody samples are first depleted via affinity enrichment (e.g., Protein A, Protein L) using milligram quantities of material. The HCP-containing flow-through is then enzymatically digested, analyzed using nano-UPLC-MS/MS, and proteins are identified through database searching. Nearly 700 HCPs were identified from samples with very low total HCP levels (< 1 ppm to ∼ 10 ppm) using this method. Quantitation of individual HCPs was performed using normalized spectral counting as the number of peptide spectrum matches (PSMs) per protein is proportional to protein abundance. Multivariate analysis tools were utilized to assess similarities between HCP profiles by: 1) quantifying overlaps between HCP identities; and 2) comparing correlations between individual protein abundances as calculated by spectral counts. Clustering analysis using these measures of dissimilarity between HCP profiles enabled high resolution differentiation of commercial grade monoclonal antibody samples generated from different cell lines, cell culture, and purification processes.
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Affiliation(s)
| | | | | | | | - Yan Yin
- a Momenta Pharmaceuticals ; Cambridge , MA USA
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Bracewell DG, Francis R, Smales CM. The future of host cell protein (HCP) identification during process development and manufacturing linked to a risk-based management for their control. Biotechnol Bioeng 2015; 112:1727-37. [PMID: 25998019 PMCID: PMC4973824 DOI: 10.1002/bit.25628] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 03/04/2015] [Accepted: 04/21/2015] [Indexed: 12/14/2022]
Abstract
The use of biological systems to synthesize complex therapeutic products has been a remarkable success. However, during product development, great attention must be devoted to defining acceptable levels of impurities that derive from that biological system, heading this list are host cell proteins (HCPs). Recent advances in proteomic analytics have shown how diverse this class of impurities is; as such knowledge and capability grows inevitable questions have arisen about how thorough current approaches to measuring HCPs are. The fundamental issue is how to adequately measure (and in turn monitor and control) such a large number of protein species (potentially thousands of components) to ensure safe and efficacious products. A rather elegant solution is to use an immunoassay (enzyme‐linked immunosorbent assay [ELISA]) based on polyclonal antibodies raised to the host cell (biological system) used to synthesize a particular therapeutic product. However, the measurement is entirely dependent on the antibody serum used, which dictates the sensitivity of the assay and the degree of coverage of the HCP spectrum. It provides one summed analog value for HCP amount; a positive if all HCP components can be considered equal, a negative in the more likely event one associates greater risk with certain components of the HCP proteome. In a thorough risk‐based approach, one would wish to be able to account for this. These issues have led to the investigation of orthogonal analytical methods; most prominently mass spectrometry. These techniques can potentially both identify and quantify HCPs. The ability to measure and monitor thousands of proteins proportionally increases the amount of data acquired. Significant benefits exist if the information can be used to determine critical HCPs and thereby create an improved basis for risk management. We describe a nascent approach to risk assessment of HCPs based upon such data, drawing attention to timeliness in relation to biosimilar initiatives. The development of such an approach requires databases based on cumulative knowledge of multiple risk factors that would require national and international regulators, standards authorities (e.g., NIST and NIBSC), industry and academia to all be involved in shaping what is the best approach to the adoption of the latest bioanalytical technology to this area, which is vital to delivering safe efficacious biological medicines of all types. Biotechnol. Bioeng. 2015;112: 1727–1737. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel G Bracewell
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK.
| | | | - C Mark Smales
- Centre for Molecular Processing, School of Biosciences, University of Kent, Canterbury, Kent, UK, CT2 7NJ
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Hogwood CEM, Bracewell DG, Smales CM. Measurement and control of host cell proteins (HCPs) in CHO cell bioprocesses. Curr Opin Biotechnol 2014; 30:153-60. [DOI: 10.1016/j.copbio.2014.06.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 06/16/2014] [Accepted: 06/22/2014] [Indexed: 11/26/2022]
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