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Millán-Martín S, Jakes C, Carillo S, Bones J. Multi-attribute method (MAM) to assess analytical comparability of adalimumab biosimilars. J Pharm Biomed Anal 2023; 234:115543. [PMID: 37385093 DOI: 10.1016/j.jpba.2023.115543] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
Adalimumab drug product (Humira ®), the first fully human monoclonal antibody (mAb) approved by FDA in 2002, led the top ten list of best-selling mAbs in 2018 and has been the most profitable drug in the world. With the expiration of patent protection in Europe in 2018 and in United States by 2023, the landscape is changing as up to 10 adalimumab biosimilars are expected to enter the market in the US. Biosimilars offer the potential to lower costs on health care systems and increase patient accessibility. The analytical similarity of seven different adalimumab biosimilars was accomplished in the present study using the multi-attribute method (MAM), a LC-MS based peptide mapping technique that allows for primary sequence assessment and evaluation of multiple quality attributes including deamidation, oxidation, succinimide formation, N- and C- terminal composition and detailed N-glycosylation analysis. In the first step, characterization of the most relevant post-translational modifications of a reference product was attained during the discovery phase of MAM. During the second step, as part of the MAM targeted monitoring phase, adalimumab batch-to batch variability was evaluated to define statistical intervals for the establishment of similarity ranges. The third step describes biosimilarity evaluation of predefined quality attributes and new peak detection for the assessment of any new or modified peak compared to the reference product. This study highlights a new perspective of the MAM approach and its underlying power for biotherapeutic comparability exercises in addition to analytical characterization. MAM offers a streamlined comparability assessment workflow based on high-confidence quality attribute analysis using high-resolution accurate mass mass spectrometry (HRAM MS) and the capability to detect any new or modified peak compared to the reference product.
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Affiliation(s)
- Silvia Millán-Martín
- National Institute for Bioprocessing Research & Training, Fosters Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
| | - Craig Jakes
- National Institute for Bioprocessing Research & Training, Fosters Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
| | - Sara Carillo
- National Institute for Bioprocessing Research & Training, Fosters Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
| | - Jonathan Bones
- National Institute for Bioprocessing Research & Training, Fosters Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland; School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4 D04 V1W8, Ireland.
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2
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Lin J, Xie M, Liu D, Gao Z, Zhao X, Ma H, Ding S, Li SM, Li S, Liu Y, Zhou F, Hu H, Chen T, Chen H, Xie M, Yang B, Cheng J, Ma M, Nan Y, Ju D. Characterization of light chain c-terminal extension sequence variant in one bispecific antibody. Front Chem 2022; 10:994472. [PMID: 36204149 PMCID: PMC9530627 DOI: 10.3389/fchem.2022.994472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Protein modifications such as post-translational modifications (PTMs) and sequence variants (SVs) occur frequently during protein biosynthesis and have received great attention by biopharma industry and regulatory agencies. In this study, an aberrant peak near light chain (LC) was observed in the non-reduced capillary electrophoresis sodium dodecyl sulfate (nrCE-SDS) electrophoretogram during cell line development of one bispecific antibody (BsAb) product, and the detected mass was about 944 Da higher than LC. The corresponding peak was then enriched by denaturing size-exclusion chromatography (SEC-HPLC) and further characterized by nrCE-SDS and peptide mapping analyses. De novo mass spectra/mass spectra (MS/MS) analysis revealed that the aberrant peak was LC related sequence variant, with the truncated C-terminal sequence “SFNR” (“GEC”deleted) linked with downstream SV40 promotor sequence “EAEAASASELFQ”. The unusual sequence was further confirmed by comparing with the direct synthetic peptide “SFNREAEAASASELFQ”. It was demonstrated by mRNA sequencing of the cell pool that the sequence variant was caused by aberrant splicing at the transcription step. The prepared product containing this extension variant maintained well-folded structure and good functional properties though the LC/Heavy chain (HC) inter-chain disulfide was not formed. Several control strategies to mitigate the risk of this LC related sequence variant were also proposed.
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Affiliation(s)
- Jun Lin
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, China
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Mengyu Xie
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Dan Liu
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Zhen Gao
- Genor Biopharma Co., Ltd., Shanghai, China
| | | | - Hongxia Ma
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Sheng Ding
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Shu mei Li
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Song Li
- Genor Biopharma Co., Ltd., Shanghai, China
| | | | - Fang Zhou
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Hao Hu
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Tao Chen
- Genor Biopharma Co., Ltd., Shanghai, China
| | - He Chen
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Min Xie
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Bo Yang
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Jun Cheng
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Mingjun Ma
- Genor Biopharma Co., Ltd., Shanghai, China
| | - Yanyang Nan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, China
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, China
- *Correspondence: Dianwen Ju,
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3
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Gramlich M, Maier S, Kaiser PD, Traenkle B, Wagner TR, Voglmeir J, Stoll D, Rothbauer U, Zeck A. A Novel PNGase Rc for Improved Protein N-Deglycosylation in Bioanalytics and Hydrogen-Deuterium Exchange Coupled With Mass Spectrometry Epitope Mapping under Challenging Conditions. Anal Chem 2022; 94:9863-9871. [PMID: 35749695 DOI: 10.1021/acs.analchem.2c01748] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-linked glycosylation is a ubiquitous posttranslational modification of proteins. While it plays an important role in the biological function of proteins, it often poses a major challenge for their analytical characterization. Currently available peptide N-glycanases (PNGases) are often inefficient at deglycosylating proteins due to sterically inaccessible N-glycosylation sites. This usually leads to poor sequence coverage in bottom-up analysis using liquid chromatography with tandem mass spectrometry and makes it impossible to obtain an intact mass signal in top-down MS analysis. In addition, most PNGases operate optimally only in the neutral to slightly acidic pH range and are severely compromised in the presence of reducing and denaturing substances, which limits their use for advanced bioanalysis based on hydrogen-deuterium exchange in combination with mass spectrometry (HDX-MS). Here, we present a novel peptide N-glycanase from Rudaea cellulosilytica (PNGase Rc) for which we demonstrate broad substrate specificity for N-glycan hydrolysis from multiply occupied and natively folded proteins. Our results show that PNGase Rc is functional even under challenging, HDX quenching conditions (pH 2.5, 0 °C) and in the presence of 0.4 M tris(2-carboxyethyl)phosphine, 4 M urea, and 1 M guanidinium chloride. Most importantly, we successfully applied the PNGase Rc in an HDX-MS workflow to determine the epitope of a nanobody targeting the extracellular domain of human signal-regulating protein alpha (SIRPα).
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Affiliation(s)
- Marius Gramlich
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Sandra Maier
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Teresa R Wagner
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen 72076, Germany
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dieter Stoll
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany.,Department of Life Sciences, University of Applied Sciences Albstadt-Sigmaringen, Sigmaringen 72488, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen 72076, Germany
| | - Anne Zeck
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
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4
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Zhang A, Chen Z, Li M, Qiu H, Lawrence S, Bak H, Li N. A general evidence-based sequence variant control limit for recombinant therapeutic protein development. MAbs 2021; 12:1791399. [PMID: 32744138 PMCID: PMC7531532 DOI: 10.1080/19420862.2020.1791399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sequence variants (SVs) resulting from unintended amino acid substitutions in recombinant therapeutic proteins have increasingly gained attention from both regulatory agencies and the biopharmaceutical industry given their potential impact on efficacy and safety. With well-optimized production systems, such sequence variants usually exist at very low levels in the final protein products due to the high fidelity of DNA replication and protein biosynthesis process in mammalian expression systems such as Chinese hamster ovary cell lines. However, their levels can be significantly elevated in cases where the selected production cell line has unexpected DNA mutations or the manufacturing process is not fully optimized, for example, if depletion of certain amino acids occurs in the cell culture media in bioreactors. Therefore, it is important to design and implement an effective monitoring and control strategy to prevent or minimize the possible risks of SVs during the early stage of product and process development. However, there is no well-established guidance from the regulatory agencies or consensus across the industry to assess and manage SV risks. A question frequently asked is: What levels of SVs can be considered acceptable during product and process development, but also have no negative effects on drug safety and efficacy in patients? To address this critical question, we have taken a holistic approach and conducted a comprehensive sequence variant analysis. To guide biologic development, a general SV control limit of 0.1% at individual amino acid sites was proposed and properly justified based on extensive literature review, SV benchmark survey of approved therapeutic proteins, and accumulated experience on SV control practice at Regeneron.
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Affiliation(s)
- Aming Zhang
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown, New York, USA
| | - Zhengwei Chen
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown, New York, USA
| | - Meinuo Li
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown, New York, USA
| | - Haibo Qiu
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown, New York, USA
| | - Shawn Lawrence
- Preclinical Manufacturing and Process Development , Tarrytown, New York, USA
| | - Hanne Bak
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown, New York, USA
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown, New York, USA
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5
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Identification, characterization and control of a sequence variant in monoclonal antibody drug product: a case study. Sci Rep 2021; 11:13233. [PMID: 34168178 PMCID: PMC8225904 DOI: 10.1038/s41598-021-92338-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Sequence variants (SV) in protein bio therapeutics can be categorized as unwanted impurities and may raise serious concerns in efficacy and safety of the product. Early detection of specific sequence modifications, that can result in altered physicochemical and or biological properties, is therefore desirable in product manufacturing. Because of their low abundance, and finite resolving power of conventional analytical techniques, they are often overlooked in early drug development. Here, we present a case study where trace amount of a sequence variant is identified in a monoclonal antibody (mAb) based therapeutic protein by LC-MS/MS and the structural and functional features of the SV containing mAb is assessed using appropriate analytical techniques. Further, a very sensitive selected reaction monitoring (SRM) technique is developed to quantify the SV which revealed both prominent and inconspicuous nature of the variant in process chromatography. We present the extensive characterization of a sequence variant in protein biopharmaceutical and first report on control of sequence variants to < 0.05% in final drug product by utilizing SRM based mass spectrometry method during the purification steps.
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6
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Scientific Best Practices for Primary Sequence Confirmation and Sequence Variant Analysis in the Development of Therapeutic Proteins. J Pharm Sci 2020; 110:619-626. [PMID: 33212163 DOI: 10.1016/j.xphs.2020.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 02/01/2023]
Abstract
In this commentary, we will provide a high-level introduction into LC-MS product characterization methodologies deployed throughout biopharmaceutical development. The ICH guidelines for early and late phase filings is broad so that it is applicable to diverse biotherapeutic products in the clinic and industry pipelines. This commentary is meant to address areas of protein primary sequence confirmation and sequence variant analysis where ambiguity exists in industry on the specific scope of work that is needed to fulfill the general guidance that is given in sections Q5b and Q6b. This commentary highlights the discussion and outcomes of two recent workshops centering on the application of LC-MS to primary structure confirmation and sequence variant analysis (SVA) that were held at the 2018 and 2019 CASSS Practical Applications of Mass Spectrometry in the Biotechnology Industry Symposia in San Francisco, CA and Chicago, IL, respectively. Recommendations from the conferences fall into two distinct but related areas; 1) consolidation of opinions amongst industry stakeholders on the specific definitions of peptide mapping and peptide sequencing for primary structure confirmation and the technologies used for both, as they relate to regulatory expectations and submissions and 2) development of fit-for-purpose strategy to define appropriate assay controls in SVA experiments.
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7
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Webster TA, Hadley BC, Dickson M, Busa JK, Jaques C, Mason C. Feedback control of two supplemental feeds during fed-batch culture on a platform process using inline Raman models for glucose and phenylalanine concentration. Bioprocess Biosyst Eng 2020; 44:127-140. [PMID: 32816075 DOI: 10.1007/s00449-020-02429-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/12/2020] [Indexed: 11/29/2022]
Abstract
The use of Raman models for glucose and phenylalanine concentrations to provide the signal for a control algorithm to continuously adjust the feed rate of two separate supplemental feeds during the fed-batch culture of a CHOK1SV GS-KO® cell line in a platform process was evaluated. Automated feed rate adjustment of the glucose feed using a Raman model for glucose concentration, maintained the glucose concentration within the desired target (average deviation ± 0.49 g/L). Automated feed rate adjustment of the nutrient feed using a Raman model for phenylalanine concentration, maintained phenylalanine concentrations within the target (average deviation ± 29.97 mg/L). The novel use of a Raman model for phenylalanine concentration, combined with a Raman model for glucose concentration, to maintain target glucose and phenylalanine concentrations through feed-rate adjustments, reduced the average cumulative glucose and nutrient feed additions (19% and 27% respectively) compared to manually adjusted cultures. Additionally, the proposed automation strategy led to lower osmolality during culture, maintained the nutrient environment more consistently, and achieved higher harvest product concentration (≈ 20% higher) compared to typical fed-batch process control for the cell line and platform process evaluated. Furthermore, the proposed feeding strategy yielded similar glycosylation and charge variant profiles compared to manually adjusted fed-batch process control. The ability to continuously adjust the feed rate addition of two separate feeds in this manner helps enable a shift away from the current daily offline sampling needed to control fed-batch mammalian cell culture during clinical and commercial manufacturing on platform processes.
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Affiliation(s)
| | - Brian C Hadley
- Lonza Biologics Inc, 101 International Dr, Portsmouth, NH, 03801, USA
| | - Marissa Dickson
- Lonza Biologics Inc, 101 International Dr, Portsmouth, NH, 03801, USA
| | - John K Busa
- Lonza Biologics Inc, 101 International Dr, Portsmouth, NH, 03801, USA
| | - Colin Jaques
- Lonza Biologics Plc, 228 Bath Road, Slough, SL14DX, UK
| | - Carrie Mason
- Lonza Biologics Inc, 101 International Dr, Portsmouth, NH, 03801, USA
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8
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Rugbjerg P, Sommer MOA. Overcoming genetic heterogeneity in industrial fermentations. Nat Biotechnol 2019; 37:869-876. [DOI: 10.1038/s41587-019-0171-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 05/28/2019] [Indexed: 12/15/2022]
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9
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Wang S, Xing T, Liu AP, He Z, Yan Y, Daly TJ, Li N. Simple Approach for Improved LC-MS Analysis of Protein Biopharmaceuticals via Modification of Desolvation Gas. Anal Chem 2019; 91:3156-3162. [PMID: 30682238 DOI: 10.1021/acs.analchem.8b05846] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
LC-MS based analysis of protein biopharmaceuticals could benefit from improved data quality, which can subsequently lead to improved drug characterization with higher confidence and less ambiguity. In this study, we created a simple device to modify the desolvation gas on a Q-Exactive mass spectrometer and to demonstrate the utility in improving both peptide mapping analysis and intact mass analysis, the two most routinely and widely applied LC-MS techniques in protein biopharmaceutical characterization. By modifying the desolvation gas with acid vapor from propionic acid (PA) and isopropanol (IPA), the ion suppression effects from trifluoroacetic acid (TFA) in a typical peptide mapping method can be effectively mitigated, thus leading to improved MS sensitivity. By modifying the desolvation gas with base vapor from triethylamine (TEA), the charge reduction effect can be achieved and utilized to improve the spectral quality from intact mass analysis of protein biopharmaceuticals. The approach and device described in this work suggests a low-cost and practical solution to improve the LC-MS characterization of protein biopharmaceuticals, which has the potential to be widely implemented in biopharmaceutical analytical laboratories.
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Affiliation(s)
- Shunhai Wang
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Tao Xing
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Anita P Liu
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Zehong He
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Yuetian Yan
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Thomas J Daly
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Ning Li
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
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10
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Xu Y, Wang D, Mason B, Rossomando T, Li N, Liu D, Cheung JK, Xu W, Raghava S, Katiyar A, Nowak C, Xiang T, Dong DD, Sun J, Beck A, Liu H. Structure, heterogeneity and developability assessment of therapeutic antibodies. MAbs 2018; 11:239-264. [PMID: 30543482 DOI: 10.1080/19420862.2018.1553476] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Increasing attention has been paid to developability assessment with the understanding that thorough evaluation of monoclonal antibody lead candidates at an early stage can avoid delays during late-stage development. The concept of developability is based on the knowledge gained from the successful development of approximately 80 marketed antibody and Fc-fusion protein drug products and from the lessons learned from many failed development programs over the last three decades. Here, we reviewed antibody quality attributes that are critical to development and traditional and state-of-the-art analytical methods to monitor those attributes. Based on our collective experiences, a practical workflow is proposed as a best practice for developability assessment including in silico evaluation, extended characterization and forced degradation using appropriate analytical methods that allow characterization with limited material consumption and fast turnaround time.
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Affiliation(s)
- Yingda Xu
- a Protein Analytics , Adimab , Lebanon , NH , USA
| | - Dongdong Wang
- b Analytical Department , Bioanalytix, Inc ., Cambridge , MA , USA
| | - Bruce Mason
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
| | - Tony Rossomando
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
| | - Ning Li
- d Analytical Chemistry , Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Dingjiang Liu
- e Formulation Development , Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Jason K Cheung
- f Pharmaceutical Sciences , MRL, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Wei Xu
- g Analytical Method Development , MRL, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Smita Raghava
- h Sterile Formulation Sciences , MRL, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Amit Katiyar
- i Analytical Development , Bristol-Myers Squibb , Pennington , NJ , USA
| | - Christine Nowak
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
| | - Tao Xiang
- j Manufacturing Sciences , Abbvie Bioresearch Center , Worcester , MA , USA
| | - Diane D Dong
- j Manufacturing Sciences , Abbvie Bioresearch Center , Worcester , MA , USA
| | - Joanne Sun
- k Product development , Innovent Biologics , Suzhou Industrial Park , China
| | - Alain Beck
- l Analytical chemistry , NBEs, Center d'immunologie Pierre Fabre , St Julien-en-Genevois Cedex , France
| | - Hongcheng Liu
- c Product Characterization , Alexion Pharmaceuticals, Inc ., New Haven , CT , USA
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11
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Rehder DS, Wisniewski CJ, Liu D, Ren D, Farnan D, Schenauer MR. Expression vector-derived heterogeneity in a therapeutic IgG4 monoclonal antibody. MAbs 2018; 11:145-152. [PMID: 30365358 DOI: 10.1080/19420862.2018.1540254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
While characterizing a therapeutic IgG4 monoclonal antibody (mAb), we observed a variant with a mass 1177 Da larger than the predominant mAb form that could not be ascribed to previously described modifications. Through successive rounds of experimentation, we localized the mass addition to the C-terminus of the heavy chain (HC). During this process we observed that when the mAb was broken down into separate domains, the Fc and the 1177 Da-modified Fc could be chromatographically separated. Separation allowed collection of native and modified Fc fractions for LC/MS peptide mapping. A unique peptide present in the modified fraction was de novo sequenced and demonstrated to be a modified form of the HC C-terminus lacking two native residues (GK) and gaining twelve additional non-native residues (EAEAASASELFQ). Aware of other mAb variants with genetic origins, we sought to understand whether this modification too had a genetic basis. In silico translation of the expression vector encoding the mAb demonstrated that a normally non-coding section of nucleotides in the + 1 reading frame relative to the HC C-terminal coding region could have led to a transcript with the non-native C-terminal extension. Two potential mechanisms for how this nucleotide sequence might have fused to the native HC coding region and led to expression of the extension product are presented.
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Affiliation(s)
- Douglas S Rehder
- a Biologics Analytical Operations , Gilead Sciences , Oceanside , CA , USA
| | - Chris J Wisniewski
- a Biologics Analytical Operations , Gilead Sciences , Oceanside , CA , USA
| | - Denfeng Liu
- a Biologics Analytical Operations , Gilead Sciences , Oceanside , CA , USA
| | - Diya Ren
- a Biologics Analytical Operations , Gilead Sciences , Oceanside , CA , USA
| | - Dell Farnan
- a Biologics Analytical Operations , Gilead Sciences , Oceanside , CA , USA
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12
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Lin TJ, Beal KM, Brown PW, DeGruttola HS, Ly M, Wang W, Chu CH, Dufield RL, Casperson GF, Carroll JA, Friese OV, Figueroa B, Marzilli LA, Anderson K, Rouse JC. Evolution of a comprehensive, orthogonal approach to sequence variant analysis for biotherapeutics. MAbs 2018; 11:1-12. [PMID: 30303443 PMCID: PMC6343769 DOI: 10.1080/19420862.2018.1531965] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Amino acid sequence variation in protein therapeutics requires close monitoring during cell line and cell culture process development. A cross-functional team of Pfizer colleagues from the Analytical and Bioprocess Development departments worked closely together for over 6 years to formulate and communicate a practical, reliable sequence variant (SV) testing strategy with state-of-the-art techniques that did not necessitate more resources or lengthen project timelines. The final Pfizer SV screening strategy relies on next-generation sequencing (NGS) and amino acid analysis (AAA) as frontline techniques to identify mammalian cell clones with genetic mutations and recognize cell culture process media/feed conditions that induce misincorporations, respectively. Mass spectrometry (MS)-based techniques had previously been used to monitor secreted therapeutic products for SVs, but we found NGS and AAA to be equally informative, faster, less cumbersome screening approaches. MS resources could then be used for other purposes, such as the in-depth characterization of product quality in the final stages of commercial-ready cell line and culture process development. Once an industry-wide challenge, sequence variation is now routinely monitored and controlled at Pfizer (and other biopharmaceutical companies) through increased awareness, dedicated cross-line efforts, smart comprehensive strategies, and advances in instrumentation/software, resulting in even higher product quality standards for biopharmaceutical products.
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Affiliation(s)
- T Jennifer Lin
- a Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Andover , MA , USA
| | - Kathryn M Beal
- a Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Andover , MA , USA
| | - Paul W Brown
- b Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Chesterfield , MO , USA
| | | | - Mellisa Ly
- a Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Andover , MA , USA
| | - Wenge Wang
- a Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Andover , MA , USA
| | - Chia H Chu
- b Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Chesterfield , MO , USA
| | - Robert L Dufield
- b Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Chesterfield , MO , USA
| | - Gerald F Casperson
- b Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Chesterfield , MO , USA
| | - James A Carroll
- b Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Chesterfield , MO , USA
| | - Olga V Friese
- b Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Chesterfield , MO , USA
| | - Bruno Figueroa
- a Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Andover , MA , USA
| | - Lisa A Marzilli
- a Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Andover , MA , USA
| | - Karin Anderson
- a Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Andover , MA , USA
| | - Jason C Rouse
- a Biotherapeutics Pharmaceutical Sciences , Pfizer, Inc , Andover , MA , USA
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13
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Háda V, Bagdi A, Bihari Z, Timári SB, Fizil Á, Szántay C. Recent advancements, challenges, and practical considerations in the mass spectrometry-based analytics of protein biotherapeutics: A viewpoint from the biosimilar industry. J Pharm Biomed Anal 2018; 161:214-238. [PMID: 30205300 DOI: 10.1016/j.jpba.2018.08.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/22/2023]
Abstract
The extensive analytical characterization of protein biotherapeutics, especially of biosimilars, is a critical part of the product development and registration. High-resolution mass spectrometry became the primary analytical tool used for the structural characterization of biotherapeutics. Its high instrumental sensitivity and methodological versatility made it possible to use this technique to characterize both the primary and higher-order structure of these proteins. However, even by using high-end instrumentation, analysts face several challenges with regard to how to cope with industrial and regulatory requirements, that is, how to obtain accurate and reliable analytical data in a time- and cost-efficient way. New sample preparation approaches, measurement techniques and data evaluation strategies are available to meet those requirements. The practical considerations of these methods are discussed in the present review article focusing on hot topics, such as reliable and efficient sequencing strategies, minimization of artefact formation during sample preparation, quantitative peptide mapping, the potential of multi-attribute methodology, the increasing role of mass spectrometry in higher-order structure characterization and the challenges of MS-based identification of host cell proteins. On the basis of the opportunities in new instrumental techniques, methodological advancements and software-driven data evaluation approaches, for the future one can envision an even wider application area for mass spectrometry in the biopharmaceutical industry.
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Affiliation(s)
- Viktor Háda
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary.
| | - Attila Bagdi
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Zsolt Bihari
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | | | - Ádám Fizil
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Csaba Szántay
- Spectroscopic Research Department, Gedeon Richter Plc, Hungary.
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14
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Popp O, Moser S, Zielonka J, Rüger P, Hansen S, Plöttner O. Development of a pre-glycoengineered CHO-K1 host cell line for the expression of antibodies with enhanced Fc mediated effector function. MAbs 2017; 10:290-303. [PMID: 29173063 PMCID: PMC5825202 DOI: 10.1080/19420862.2017.1405203] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Novel biotherapeutic glycoproteins, like recombinant monoclonal antibodies (mAbs) are widely used for the treatment of numerous diseases. The N-glycans attached to the constant region of an antibody have been demonstrated to be crucial for the biological efficacy. Even minor modifications of the N-glycan structure can dictate the potency of IgG effector functions such as the antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). Here, we present the development of a glycoengineered CHO-K1 host cell line (HCL), stably expressing β1,4-N-Acetylglucoseaminyltransferase III (GnT-III) and α-mannosidase II (Man-II), for the expression of a-fucosylated antibodies with enhanced Fc-mediated effector function. Glycoengineered HCLs were generated in a two-step strategy, starting with generating parental HCLs by stable transfection of CHO-K1 cells with GnT-III and Man-II. In a second step, parental HCLs were stably transfected a second time with these two transgenes to increase their copy number in the genetic background. Generated glycoengineered CHO-K1 cell lines expressing two different mAbs deliver antibody products with a content of more than 60% a-fucosylated glycans. In-depth analysis of the N-glycan structure revealed that the majority of the Fc-attached glycans of the obtained mAbs were of complex bisected type. Furthermore, we showed the efficient use of FcγRIIIa affinity chromatography as a novel method for the fast assessment of the mAbs a-fucosylation level. By testing different cultivation conditions for the pre-glycoengineered recombinant CHO-K1 clones, we identified key components essential for the production of a-fucosylated mAbs. The prevalent effect could be attributed to the trace element manganese, which leads to a strong increase of a-fucosylated complex- and hybrid-type glycans. In conclusion, the novel pre-glycoengineered CHO-K1 HCL can be used for the production of antibodies with high ratios of a-fucosylated Fc-attached N-glycans. Application of our newly developed FcγRIIIa affinity chromatography method during cell line development and use of optimized cultivation conditions can ultimately support the efficient development of a-fucosylated mAbs.
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Affiliation(s)
- Oliver Popp
- a Roche Pharma Research and Early Development , Large Molecule Research, Roche Innovation Center Munich , Nonnenwald 2, Penzberg , Germany
| | - Samuel Moser
- b Roche Pharma Research and Early Development , Large Molecule Research, Roche Innovation Center Zurich , Wagistrasse 18, Schlieren , Switzerland
| | - Jörg Zielonka
- b Roche Pharma Research and Early Development , Large Molecule Research, Roche Innovation Center Zurich , Wagistrasse 18, Schlieren , Switzerland
| | - Petra Rüger
- a Roche Pharma Research and Early Development , Large Molecule Research, Roche Innovation Center Munich , Nonnenwald 2, Penzberg , Germany
| | - Silke Hansen
- a Roche Pharma Research and Early Development , Large Molecule Research, Roche Innovation Center Munich , Nonnenwald 2, Penzberg , Germany
| | - Oliver Plöttner
- a Roche Pharma Research and Early Development , Large Molecule Research, Roche Innovation Center Munich , Nonnenwald 2, Penzberg , Germany
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15
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Wong HE, Huang CJ, Zhang Z. Amino acid misincorporation in recombinant proteins. Biotechnol Adv 2017; 36:168-181. [PMID: 29107148 DOI: 10.1016/j.biotechadv.2017.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/12/2017] [Accepted: 10/24/2017] [Indexed: 11/26/2022]
Abstract
Proteins provide the molecular basis for cellular structure, catalytic activity, signal transduction, and molecular transport in biological systems. Recombinant protein expression is widely used to prepare and manufacture novel proteins that serve as the foundation of many biopharmaceutical products. However, protein translation bioprocesses are inherently prone to low-level errors. These sequence variants caused by amino acid misincorporation have been observed in both native and recombinant proteins. Protein sequence variants impact product quality, and their presence can be exacerbated through cellular stress, overexpression, and nutrient starvation. Therefore, the cell line selection process, which is used in the biopharmaceutical industry, is not only directed towards maximizing productivity, but also focuses on selecting clones which yield low sequence variant levels, thereby proactively avoiding potentially inauspicious patient safety and efficacy outcomes. Here, we summarize a number of hallmark studies aimed at understanding the mechanisms of amino acid misincorporation, as well as exacerbating factors, and mitigation strategies. We also describe key advances in analytical technologies in the identification and quantification of sequence variants, and some practical considerations when using LC-MS/MS for detecting sequence variants.
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Affiliation(s)
- H Edward Wong
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Chung-Jr Huang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Zhongqi Zhang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States.
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16
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Griaud F, Winter A, Denefeld B, Lang M, Hensinger H, Straube F, Sackewitz M, Berg M. Identification of multiple serine to asparagine sequence variation sites in an intended copy product of LUCENTIS® by mass spectrometry. MAbs 2017; 9:1337-1348. [PMID: 28846476 PMCID: PMC5680803 DOI: 10.1080/19420862.2017.1366395] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Patent expiration of first-generation biologics and the high cost of innovative biologics are 2 drivers for the development of biosimilar products. There are, however, technical challenges to the production of exact copies of such large molecules. In this study, we performed a head-to-head comparison between the originator anti-VEGF-A Fab product LUCENTIS® (ranibizumab) and an intended copy product using an integrated analytical approach. While no differences could be observed using size-exclusion chromatography, capillary electrophoresis-sodium dodecyl sulfate and potency assays, different acidic peaks were identified with cation ion exchange chromatography and capillary zone electrophoresis. Further investigation of the intact Fab, subunits and primary sequence with mass spectrometry demonstrated the presence of a modified light chain variant in the intended copy product batches. This variant was characterized with a mass increase of 27.01 Da compared to the originator sequence and its abundance was estimated in the range of 6–9% of the intended copy product light chain. MS/MS spectra interrogation confirmed that this modification relates to a serine to asparagine sequence variant found in the intended copy product light chain. We demonstrated that the integration of high-resolution and sensitive orthogonal technologies was beneficial to assess the similarity of an originator and an intended copy product.
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Affiliation(s)
- François Griaud
- a Analytical Development and Characterization NBEs, Biopharmaceutical Product and Process Development, Biologics Technical Development and Manufacturing, Novartis Pharma AG , Basel , Basel-Stadt, Switzerland
| | - Andrej Winter
- a Analytical Development and Characterization NBEs, Biopharmaceutical Product and Process Development, Biologics Technical Development and Manufacturing, Novartis Pharma AG , Basel , Basel-Stadt, Switzerland
| | - Blandine Denefeld
- a Analytical Development and Characterization NBEs, Biopharmaceutical Product and Process Development, Biologics Technical Development and Manufacturing, Novartis Pharma AG , Basel , Basel-Stadt, Switzerland
| | - Manuel Lang
- a Analytical Development and Characterization NBEs, Biopharmaceutical Product and Process Development, Biologics Technical Development and Manufacturing, Novartis Pharma AG , Basel , Basel-Stadt, Switzerland
| | - Héloïse Hensinger
- a Analytical Development and Characterization NBEs, Biopharmaceutical Product and Process Development, Biologics Technical Development and Manufacturing, Novartis Pharma AG , Basel , Basel-Stadt, Switzerland
| | - Frank Straube
- a Analytical Development and Characterization NBEs, Biopharmaceutical Product and Process Development, Biologics Technical Development and Manufacturing, Novartis Pharma AG , Basel , Basel-Stadt, Switzerland
| | - Mirko Sackewitz
- a Analytical Development and Characterization NBEs, Biopharmaceutical Product and Process Development, Biologics Technical Development and Manufacturing, Novartis Pharma AG , Basel , Basel-Stadt, Switzerland
| | - Matthias Berg
- a Analytical Development and Characterization NBEs, Biopharmaceutical Product and Process Development, Biologics Technical Development and Manufacturing, Novartis Pharma AG , Basel , Basel-Stadt, Switzerland
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17
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Abstract
Sequence variant analysis (SVA) is critical in therapeutic protein development because it ensures the absence of genetic mutations of a production clone or high-level misincorporations during cell culture. While software for searching sequence variants from mass spectrometry data are available, effectively distinguishing true positives from a large number of false positives in the reported hits or identifications found in the error tolerant search mode is a challenge. This verification process must be done manually and can take several days or even weeks to accomplish. We report here the use of a Perl-based script to evaluate every identified hit to remove the false positives from the search results of PepFinder™ (also known as MassAnalyzer) based on orthogonal criteria. Our data show that the false positives from PepFinder™ output were reduced ∼4-fold without loss of accuracy in the detection of true identifications, representing a more than 70% reduction in time compared with the manual data verification process.
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Affiliation(s)
- Wenzhou Li
- a Attribute Sciences, Amgen Inc. , Thousand Oaks , CA , USA
| | - Jette Wypych
- a Attribute Sciences, Amgen Inc. , Thousand Oaks , CA , USA
| | - Robert J Duff
- a Attribute Sciences, Amgen Inc. , Thousand Oaks , CA , USA
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18
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Lin TJ, Beal KM, DeGruttola HS, Brennan S, Marzilli LA, Anderson K. Utilization of sequence variants as biomarkers to analyze population dynamics in cloned cell lines. Biotechnol Bioeng 2017; 114:1744-1752. [DOI: 10.1002/bit.26298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/16/2017] [Accepted: 03/24/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Tzihsuan Jennifer Lin
- Cell Line Development, Bioprocess R&D; Biotherapeutics Pharmaceutical Sciences, Pfizer Inc; Andover 01810 Massachusetts
- Mass Spectrometry and Biophysical Characterization, Analytical R&D; Biotherapeutics Pharmaceutical Sciences, Pfizer, Inc; Andover Massachusetts
| | - Kathryn M. Beal
- Cell Line Development, Bioprocess R&D; Biotherapeutics Pharmaceutical Sciences, Pfizer Inc; Andover 01810 Massachusetts
| | | | - Steven Brennan
- Cell Line Development, Bioprocess R&D; Biotherapeutics Pharmaceutical Sciences, Pfizer Inc; Andover 01810 Massachusetts
| | - Lisa A. Marzilli
- Mass Spectrometry and Biophysical Characterization, Analytical R&D; Biotherapeutics Pharmaceutical Sciences, Pfizer, Inc; Andover Massachusetts
| | - Karin Anderson
- Cell Line Development, Bioprocess R&D; Biotherapeutics Pharmaceutical Sciences, Pfizer Inc; Andover 01810 Massachusetts
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19
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Popp O, Müller D, Didzus K, Paul W, Lipsmeier F, Kirchner F, Niklas J, Mauch K, Beaucamp N. A hybrid approach identifies metabolic signatures of high-producers for chinese hamster ovary clone selection and process optimization. Biotechnol Bioeng 2016; 113:2005-19. [DOI: 10.1002/bit.25958] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/01/2015] [Accepted: 02/14/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Oliver Popp
- Pharma Research and Early Development; Cell Culture Research, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Nonnenwald 2 D-82377 Penzberg Germany
| | - Dirk Müller
- Insilico Biotechnology AG; Stuttgart Germany
| | - Katharina Didzus
- Pharma Research and Early Development; Cell Culture Research, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Nonnenwald 2 D-82377 Penzberg Germany
| | - Wolfgang Paul
- Pharma Research and Early Development; Cell Culture Research, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Nonnenwald 2 D-82377 Penzberg Germany
| | - Florian Lipsmeier
- Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Penzberg Germany
| | | | - Jens Niklas
- Insilico Biotechnology AG; Stuttgart Germany
| | - Klaus Mauch
- Insilico Biotechnology AG; Stuttgart Germany
| | - Nicola Beaucamp
- Pharma Research and Early Development; Cell Culture Research, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Nonnenwald 2 D-82377 Penzberg Germany
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20
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Lian Z, Wu Q, Wang T. Identification and characterization of a -1 reading frameshift in the heavy chain constant region of an IgG1 recombinant monoclonal antibody produced in CHO cells. MAbs 2015; 8:358-70. [PMID: 26652198 PMCID: PMC4966638 DOI: 10.1080/19420862.2015.1116658] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/27/2015] [Accepted: 11/01/2015] [Indexed: 01/16/2023] Open
Abstract
Frameshifts lead to complete alteration of the intended amino acid sequences, and therefore may affect the biological activities of protein therapeutics and pose potential immunogenicity risks. We report here the identification and characterization of a novel -1 frameshift variant in a recombinant IgG1 therapeutic monoclonal antibody (mAb) produced in Chinese hamster ovary cells during the cell line selection studies. The variant was initially observed as an atypical post-monomer fragment peak in size exclusion chromatography. Characterization of the fragment peak using intact and reduced liquid chromatography-mass spectrometry (LC-MS) analyses determined that the fragment consisted of a normal light chain disulfide-linked to an aberrant 26 kDa fragment that could not be assigned to any HC fragment even after considering common modifications. Further analysis using LC-MS/MS peptide mapping revealed that the aberrant fragment contained the expected HC amino acid sequence (1-232) followed by a 20-mer novel sequence corresponding to expression of heavy chain DNA sequence in the -1 reading frame. Examination of the DNA sequence around the frameshift initiation site revealed that a mononucleotide repeat GGGGGG located in the IgG1 HC constant region was most likely the structural root cause of the frameshift. Rapid identification of the frameshift allowed us to avoid use of a problematic cell line containing the frameshift as the production cell line. The frameshift reported here may be observed in other mAb products and the hypothesis-driven analytical approaches employed here may be valuable for rapid identification and characterization of frameshift variants in other recombinant proteins.
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Affiliation(s)
- Zhirui Lian
- Bioproduct Research and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Qindong Wu
- Bioproduct Research and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Tongtong Wang
- Bioproduct Research and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
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21
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Scott RA, Rogers R, Balland A, Brady LJ. Rapid identification of an antibody DNA construct rearrangement sequence variant by mass spectrometry. MAbs 2015; 6:1453-63. [PMID: 25484040 DOI: 10.4161/mabs.36222] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
During cell line development for an IgG1 antibody candidate (mAb1), a C-terminal extension was identified in 2 product candidate clones expressed in CHO-K1 cell line. The extension was initially observed as the presence of anomalous new peaks in these clones after analysis by cation exchange chromatography (CEX-HPLC) and reduced capillary electrophoresis (rCE-SDS). Reduced mass analysis of these CHO-K1 clones revealed that a larger than expected mass was present on a sub-population of the heavy chain species, which could not be explained by any known chemical or post-translational modifications. It was suspected that this additional mass on the heavy chain was due to the presence of an additional amino acid sequence. To identify the suspected additional sequence, de novo sequencing in combination with proteomic searching was performed against translated DNA vectors for the heavy chain and light chain. Peptides unique to the clones containing the extension were identified matching short sequences (corresponding to 9 and 35 amino acids, respectively) from 2 non-coding sections of the light chain vector construct. After investigation, this extension was observed to be due to the re-arrangement of the DNA construct, with the addition of amino acids derived from the light chain vector non-translated sequence to the C-terminus of the heavy chain. This observation showed the power of proteomic mass spectrometric techniques to identify an unexpected antibody sequence variant using de novo sequencing combined with database searching, and allowed for rapid identification of the root cause for new peaks in the cation exchange and rCE-SDS assays.
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Key Words
- C-terminal extension
- CAN, acetonitrile
- CEX, cation exchange
- CHO, Chinese hamster ovary
- DNA, deoxyribonucleic acid
- DTT, dithiothreitol
- Da, Dalton
- FDR, false discovery rate
- HC, heavy chain
- HPLC, high performance liquid chromatography
- LC, light chain
- MS, mass spectrometer
- MS/MS, tandem mass spectrometry
- MW, molecular weight
- NCBI, National Center for Biotechnology Information
- NCG, non-concensus glycosylation
- PSM, peptide-spectrum matches
- RP-UPLC, reversed phase ultra-high pressure liquid chromatography
- SEC, size exclusion chromatography
- TFA, trifluoracetic acid
- TOF, time of flight mass spectrometer
- UV, ultraviolet
- aa, amino acids
- mass spectrometry
- ppm, parts per million
- rCE-SDS, reduced capillary electrophoresis-sodium dodecyl sulfate
- sequence variant
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22
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Zhang S, Bartkowiak L, Nabiswa B, Mishra P, Fann J, Ouellette D, Correia I, Regier D, Liu J. Identifying low-level sequence variants via next generation sequencing to aid stable CHO cell line screening. Biotechnol Prog 2015; 31:1077-85. [DOI: 10.1002/btpr.2119] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/04/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Sheng Zhang
- Process Sciences Cell Culture, Abbvie Bioresearch Center; 100 Research Drive Worcester MA 01605
| | - Lisa Bartkowiak
- Process Sciences Cell Culture, Abbvie Bioresearch Center; 100 Research Drive Worcester MA 01605
| | - Bernard Nabiswa
- Process Sciences Cell Culture, Abbvie Bioresearch Center; 100 Research Drive Worcester MA 01605
| | - Pratibha Mishra
- Process Sciences Cell Culture, Abbvie Bioresearch Center; 100 Research Drive Worcester MA 01605
| | - John Fann
- Process Sciences Cell Culture, Abbvie Bioresearch Center; 100 Research Drive Worcester MA 01605
| | - David Ouellette
- Process Sciences Analytics, Abbvie Bioresearch Center; 100 Research Drive Worcester MA 01605
| | - Ivan Correia
- Process Sciences Analytics, Abbvie Bioresearch Center; 100 Research Drive Worcester MA 01605
| | - Dean Regier
- Protein Science, Abbvie Bioresearch Center; 100 Research Drive Worcester MA 01605
| | - Junjian Liu
- Protein Science, Abbvie Bioresearch Center; 100 Research Drive Worcester MA 01605
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23
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Kaas CS, Bolt G, Hansen JJ, Andersen MR, Kristensen C. Deep sequencing reveals different compositions of mRNA transcribed from the F8 gene in a panel of FVIII-producing CHO cell lines. Biotechnol J 2015; 10:1081-9. [PMID: 25963793 DOI: 10.1002/biot.201400667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/27/2015] [Accepted: 05/08/2015] [Indexed: 12/15/2022]
Abstract
Coagulation factor VIII (FVIII) is one of the most complex biopharmaceuticals due to the large size, poor protein stability and extensive post-translational modifications. As a consequence, efficient production of FVIII in mammalian cells poses a major challenge, with typical yields two to three orders of magnitude lower than for antibodies. In the present study we investigated CHO DXB11 cells transfected with a plasmid encoding human coagulation factor VIII. Single cell clones were isolated from the pool of transfectants and a panel of 14 clones representing a dynamic range of FVIII productivities was selected for RNA sequencing analysis. The analysis showed distinct differences in F8 RNA composition between the clones. The exogenous F8-dhfr transcript was found to make up the most abundant transcript in the present clones. No correlation was seen between F8 mRNA levels and the measured FVIII productivity. It was found that three MTX resistant, nonproducing clones had different truncations of the F8 transcripts. We find that by using deep sequencing, in contrast to microarray technology, for determining the transcriptome from CHO transfectants, we are able to accurately deduce the mature mRNA composition of the transgene and identify significant truncations that would probably otherwise have remained undetected.
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Affiliation(s)
- Christian S Kaas
- Mammalian Cell Technology, Novo Nordisk A/S, Maaloev, Denmark. .,Department of Systems Biology, Technical University of Denmark, Kgs Lyngby, Denmark.
| | - Gert Bolt
- Mammalian Cell Technology, Novo Nordisk A/S, Maaloev, Denmark
| | - Jens J Hansen
- Mammalian Cell Technology, Novo Nordisk A/S, Maaloev, Denmark
| | - Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Claus Kristensen
- Mammalian Cell Technology, Novo Nordisk A/S, Maaloev, Denmark.,Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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24
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An optimized approach to the rapid assessment and detection of sequence variants in recombinant protein products. Anal Bioanal Chem 2015; 407:3851-60. [PMID: 25795027 DOI: 10.1007/s00216-015-8618-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 02/26/2015] [Accepted: 03/03/2015] [Indexed: 01/01/2023]
Abstract
The development of sensitive techniques to detect sequence variants (SVs), which naturally arise due to DNA mutations and errors in transcription/translation (amino acid misincorporations), has resulted in increased attention to their potential presence in protein-based biologic drugs in recent years. Often, these SVs may be below 0.1%, adding challenges for consistent and accurate detection. Furthermore, the presence of false-positive (FP) signals, a hallmark of SV analysis, requires time-consuming analyst inspection of the data to sort true from erroneous signal. Consequently, gaps in information about the prevalence, type, and impact of SVs in marketed and in-development products are significant. Here, we report the results of a simple, straightforward, and sensitive approach to sequence variant analysis. This strategy employs mixing of two samples of an antibody or protein with the same amino acid sequence in a dilution series followed by subsequent sequence variant analysis. Using automated peptide map analysis software, a quantitative assessment of the levels of SVs in each sample can be made based on the signal derived from the mass spectrometric data. We used this strategy to rapidly detect differences in sequence variants in a monoclonal antibody after a change in process scale, and in a comparison of three mAbs as part of a biosimilar program. This approach is powerful, as true signals can be readily distinguished from FP signal, even at a level well below 0.1%, by using a simple linear regression analysis across the data set with none to minimal inspection of the MS/MS data. Additionally, the data produced from these studies can also be used to make a quantitative assessment of relative levels of product quality attributes. The information provided here extends the published knowledge about SVs and provides context for the discussion around the potential impact of these SVs on product heterogeneity and immunogenicity.
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25
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Popp O, Larraillet V, Kettenberger H, Gorr IH, Hilger M, Lipsmeier F, Zeck A, Beaucamp N. Molecular polygamy: The promiscuity of l-phenylalanyl-tRNA-synthetase triggers misincorporation of meta- and ortho-tyrosine in monoclonal antibodies expressed by Chinese hamster ovary cells. Biotechnol Bioeng 2015; 112:1187-99. [PMID: 25545851 DOI: 10.1002/bit.25528] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 01/03/2023]
Abstract
In-depth analytical characterization of biotherapeutics originating from different production batches is mandatory to ensure product safety and consistent molecule efficacy. Previously, we have shown unintended incorporation of tyrosine (Tyr) and leucine/isoleucine (Leu/Ile) at phenylalanine (Phe) positions in a recombinant produced monoclonal antibody (mAb) using an orthogonal MASCOT/SIEVE based approach for mass spectrometry data analysis. The misincorporation could be avoided by sufficient supply of phenylalanine throughout the process. Several non-annotated signals in the primarily chromatographic peptide separation step for apparently single Phe→Tyr sequence variants (SVs) suggest a role for isobar tyrosine isoforms. Meta- and ortho-Tyr are spontaneously generated during aerobic fed-batch production processes using Chinese hamster ovary (CHO) cell lines. Process induced meta- and ortho-Tyr but not proteinogenic para-Tyr are incorporated at Phe locations in Phe-starved CHO cultures expressing a recombinant mAb. Furthermore, meta- and ortho-Tyr are preferably misincorporated over Leu. Structural modeling of the l-phenylalanyl-tRNA-synthetase (PheRS) substrate activation site indicates a possible fit of non-cognate ortho-Tyr and meta-Tyr substrates. Dose-dependent misincorporations of Tyr isoforms support the hypothesis that meta- and ortho-Tyr are competing, alternative substrates for PheRS in CHO processes. Finally, easily accessible at-line surrogate markers for Phe→Tyr SV formation in biotherapeutic production were defined by the calculation of critical ratios for meta-Tyr/Phe and ortho-Tyr/Phe to support early prediction of SV probability, and finally, to allow for immediate process controlled Phe→Tyr SV prevention.
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Affiliation(s)
- Oliver Popp
- Pharma Research and Early Development, Cell Culture Research, Roche Innovation Center Penzberg, Nonnenwald 2, 82377 Penzberg, Germany.
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26
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Ragionieri L, Vitorino R, Frommlet J, Oliveira JL, Gaspar P, Ribas de Pouplana L, Santos MAS, Moura GR. Improving the accuracy of recombinant protein production through integration of bioinformatics, statistical and mass spectrometry methodologies. FEBS J 2015; 282:769-87. [DOI: 10.1111/febs.13181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 10/09/2014] [Accepted: 12/16/2014] [Indexed: 02/05/2023]
Affiliation(s)
- Lapo Ragionieri
- RNA and Genome Biology Laboratories; Department of Biology/Health Sciences; Centro de Estudos do Ambiente e do Mar iBiMED; University of Aveiro; Portugal
| | - Rui Vitorino
- Department of Chemistry; University of Aveiro; Portugal
| | - Joerg Frommlet
- Department of Biology and Centro de Estudos do Ambiente e do Mar; University of Aveiro; Portugal
| | - José L. Oliveira
- Department of Electronics; Telecommunications and Informatics and Instituto de Engenharia Electrónica e Telemática de Aveiro; University of Aveiro; Portugal
| | - Paulo Gaspar
- Department of Electronics; Telecommunications and Informatics and Instituto de Engenharia Electrónica e Telemática de Aveiro; University of Aveiro; Portugal
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine; Barcelona Spain
- Catalan Institution for Research and Advanced Studies; Barcelona Spain
| | - Manuel A. Silva Santos
- RNA and Genome Biology Laboratories; Department of Biology/Health Sciences; Centro de Estudos do Ambiente e do Mar iBiMED; University of Aveiro; Portugal
| | - Gabriela Ribeiro Moura
- RNA and Genome Biology Laboratories; Department of Biology/Health Sciences; Centro de Estudos do Ambiente e do Mar iBiMED; University of Aveiro; Portugal
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Borisov OV, Alvarez M, Carroll JA, Brown PW. Sequence Variants and Sequence Variant Analysis in Biotherapeutic Proteins. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1201.ch002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Oleg V. Borisov
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - Melissa Alvarez
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - James A. Carroll
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - Paul W. Brown
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
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Sandra K, Vandenheede I, Sandra P. Modern chromatographic and mass spectrometric techniques for protein biopharmaceutical characterization. J Chromatogr A 2014; 1335:81-103. [DOI: 10.1016/j.chroma.2013.11.057] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 10/25/2022]
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Biermann M, Linnemann J, Knüpfer U, Vollstädt S, Bardl B, Seidel G, Horn U. Trace element associated reduction of norleucine and norvaline accumulation during oxygen limitation in a recombinant Escherichia coli fermentation. Microb Cell Fact 2013; 12:116. [PMID: 24261588 PMCID: PMC3842802 DOI: 10.1186/1475-2859-12-116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 10/25/2013] [Indexed: 12/21/2022] Open
Abstract
Background Norleucine and norvaline belong to a group of non-canonical amino acids which are synthesized as byproducts in the branched chain amino acid metabolism of Escherichia coli. The earlier observed misincorporation of these rare amino acids into recombinant proteins has attracted increasing attention due to the rising use of protein based biopharmaceuticals in clinical application. Experimental data revealed pyruvate overflow inducing conditions, which typically occur in oxygen limited zones of large-scale fermentations as a major reason leading to norvaline and norleucine synthesis during E. coli cultivation. Previous approaches to suppress misincorporation of norleucine and norvaline considered growth media supplementation with the relevant canonical isostructural compounds, but no research was performed on the impact of the overflow metabolism related trace elements molybdenum, nickel and selenium. These elements form essential parts of the formate hydrogen lyase (FHL) metalloprotein complex, which is a key enzyme of anaerobic pyruvate metabolism in E. coli and could therefore represent a crucial connection to the pyruvate accumulation associated biosynthesis of rare amino acids. Results In this study, the trace element associated response of recombinant antibody producing E. coli to oxygen limitation at high glucose concentration with a special focus on non-canonical amino acids was analysed. During fed-batch cultivation with provoked oxygen limitation and glucose excess norleucine and norvaline were only accumulated in the absence of molybdenum, nickel and selenium. In contrast, the trace element supplemented stress fermentation showed significantly reduced concentrations of these rare amino acids and the major signature fermentation product formate, supporting the correlation between a functional formate hydrogen lyase complex and low unspecific amino acid synthesis under oxygen limitation at high glucose concentration. Conclusions The formation of norleucine and norvaline by recombinant E. coli during cultivation with provoked oxygen limitation and glucose excess can be reduced to levels at the detection limit by adding the trace elements molybdenum, selenium and nickel to the fermentation medium. Even under the metabolic burden during induction phase the physiologically available concentrations of non-canonical amino acids remained low. Since our results allow facile process changes that can be easily implemented to avoid the undesirable accumulation of norleucine and norvaline, we consider this study highly interesting for improved process development in E. coli based recombinant drug production and the future development of possible mechanisms to reduce misincorporation events into protein based biopharmaceuticals.
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Affiliation(s)
- Michael Biermann
- Leibniz-Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany.
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Noh SM, Sathyamurthy M, Lee GM. Development of recombinant Chinese hamster ovary cell lines for therapeutic protein production. Curr Opin Chem Eng 2013. [DOI: 10.1016/j.coche.2013.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Rosati S, Thompson NJ, Heck AJ, Rosati S, Thompson NJ, Heck AJ. Tackling the increasing complexity of therapeutic monoclonal antibodies with mass spectrometry. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Gramer MJ. Product Quality Considerations for Mammalian Cell Culture Process Development and Manufacturing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 139:123-66. [DOI: 10.1007/10_2013_214] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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