1
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Mass spectrometry-based multi-attribute method for mutation analysis in the early development of therapeutic proteins. J Pharm Biomed Anal 2022; 220:115018. [PMID: 36030755 DOI: 10.1016/j.jpba.2022.115018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/22/2022]
Abstract
The early intervention is essential, and later development cannot compensate for this initial generation of an antibody drug. Especially for sequence variants (SVs), should cause concern during the early bioprocess development. The advancement of bioprocess development is paralleled by development of state-of-the-art analytical methods that will provide further information. In the present study, a mass spectrometry (MS)-based multi-attribute method (MAM) was used to simultaneously monitor the SVs and other quality attributes in the early bioprocess development of ofatumumab, and a sequence variant (SV) was detected by a subunit-based MAM. Subsequently, the variant was further identified by MS/MS and confirmed by adding a synthetic peptide. Furthermore, the content of the SV was detected via DNA sequencing. The levels of the variant (T175A mutant) in the light chain were demonstrate to be nearly consistent at the DNA and protein levels, suggesting that the mutation may have negligible effect on both the transcriptional and translational levels. Collectively, these results indicate that broad-spectrum, rapid, and accurate platform such as MS-based MAM should be implemented to quality control for the early development of therapeutic proteins, it will also be important to establish an effective and integrated MAM to control SVs during therapeutic proteins development.
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2
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Greer T, Johnson RO, Nie S, Cejkov M, Zheng X, Li N. High Throughput and High Confidence Sequence Variant Analysis in Therapeutic Antibodies using Evosep One Liquid Chromatography Tandem Mass Spectrometry with Synthetic Heavy Peptides. J Pharm Biomed Anal 2022; 219:114925. [DOI: 10.1016/j.jpba.2022.114925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 11/25/2022]
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3
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Jakes C, Millán-Martín S, Carillo S, Scheffler K, Zaborowska I, Bones J. Tracking the Behavior of Monoclonal Antibody Product Quality Attributes Using a Multi-Attribute Method Workflow. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1998-2012. [PMID: 33513021 DOI: 10.1021/jasms.0c00432] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The multi-attribute method (MAM) is a liquid chromatography-mass spectrometry based method that is used to directly characterize and monitor many product quality attributes and impurities on biotherapeutics, most commonly at the peptide level. It utilizes high-resolution accurate mass spectral data which are analyzed in an automated fashion. MAM is a promising approach that is intended to replace or supplement several conventional assays with a single LC-MS analysis and can be implemented in a Current Good Manufacturing Practice environment. MAM provides accurate site-specific quantitation information on targeted attributes and the nontargeted new peak detection function allows to detect new peaks as impurities, modifications, or sequence variants when comparing to a reference sample. The high resolution MAM workflow was applied here for three independent case studies. First, to monitor the behavior of monoclonal antibody product quality attributes over the course of a 12-day cell culture experiment providing an insight into the behavior and dynamics of product attributes throughout the process. Second, the workflow was applied to test the purity and identity of a product through analysis of samples spiked with host cell proteins. Third, through the comparison of a drug product and a biosimilar with known sequence variants. The three case studies presented here, clearly demonstrate the robustness and accuracy of the MAM workflow that implies suitability for deployment in the regulated environment.
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Affiliation(s)
- Craig Jakes
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co., Dublin, A94 X099 Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - Silvia Millán-Martín
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co., Dublin, A94 X099 Ireland
| | - Sara Carillo
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co., Dublin, A94 X099 Ireland
| | - Kai Scheffler
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Izabela Zaborowska
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co., Dublin, A94 X099 Ireland
| | - Jonathan Bones
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co., Dublin, A94 X099 Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
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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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Groot J, Zhou Y, Marshall E, Cullen P, Carlile T, Lin D, Xu CF, Crisafulli J, Sun C, Casey F, Zhang B, Alves C. Benchmarking and optimization of a high-throughput sequencing based method for transgene sequence variant analysis in biotherapeutic cell line development. Biotechnol J 2021; 16:e2000548. [PMID: 34018310 DOI: 10.1002/biot.202000548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022]
Abstract
In recent years, High-Throughput Sequencing (HTS) based methods to detect mutations in biotherapeutic transgene products have become a key quality step deployed during the development of manufacturing cell line clones. Previously we reported on a higher throughput, rapid mutation detection method based on amplicon sequencing (targeting transgene RNA) and detailed its implementation to facilitate cell line clone selection. By gaining experience with our assay in a diverse set of cell line development programs, we improved the computational analysis as well as experimental protocols. Here we report on these improvements as well as on a comprehensive benchmarking of our assay. We evaluated assay performance by mixing amplicon samples of a verified mutated antibody clone with a non-mutated antibody clone to generate spike-in mutations from ∼60% down to ∼0.3% frequencies. We subsequently tested the effect of 16 different sample and HTS library preparation protocols on the assay's ability to quantify mutations and on the occurrence of false-positive background error mutations (artifacts). Our evaluation confirmed assay robustness, established a high confidence limit of detection of ∼0.6%, and identified protocols that reduce error levels thereby significantly reducing a source of false positives that bottlenecked the identification of low-level true mutations.
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Affiliation(s)
- Joost Groot
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA.,Inzen Therapeutics, Cambridge, Massachusetts, USA
| | - Yizhou Zhou
- Protein Development, Biogen, Cambridge, Massachusetts, USA
| | - Eric Marshall
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Patrick Cullen
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Thomas Carlile
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Dongdong Lin
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Chong-Feng Xu
- Analytical Development, Biogen, Cambridge, Massachusetts, USA
| | | | - Chao Sun
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Fergal Casey
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Baohong Zhang
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
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6
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Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
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7
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Carrara SC, Ulitzka M, Grzeschik J, Kornmann H, Hock B, Kolmar H. From cell line development to the formulated drug product: The art of manufacturing therapeutic monoclonal antibodies. Int J Pharm 2020; 594:120164. [PMID: 33309833 DOI: 10.1016/j.ijpharm.2020.120164] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/23/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023]
Abstract
Therapeutic monoclonal antibodies and related products have steadily grown to become the dominant product class within the biopharmaceutical market. Production of antibodies requires special precautions to ensure safety and efficacy of the product. In particular, minimizing antibody product heterogeneity is crucial as drug substance variants may impair the activity, efficacy, safety, and pharmacokinetic properties of an antibody, consequently resulting in the failure of a product in pre-clinical and clinical development. This review will cover the manufacturing and formulation challenges and advances of therapeutic monoclonal antibodies, focusing on improved processes to minimize variants and ensure batch-to-batch consistency. Processes put in place by regulatory agencies, such as Quality-by-Design (QbD) and current Good Manufacturing Practices (cGMP), and how their implementation has aided drug development in pharmaceutical companies will be reviewed. Advances in formulation and considerations on the intended use of a therapeutic antibody, including the route of administration and patient compliance, will be discussed.
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Affiliation(s)
- Stefania C Carrara
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany; Ferring Darmstadt Laboratory, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Michael Ulitzka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany; Ferring Darmstadt Laboratory, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Julius Grzeschik
- Ferring Darmstadt Laboratory, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Henri Kornmann
- Ferring International Center SA, CH-1162 Saint-Prex, Switzerland
| | - Björn Hock
- Ferring International Center SA, CH-1162 Saint-Prex, Switzerland.
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany.
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8
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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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9
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Boddapati S, Gilmore J, Boone K, Bushey J, Ross J, Gfeller B, McFee W, Rao R, Corrigan G, Chen A, Clarke H, Valliere-Douglass J, Bhargava S. Evidence for co-translational misincorporation of non-canonical amino acid hydroxyproline in recombinant antibodies produced in Chinese Hamster Ovary (CHO) cell lines. PLoS One 2020; 15:e0241250. [PMID: 33119652 PMCID: PMC7595273 DOI: 10.1371/journal.pone.0241250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/09/2020] [Indexed: 02/03/2023] Open
Abstract
With the advent of highly sensitive technologies such as tandem mass spectrometry and next-generation sequencing, recombinant antibodies are now routinely analyzed for the presence of low-level sequence variants including amino acid misincorporations. During mAb cell culture process development, we found that proline was replaced with the non-canonical amino acid, hydroxyproline, in the protein sequence. We investigated the relationship between proline content in the cell culture media and proline sequence variants and found that the proline concentration was inversely correlated with the amount of sequence variants detected in the protein sequence. Hydroxyproline incorporation has been previously reported in recombinant proteins produced in mammalian expression systems as a post-translational modification. Given the dependency on proline levels, the mechanism was then investigated. To address the possibility of co-translational misincorporation of hydroxyproline, we used tandem mass spectrometry to measure incorporation of stable-isotope labelled hydroxyproline added to the feed of a production bioreactor. We discovered co-translational misincorporation of labelled hydroxyproline in the recombinant antibody. These findings are significant, since they underscore the need to track non-canonical amino acid incorporation as a co-translational event in CHO cells. Understanding the mechanism of hydroxyproline incorporation is crucial in developing an appropriate control strategy during biologics production.
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Affiliation(s)
- Shanta Boddapati
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
- * E-mail:
| | - Jason Gilmore
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
| | - Kyle Boone
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
| | - John Bushey
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
| | - Jonathan Ross
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
| | - Brian Gfeller
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
| | - William McFee
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
| | - Romesh Rao
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
| | - Greg Corrigan
- Upstream Manufacturing, Seattle Genetics Inc, Bothell, WA, United States of America
| | - Aaron Chen
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
| | - Howard Clarke
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
| | | | - Swapnil Bhargava
- Process Sciences, Seattle Genetics Inc, Bothell, WA, United States of America
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10
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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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11
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Towards in situ continuous feeding via controlled release of complete nutrients for fed-batch culture of animal cells. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Harris C, Xu W, Grassi L, Wang C, Markle A, Hardman C, Stevens R, Miro-Quesada G, Hatton D, Wang J. Identification and characterization of an IgG sequence variant with an 11 kDa heavy chain C-terminal extension using a combination of mass spectrometry and high-throughput sequencing analysis. MAbs 2019; 11:1452-1463. [PMID: 31570042 PMCID: PMC6816433 DOI: 10.1080/19420862.2019.1667740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein primary structure is a potential critical quality attribute for biotherapeutics. Identifying and characterizing any sequence variants present is essential for product development. A sequence variant ~11 kDa larger than the expected IgG mass was observed by size-exclusion chromatography and two-dimensional liquid chromatography coupled with online mass spectrometry. Further characterization indicated that the 11 kDa was added to the heavy chain (HC) Fc domain. Despite the relatively large mass addition, only one unknown peptide was detected by peptide mapping. To decipher the sequence, the transcriptome of the manufacturing cell line was characterized by Illumina RNA-seq. Transcriptome reconstruction detected an aberrant fusion transcript, where the light chain (LC) constant domain sequence was fused to the 3ʹ end of the HC transcript. Translation of this fusion transcript generated an extended peptide sequence at the HC C-terminus corresponding to the observed 11 kDa mass addition. Nanopore-based genome sequencing showed multiple copies of the plasmid had integrated in tandem with one copy missing the 5ʹ end of the plasmid, deleting the LC variable domain. The fusion transcript was due to read-through of the HC terminator sequence into the adjacent partial LC gene and an unexpected splicing event between a cryptic splice-donor site at the 3ʹ end of the HC and the splice acceptor site at the 5ʹ end of the LC constant domain. Our study demonstrates that combining protein physicochemical characterization with genomic and transcriptomic analysis of the manufacturing cell line greatly improves the identification of sequence variants and understanding of the underlying molecular mechanisms.
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Affiliation(s)
- Claire Harris
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Weichen Xu
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Luigi Grassi
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Chunlei Wang
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Abigail Markle
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Colin Hardman
- Data Science & Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Richard Stevens
- Antibody Discovery and Protein Engineering, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Guillermo Miro-Quesada
- Data & Quantitative Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Diane Hatton
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Jihong Wang
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
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13
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Sequence Variant and Posttranslational Modification Analysis During Cell Line Selection via High-Throughput Peptide Mapping. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 31347050 DOI: 10.1007/978-3-030-15950-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Selection of high-producing lead and backup cell lines with high-fidelity primary structure is a major goal of cell line development of protein therapeutics. Conventional techniques for sequence variant analysis, such as mass spectrometry (MS) and next-generation sequencing (NGS) have limitations on the sample number and turnaround time, thus often are only applied at the final stages of development, where an undesired lead or backup clone could cause a significant delay in project timeline. Here we presented a high-throughput (HT) peptide mapping workflow which can be applied at early stages of cell line selection for testing of a batch of 30-40 clones within 2-week turnaround while reporting valuable information on sequence variants and posttranslational modifications (PTMs). The successful application of this workflow was demonstrated for two mAb programs. Multiple clones were removed from a total of 33 mAb-1 clones using various criteria: nine clones contained at least one >1% upregulated unknown peptide ions, 11 clones contained at least eight >0.1% upregulated unknowns, and six clones contained upregulated critical PTMs. For mAb-2, light chain (LC) sequence extension of approximately 30 amino acids were detected in 6 out of 36 clones at levels up to 11%. Besides, a Q to H mutation at ~30% was detected in the heavy chain (HC) of a single clone. Q to H mutation has mass change of 9.00 Da and failed to be detected by intact mass analysis. Rapid PTM quantitation also facilitated the selection of clones with desirable quality attributes, such as N-glycan profile. Hence, we demonstrated a risk-reducing strategy where abnormal clones could be detected at earlier stages of cell line selection, which should result in reduced and more predictable timeline of cell line development.
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14
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Aeschlimann SH, Graf C, Mayilo D, Lindecker H, Urda L, Kappes N, Burr AL, Simonis M, Splinter E, Min M, Laux H. Enhanced CHO Clone Screening: Application of Targeted Locus Amplification and Next‐Generation Sequencing Technologies for Cell Line Development. Biotechnol J 2019; 14:e1800371. [DOI: 10.1002/biot.201800371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Samuel H. Aeschlimann
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Christian Graf
- Novartis Technical R&D, Technical Development BiosimilarsHexal AG, Keltenring 1+3 82041 Oberhaching Germany
| | - Dmytro Mayilo
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Hélène Lindecker
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Lorena Urda
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Nora Kappes
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Alicia Leone Burr
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | | | - Erik Splinter
- Cergentis B.VYalelaan 62 3584 CM Utrecht The Netherlands
| | - Max Min
- Cergentis B.VYalelaan 62 3584 CM Utrecht The Netherlands
| | - Holger Laux
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
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15
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Stadnik D, Bierczyńska-Krzysik A, Zielińska J, Antosik J, Borowicz P, Bednarek E, Bocian W, Sitkowski J, Kozerski L. Identification of Lysine Misincorporation at Asparagine Position in Recombinant Insulin Analogs Produced in E. coli. Pharm Res 2019; 36:79. [PMID: 30949841 PMCID: PMC6449291 DOI: 10.1007/s11095-019-2601-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/03/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE Identification of human insulin analogs' impurity with a mass shift +14 Da in comparison to a parent protein. METHODS The protein sequence variant was detected and identified with the application of peptide mapping, liquid chromatography, tandem mass spectrometric analysis, nuclear magnetic resonance spectroscopy (NMR) and Edman sequencing. RESULTS The misincorporated lysine (Lys) at asparagine (Asn) position A21 was detected in recombinant human insulin and its analogs. CONCLUSIONS Although there are three asparagine residues in the insulin derivative, the misincorporation of lysine occurred only at position A21. The process involves G/U or A/U wobble base pairing.
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Affiliation(s)
- Dorota Stadnik
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland.
| | - Anna Bierczyńska-Krzysik
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland
| | - Joanna Zielińska
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland
| | - Jarosław Antosik
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland
| | - Piotr Borowicz
- Łukasiewicz Research Network - Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516, Warsaw, Poland
| | - Elżbieta Bednarek
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Wojciech Bocian
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Jerzy Sitkowski
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Lech Kozerski
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
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16
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Beck A, Liu H. Macro- and Micro-Heterogeneity of Natural and Recombinant IgG Antibodies. Antibodies (Basel) 2019; 8:antib8010018. [PMID: 31544824 PMCID: PMC6640695 DOI: 10.3390/antib8010018] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/19/2019] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
Recombinant monoclonal antibodies (mAbs) intended for therapeutic usage are required to be thoroughly characterized, which has promoted an extensive effort towards the understanding of the structures and heterogeneity of this major class of molecules. Batch consistency and comparability are highly relevant to the successful pharmaceutical development of mAbs and related products. Small structural modifications that contribute to molecule variants (or proteoforms) differing in size, charge or hydrophobicity have been identified. These modifications may impact (or not) the stability, pharmacokinetics, and efficacy of mAbs. The presence of the same type of modifications as found in endogenous immunoglobulin G (IgG) can substantially lower the safety risks of mAbs. The knowledge of modifications is also critical to the ranking of critical quality attributes (CQAs) of the drug and define the Quality Target Product Profile (QTPP). This review provides a summary of the current understanding of post-translational and physico-chemical modifications identified in recombinant mAbs and endogenous IgGs at physiological conditions.
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Affiliation(s)
- Alain Beck
- Biologics CMC and developability, IRPF, Center d'immunologie Pierre Fabre, St Julien-en-Genevois CEDEX, 74160 Saint-Julien en Genevois, France.
| | - Hongcheng Liu
- Anokion, 50 Hampshire Street, Suite 402, Cambridge, MA 02139, USA.
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17
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Joshi K, Cao L, Farabaugh PJ. The problem of genetic code misreading during protein synthesis. Yeast 2019; 36:35-42. [DOI: 10.1002/yea.3374] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 02/01/2023] Open
Affiliation(s)
- Kartikeya Joshi
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland, USA
| | - Ling Cao
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland, USA
| | - Philip J. Farabaugh
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland, USA
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18
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Calmels C, McCann A, Malphettes L, Andersen MR. Application of a curated genome-scale metabolic model of CHO DG44 to an industrial fed-batch process. Metab Eng 2019; 51:9-19. [DOI: 10.1016/j.ymben.2018.09.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/17/2018] [Accepted: 09/14/2018] [Indexed: 01/08/2023]
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19
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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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20
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Wong HE, Huang CJ, Zhang Z. Amino Acid Misincorporation Propensities Revealed through Systematic Amino Acid Starvation. Biochemistry 2018; 57:6767-6779. [DOI: 10.1021/acs.biochem.8b00976] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- H. Edward Wong
- Process Development, Amgen, Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Chung-Jr Huang
- Process Development, Amgen, Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Zhongqi Zhang
- Process Development, Amgen, Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
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21
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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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22
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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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23
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Cartwright JF, Anderson K, Longworth J, Lobb P, James DC. Highly sensitive detection of mutations in CHO cell recombinant DNA using multi-parallel single molecule real-time DNA sequencing. Biotechnol Bioeng 2018; 115:1485-1498. [DOI: 10.1002/bit.26561] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/01/2017] [Accepted: 02/04/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Joseph F. Cartwright
- Department of Chemical and Biological Engineering; University of Sheffield; Sheffield UK
| | - Karin Anderson
- Cell Line Development; BioTherapeutic Pharmaceutical Sciences; Pfizer Inc; Andover Massachusetts
| | - Joseph Longworth
- Department of Chemical and Biological Engineering; University of Sheffield; Sheffield UK
| | | | - David C. James
- Department of Chemical and Biological Engineering; University of Sheffield; Sheffield UK
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24
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Magnenat L, Palmese A, Fremaux C, D'Amici F, Terlizzese M, Rossi M, Chevalet L. Demonstration of physicochemical and functional similarity between the proposed biosimilar adalimumab MSB11022 and Humira®. MAbs 2017; 9:127-139. [PMID: 27854156 PMCID: PMC5240642 DOI: 10.1080/19420862.2016.1259046] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biosimilars are biological products that are highly similar to existing products approved by health authorities. Demonstration of similarity starts with the comprehensive analysis of the reference product and its proposed biosimilar at the physicochemical and functional levels. Here, we report the results of a comparative analysis of a proposed biosimilar adalimumab MSB11022 and its reference product, Humira®. Three batches of MSB11022 and up to 23 batches of Humira® were analyzed by a set of state-of-the-art orthogonal methods. Primary and higher order structure analysis included N/C-terminal modifications, molecular weight of heavy and light chains, C-terminal lysine truncation, disulfide bridges, secondary and tertiary structures, and thermal stability. Purity ranged from 98.4%–98.8% for MSB11022 batches (N = 3) and from 98.4%–99.6% for Humira® batches (N = 19). Isoform analysis showed 5 isoform clusters within the pI range of 7.94–9.14 and 100% glycan site occupancy for both MSB11022 and Humira®. Functional analysis included Fab-dependent inhibition of tumor necrosis factor (TNF)-induced cytotoxicity in L929-A9 cell line and affinity to soluble and transmembrane forms of TNF, as well as Fc-dependent binding to Fcγ and neonatal Fc receptors and C1q complement proteins. All tested physicochemical and functional parameters demonstrated high similarity of MSB11022 and Humira®, with lower variability between MSB11022 and Humira® batches compared with variability within individual batches of Humira®. Based on these results, MSB11022 is anticipated to have safety and efficacy comparable to those of Humira®.
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Affiliation(s)
- Laurent Magnenat
- a Non clinical Pharmacology, Merck Biosimilars , Aubonne , Switzerland
| | - Angelo Palmese
- b Department of Protein Chemistry , Merck, Guidonia Montecelio - Rome , Italy
| | - Christèle Fremaux
- c Non clinical Pharmacology, Merck Biosimilars , Corsier-sur-Vevey , Switzerland
| | - Fabio D'Amici
- d Bioanalytical Development, Pharmaceutical & Analytical Development Biotech Products, Merck, Guidonia Montecelio - Rome , Italy
| | - Mariagrazia Terlizzese
- d Bioanalytical Development, Pharmaceutical & Analytical Development Biotech Products, Merck, Guidonia Montecelio - Rome , Italy
| | - Mara Rossi
- b Department of Protein Chemistry , Merck, Guidonia Montecelio - Rome , Italy
| | - Laurent Chevalet
- e Analytical and Pharmaceutical Development, Merck Biosimilars , Aubonne , Switzerland
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25
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Jiang T, Song H, Slaney TR, Wu W, Langsdorf E, Gupta G, Ludwig R, Tao L, McVey D, Das TK. Codon-Directed Determination of the Biological Causes of Sequence Variants in Therapeutic Proteins. Anal Chem 2017; 89:12749-12755. [DOI: 10.1021/acs.analchem.7b02914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Tao Jiang
- Department
of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Hangtian Song
- Analytical,
Cell Line and Process Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky
Hill Road, Pennington, New
Jersey 08534, United States
| | - Thomas R. Slaney
- Analytical,
Cell Line and Process Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky
Hill Road, Pennington, New
Jersey 08534, United States
| | - Wei Wu
- Analytical,
Cell Line and Process Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky
Hill Road, Pennington, New
Jersey 08534, United States
| | - Erik Langsdorf
- Analytical,
Cell Line and Process Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky
Hill Road, Pennington, New
Jersey 08534, United States
| | - Gargi Gupta
- Analytical,
Cell Line and Process Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky
Hill Road, Pennington, New
Jersey 08534, United States
| | - Richard Ludwig
- Analytical,
Cell Line and Process Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky
Hill Road, Pennington, New
Jersey 08534, United States
| | - Li Tao
- Analytical,
Cell Line and Process Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky
Hill Road, Pennington, New
Jersey 08534, United States
| | - Duncan McVey
- Analytical,
Cell Line and Process Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky
Hill Road, Pennington, New
Jersey 08534, United States
| | - Tapan K. Das
- Analytical,
Cell Line and Process Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky
Hill Road, Pennington, New
Jersey 08534, United States
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26
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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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27
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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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28
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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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29
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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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Mulukutla BC, Kale J, Kalomeris T, Jacobs M, Hiller GW. Identification and control of novel growth inhibitors in fed-batch cultures of Chinese hamster ovary cells. Biotechnol Bioeng 2017; 114:1779-1790. [DOI: 10.1002/bit.26313] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/19/2017] [Accepted: 04/09/2017] [Indexed: 02/01/2023]
Affiliation(s)
| | - Jaitashree Kale
- Cell Culture Process Development; Pfizer Inc.; One Burtt Road Andover 01810 Massachusetts
| | - Taylor Kalomeris
- Cell Culture Process Development; Pfizer Inc.; One Burtt Road Andover 01810 Massachusetts
| | - Michaela Jacobs
- Cell Culture Process Development; Pfizer Inc.; One Burtt Road Andover 01810 Massachusetts
| | - Gregory W. Hiller
- Cell Culture Process Development; Pfizer Inc.; One Burtt Road Andover 01810 Massachusetts
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31
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Bandyopadhyay AA, Khetan A, Malmberg LH, Zhou W, Hu WS. Advancement in bioprocess technology: parallels between microbial natural products and cell culture biologics. J Ind Microbiol Biotechnol 2017; 44:785-797. [PMID: 28185098 DOI: 10.1007/s10295-017-1913-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/29/2017] [Indexed: 10/20/2022]
Abstract
The emergence of natural products and industrial microbiology nearly eight decades ago propelled an era of bioprocess innovation. Half a century later, recombinant protein technology spurred the tremendous growth of biologics and added mammalian cells to the forefront of industrial producing cells in terms of the value of products generated. This review highlights the process technology of natural products and protein biologics. Despite the separation in time, there is a remarkable similarity in their progression. As the new generation of therapeutics for gene and cell therapy emerges, its process technology development can take inspiration from that of natural products and biologics.
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Affiliation(s)
- Arpan A Bandyopadhyay
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN, 55455-0132, USA
| | - Anurag Khetan
- Biological Process Development, Bristol Myers Squibb, 521 NJ-173, Bloomsbury, NJ, 08804, USA
| | - Li-Hong Malmberg
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA, 01605, USA
| | | | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN, 55455-0132, USA.
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Mistranslation: from adaptations to applications. Biochim Biophys Acta Gen Subj 2017; 1861:3070-3080. [PMID: 28153753 DOI: 10.1016/j.bbagen.2017.01.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. SCOPE OF REVIEW This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. MAJOR CONCLUSIONS The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. GENERAL SIGNIFICANCE Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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33
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Tinoco I, Kim HK, Yan S. Frameshifting dynamics. Biopolymers 2016; 99:1147-66. [PMID: 23722586 DOI: 10.1002/bip.22293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/14/2013] [Accepted: 05/20/2013] [Indexed: 01/26/2023]
Abstract
Translation of messenger RNA by a ribosome occurs three nucleotides at a time from start signal to stop. However, a frameshift means that some nucleotides are read twice or some are skipped, and the following sequence of amino acids is completely different from the sequence in the original frame. In some messenger RNAs, including viral RNAs, frameshifting is programmed with RNA signals to produce specific ratios of proteins vital to the replication of the organism. The mechanisms that cause frameshifting have been studied for many years, but there are no definitive conclusions. We review ribosome structure and dynamics in relation to frameshifting dynamics provided by classical ensemble studies, and by new single-molecule methods using optical tweezers and FRET.
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Affiliation(s)
- Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460
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34
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Li Y, Fu T, Liu T, Guo H, Guo Q, Xu J, Zhang D, Qian W, Dai J, Li B, Guo Y, Hou S, Wang H. Characterization of alanine to valine sequence variants in the Fc region of nivolumab biosimilar produced in Chinese hamster ovary cells. MAbs 2016; 8:951-60. [PMID: 27050807 DOI: 10.1080/19420862.2016.1172150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Nivolumab is a therapeutic fully human IgG4 antibody to programmed death 1 (PD-1). In this study, a nivolumab biosimilar, which was produced in our laboratory, was analyzed and characterized. Sequence variants that contain undesired amino acid sequences may cause concern during biosimilar bioprocess development. We found that low levels of sequence variants were detected in the heavy chain of the nivolumab biosimilar by ultra performance liquid chromatography (UPLC) and tandem mass spectrometry. It was further identified with UPLC-MS/MS by IdeS or trypsin digestion. The sequence variant was confirmed through addition of synthetic mutant peptide. Subsequently, the mixing base signal of normal and mutant sequence was detected through DNA sequencing. The relative levels of mutant A424V in the Fc region of the heavy chain have been detected and demonstrated to be 12.25% and 13.54%, via base peak intensity (BPI) and UV chromatography of the tryptic peptide mapping, respectively. A424V variant was also quantified by real-time PCR (RT-PCR) at the DNA and RNA level, which was 19.2% and 16.8%, respectively. The relative content of the mutant was consistent at the DNA, RNA and protein level, indicating that the A424V mutation may have little influence at transcriptional or translational levels. These results demonstrate that orthogonal state-of-the-art techniques such as LC- UV- MS and RT-PCR should be implemented to characterize recombinant proteins and cell lines for development of biosimilars. Our study suggests that it is important to establish an integrated and effective analytical method to monitor and characterize sequence variants during antibody drug development, especially for antibody biosimilar products.
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Affiliation(s)
- Yantao Li
- a International Joint Cancer Institute, Second Military Medical University , Shanghai , China.,b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China
| | - Tuo Fu
- a International Joint Cancer Institute, Second Military Medical University , Shanghai , China.,b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China
| | - Tao Liu
- a International Joint Cancer Institute, Second Military Medical University , Shanghai , China.,b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China
| | - Huaizu Guo
- b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China.,c Shanghai Zhangjiang Biotechnology Co
| | - Qingcheng Guo
- a International Joint Cancer Institute, Second Military Medical University , Shanghai , China.,b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China
| | - Jin Xu
- b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China.,c Shanghai Zhangjiang Biotechnology Co
| | - Dapeng Zhang
- a International Joint Cancer Institute, Second Military Medical University , Shanghai , China.,b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China
| | - Weizhu Qian
- b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China.,c Shanghai Zhangjiang Biotechnology Co
| | - Jianxin Dai
- a International Joint Cancer Institute, Second Military Medical University , Shanghai , China.,b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China
| | - Bohua Li
- a International Joint Cancer Institute, Second Military Medical University , Shanghai , China.,b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China
| | - Yajun Guo
- b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China.,d School of Pharmacy, Liaocheng University , Liaocheng , China.,e School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Sheng Hou
- a International Joint Cancer Institute, Second Military Medical University , Shanghai , China.,b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China
| | - Hao Wang
- a International Joint Cancer Institute, Second Military Medical University , Shanghai , China.,b State Key Laboratory of Antibody Medicine and Targeted Therapy , Shanghai , China.,d School of Pharmacy, Liaocheng University , Liaocheng , China
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35
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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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36
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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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37
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Brühlmann D, Jordan M, Hemberger J, Sauer M, Stettler M, Broly H. Tailoring recombinant protein quality by rational media design. Biotechnol Prog 2015; 31:615-29. [DOI: 10.1002/btpr.2089] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/04/2015] [Indexed: 02/07/2023]
Affiliation(s)
- David Brühlmann
- Merck Serono SA, Corsier-sur-Vevey, Biotech Process Sciences, Zone Industrielle B; CH-1809 Fenil-sur-Corsier Switzerland
- Dept. of Biotechnology and Biophysics; Julius-Maximilians-Universität Würzburg, Biozentrum; Am Hubland DE-97074 Würzburg Germany
| | - Martin Jordan
- Merck Serono SA, Corsier-sur-Vevey, Biotech Process Sciences, Zone Industrielle B; CH-1809 Fenil-sur-Corsier Switzerland
| | - Jürgen Hemberger
- Inst. for Biochemical Engineering and Analytics; University of Applied Sciences Giessen; Wiesenstrasse 14, DE-35390 Giessen Germany
| | - Markus Sauer
- Dept. of Biotechnology and Biophysics; Julius-Maximilians-Universität Würzburg, Biozentrum; Am Hubland DE-97074 Würzburg Germany
| | - Matthieu Stettler
- Merck Serono SA, Corsier-sur-Vevey, Biotech Process Sciences, Zone Industrielle B; CH-1809 Fenil-sur-Corsier Switzerland
| | - Hervé Broly
- Merck Serono SA, Corsier-sur-Vevey, Biotech Process Sciences, Zone Industrielle B; CH-1809 Fenil-sur-Corsier Switzerland
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38
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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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39
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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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40
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Liu H, Ponniah G, Zhang HM, Nowak C, Neill A, Gonzalez-Lopez N, Patel R, Cheng G, Kita AZ, Andrien B. In vitro and in vivo modifications of recombinant and human IgG antibodies. MAbs 2014; 6:1145-54. [PMID: 25517300 DOI: 10.4161/mabs.29883] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tremendous knowledge has been gained in the understanding of various modifications of IgG antibodies, driven mainly by the fact that antibodies are one of the most important groups of therapeutic molecules and because of the development of advanced analytical techniques. Recombinant monoclonal antibody (mAb) therapeutics expressed in mammalian cell lines and endogenous IgG molecules secreted by B cells in the human body share some modifications, but each have some unique modifications. Modifications that are common to recombinant mAb and endogenous IgG molecules are considered to pose a lower risk of immunogenicity. On the other hand, modifications that are unique to recombinant mAbs could potentially pose higher risk. The focus of this review is the comparison of frequently observed modifications of recombinant monoclonal antibodies to those of endogenous IgG molecules.
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Affiliation(s)
- Hongcheng Liu
- a Protein Characterization; Alexion Pharmaceuticals Inc .; Cheshire , CT USA
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41
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Harris RP, Kilby PM. Amino acid misincorporation in recombinant biopharmaceutical products. Curr Opin Biotechnol 2014; 30:45-50. [PMID: 24922333 DOI: 10.1016/j.copbio.2014.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022]
Abstract
Microbial and mammalian host systems have been used extensively for the production of protein biotherapeutics. Generally these systems rely on the production of a specific gene sequence encoding one therapeutic product. Analysis of these protein products over many years has proven that this was not always the case, with multiple species of the intended product being produced due to amino acid misincorporation or mistranslation during biosynthesis of the protein. This review is the first to give a comprehensive overview of the occurrence and analysis of these misincorporations. Furthermore, using the latest data on misincorporation in native human proteins we explore potential considerations for producing a specification for misincorporation for the development of a human biotherapeutic protein product in a production environment.
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Affiliation(s)
- Robert P Harris
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks RG42 6EY, UK.
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks RG42 6EY, UK
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42
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Raina M, Moghal A, Kano A, Jerums M, Schnier PD, Luo S, Deshpande R, Bondarenko PV, Lin H, Ibba M. Reduced amino acid specificity of mammalian tyrosyl-tRNA synthetase is associated with elevated mistranslation of Tyr codons. J Biol Chem 2014; 289:17780-90. [PMID: 24828507 DOI: 10.1074/jbc.m114.564609] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Quality control operates at different steps in translation to limit errors to approximately one mistranslated codon per 10,000 codons during mRNA-directed protein synthesis. Recent studies have suggested that error rates may actually vary considerably during translation under different growth conditions. Here we examined the misincorporation of Phe at Tyr codons during synthesis of a recombinant antibody produced in tyrosine-limited Chinese hamster ovary (CHO) cells. Tyr to Phe replacements were previously found to occur throughout the antibody at a rate of up to 0.7% irrespective of the identity or context of the Tyr codon translated. Despite this comparatively high mistranslation rate, no significant change in cellular viability was observed. Monitoring of Phe and Tyr levels revealed that changes in error rates correlated with changes in amino acid pools, suggesting that mischarging of tRNA(Tyr) with noncognate Phe by tyrosyl-tRNA synthetase was responsible for mistranslation. Steady-state kinetic analyses of CHO cytoplasmic tyrosyl-tRNA synthetase revealed a 25-fold lower specificity for Tyr over Phe as compared with previously characterized bacterial enzymes, consistent with the observed increase in translation error rates during tyrosine limitation. Functional comparisons of mammalian and bacterial tyrosyl-tRNA synthetase revealed key differences at residues responsible for amino acid recognition, highlighting differences in evolutionary constraints for translation quality control.
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Affiliation(s)
- Medha Raina
- From the Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210-1292 and
| | - Adil Moghal
- From the Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210-1292 and
| | - Amanda Kano
- Amgen Incorporated, Thousand Oaks, California 91320-1799
| | - Mathew Jerums
- Amgen Incorporated, Thousand Oaks, California 91320-1799
| | - Paul D Schnier
- Amgen Incorporated, Thousand Oaks, California 91320-1799
| | - Shun Luo
- Amgen Incorporated, Thousand Oaks, California 91320-1799
| | | | | | - Henry Lin
- Amgen Incorporated, Thousand Oaks, California 91320-1799
| | - Michael Ibba
- From the Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210-1292 and
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43
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Rouiller Y, Périlleux A, Vesin MN, Stettler M, Jordan M, Broly H. Modulation of mAb quality attributes using microliter scale fed-batch cultures. Biotechnol Prog 2014; 30:571-83. [DOI: 10.1002/btpr.1921] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/23/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Yolande Rouiller
- Biotech Process Sciences, Merck Serono SA; Route de Fenil 25, ZI B 1804 Corsier-sur-Vevey Switzerland
| | - Arnaud Périlleux
- Biotech Process Sciences, Merck Serono SA; Route de Fenil 25, ZI B 1804 Corsier-sur-Vevey Switzerland
| | - Marie-Noëlle Vesin
- Biotech Process Sciences, Merck Serono SA; Route de Fenil 25, ZI B 1804 Corsier-sur-Vevey Switzerland
| | - Matthieu Stettler
- Biotech Process Sciences, Merck Serono SA; Route de Fenil 25, ZI B 1804 Corsier-sur-Vevey Switzerland
| | - Martin Jordan
- Biotech Process Sciences, Merck Serono SA; Route de Fenil 25, ZI B 1804 Corsier-sur-Vevey Switzerland
| | - Hervé Broly
- Biotech Process Sciences, Merck Serono SA; Route de Fenil 25, ZI B 1804 Corsier-sur-Vevey Switzerland
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44
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Barton C, Spencer D, Levitskaya S, Feng J, Harris R, Schenerman MA. Heterogeneity of IgGs: Role of Production, Processing, and Storage on Structure and Function. ACS SYMPOSIUM SERIES 2014. [DOI: 10.1021/bk-2014-1176.ch003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Chris Barton
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - David Spencer
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - Sophia Levitskaya
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - Jinhua Feng
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - Reed Harris
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
| | - Mark A. Schenerman
- Analytical Biotechnology, MedImmune, Gaithersburg, Maryland 20878, United States
- Genentech, Inc., South San Francisco, California 94080, United States
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45
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Fomina-Yadlin D, Gosink JJ, McCoy R, Follstad B, Morris A, Russell CB, McGrew JT. Cellular responses to individual amino-acid depletion in antibody-expressing and parental CHO cell lines. Biotechnol Bioeng 2013; 111:965-79. [DOI: 10.1002/bit.25155] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/10/2013] [Accepted: 11/12/2013] [Indexed: 02/06/2023]
Affiliation(s)
| | - John J. Gosink
- Molecular Sciences & Computational Biology; Seattle Washington
| | - Rebecca McCoy
- Cell Sciences & Technology; Amgen, Inc.; Seattle Washington 98119
| | - Brian Follstad
- Cell Sciences & Technology; Amgen, Inc.; Seattle Washington 98119
| | - Arvia Morris
- Cell Sciences & Technology; Amgen, Inc.; Seattle Washington 98119
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46
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Zhang Z, Shah B, Bondarenko PV. G/U and Certain Wobble Position Mismatches as Possible Main Causes of Amino Acid Misincorporations. Biochemistry 2013; 52:8165-76. [DOI: 10.1021/bi401002c] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Zhongqi Zhang
- Process and Product Development, Amgen Inc., Thousand
Oaks, California 91320, United States
| | - Bhavana Shah
- Process and Product Development, Amgen Inc., Thousand
Oaks, California 91320, United States
| | - Pavel V. Bondarenko
- Process and Product Development, Amgen Inc., Thousand
Oaks, California 91320, United States
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47
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Abstract
The composition of the cellular proteome is commonly thought to strictly adhere to the genetic code. However, accumulating evidence indicates that cells also regulate the synthesis of mutant protein molecules that deviate from the genetic code. Production of mutant proteins generally occurs when cells are stressed or when they undergo environmental adaptation, but production varies in amounts and specificity. The deliberate synthesis of mutant proteins suggests that some of these proteins can be useful in cellular stress response and adaptation. This review describes the occurrence of, the translation mechanisms for, and the functional hypotheses on regulated synthesis of mutant proteins.
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Affiliation(s)
- Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
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48
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Feeney L, Carvalhal V, Yu XC, Chan B, Michels DA, Wang YJ, Shen A, Ressl J, Dusel B, Laird MW. Eliminating tyrosine sequence variants in CHO cell lines producing recombinant monoclonal antibodies. Biotechnol Bioeng 2013; 110:1087-97. [PMID: 23108857 DOI: 10.1002/bit.24759] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/08/2012] [Indexed: 12/21/2022]
Abstract
Amino acid sequence variants are defined as unintended amino acid sequence changes that contribute to product variation with potential impact to product safety, immunogenicity, and efficacy. Therefore, it is important to understand the propensity for sequence variant (SV) formation during the production of recombinant proteins for therapeutic use. During the development of clinical therapeutic products, several monoclonal antibodies (mAbs) produced from Chinese Hamster Ovary (CHO) cells exhibited SVs at low levels (≤3%) in multiple locations throughout the mAbs. In these examples, the cell culture process depleted tyrosine, and the tyrosine residues in the recombinant mAbs were replaced with phenylalanine or histidine. In this work, it is demonstrated that tyrosine supplementation eliminated the tyrosine SVs, while early tyrosine starvation significantly increased the SV level in all mAbs tested. Additionally, it was determined that phenylalanine is the amino acid preferentially misincorporated in the absence of tyrosine over histidine, with no other amino acid misincorporated in the absence of tyrosine, phenylalanine, and histidine. The data support that the tyrosine SVs are due to mistranslation and not DNA mutation, most likely due to tRNA(Tyr) mischarging due to the structural similarities between tyrosine and phenylalanine.
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Affiliation(s)
- Lauren Feeney
- Department of Late Stage Cell Culture, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080-4990, USA
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49
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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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50
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Beck A, Wagner-Rousset E, Ayoub D, Van Dorsselaer A, Sanglier-Cianférani S. Characterization of Therapeutic Antibodies and Related Products. Anal Chem 2012; 85:715-36. [DOI: 10.1021/ac3032355] [Citation(s) in RCA: 445] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alain Beck
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Elsa Wagner-Rousset
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Daniel Ayoub
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie
de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France and CNRS, UMR7178, 67037 Strasbourg, France
| | - Sarah Sanglier-Cianférani
- Laboratoire de Spectrométrie
de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France and CNRS, UMR7178, 67037 Strasbourg, France
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