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Lakshmanan M, Chia S, Pang KT, Sim LC, Teo G, Mak SY, Chen S, Lim HL, Lee AP, Bin Mahfut F, Ng SK, Yang Y, Soh A, Tan AHM, Choo A, Ho YS, Nguyen-Khuong T, Walsh I. Antibody glycan quality predicted from CHO cell culture media markers and machine learning. Comput Struct Biotechnol J 2024; 23:2497-2506. [PMID: 38966680 PMCID: PMC11222931 DOI: 10.1016/j.csbj.2024.05.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 07/06/2024] Open
Abstract
N-glycosylation can have a profound effect on the quality of mAb therapeutics. In biomanufacturing, one of the ways to influence N-glycosylation patterns is by altering the media used to grow mAb cell expression systems. Here, we explore the potential of machine learning (ML) to forecast the abundances of N-glycan types based on variables related to the growth media. The ML models exploit a dataset consisting of detailed glycomic characterisation of Anti-HER fed-batch bioreactor cell cultures measured daily under 12 different culture conditions, such as changes in levels of dissolved oxygen, pH, temperature, and the use of two different commercially available media. By performing spent media quantitation and subsequent calculation of pseudo cell consumption rates (termed media markers) as inputs to the ML model, we were able to demonstrate a small subset of media markers (18 selected out of 167 mass spectrometry peaks) in a Chinese Hamster Ovary (CHO) cell cultures are important to model N-glycan relative abundances (Regression - correlations between 0.80-0.92; Classification - AUC between 75.0-97.2). The performances suggest the ML models can infer N-glycan critical quality attributes from extracellular media as a proxy. Given its accuracy, we envisage its potential applications in biomaufactucuring, especially in areas of process development, downstream and upstream bioprocessing.
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Affiliation(s)
- Meiyappan Lakshmanan
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, India
- Centre for Integrative Biology and Systems medicinE (IBSE), Indian Institute of Technology Madras, India
- Robert Bosch Centre for Data Science and AI (RBCDSAI), Indian Institute of Technology Madras, India
| | - Sean Chia
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Kuin Tian Pang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Lyn Chiin Sim
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Gavin Teo
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Shi Ya Mak
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Hsueh Lee Lim
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Alison P. Lee
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Farouq Bin Mahfut
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Say Kong Ng
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Yuansheng Yang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Annie Soh
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Andy Hee-Meng Tan
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Andre Choo
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Terry Nguyen-Khuong
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
| | - Ian Walsh
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06–01 Centros, Singapore 138668, Republic of Singapore
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2
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Sołowińska K, Holec-Gąsior L. Single Cell Expression Systems for the Production of Recombinant Proteins for Immunodiagnosis and Immunoprophylaxis of Toxoplasmosis. Microorganisms 2024; 12:1731. [PMID: 39203573 PMCID: PMC11357668 DOI: 10.3390/microorganisms12081731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/31/2024] [Accepted: 08/21/2024] [Indexed: 09/03/2024] Open
Abstract
Toxoplasmosis represents a significant public health and veterinary concern due to its widespread distribution, zoonotic transmission, and potential for severe health impacts in susceptible individuals and animal populations. The ability to design and produce recombinant proteins with precise antigenic properties is fundamental, as they serve as tools for accurate disease detection and effective immunization strategies, contributing to improved healthcare outcomes and disease control. Most commonly, a prokaryotic expression system is employed for the production of both single antigens and multi-epitope chimeric proteins; however, the cloning strategies, bacterial strain, vector, and expression conditions vary. Moreover, literature reports show the use of alternative microbial systems such as yeast or Leishmania tarentolae. This review provides an overview of the methods and strategies employed for the production of recombinant Toxoplasma gondii antigenic proteins for the serological detection of T. gondii infection and vaccine development.
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Affiliation(s)
- Karolina Sołowińska
- Department of Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland
| | - Lucyna Holec-Gąsior
- Department of Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland
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3
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Rauniyar N, Khetani J, Han X. Comparative analysis of Herceptin N-Linked glycosylation by HILIC-FLD and LC-MS/MS methods. J Pharm Biomed Anal 2024; 244:116123. [PMID: 38554555 DOI: 10.1016/j.jpba.2024.116123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/26/2024] [Accepted: 03/17/2024] [Indexed: 04/01/2024]
Abstract
Monoclonal antibodies like Herceptin play a pivotal role in modern therapeutics, with their glycosylation patterns significantly influencing their bioactivity. To characterize the N-glycan profile and their relative abundance in Herceptin, we employed two analytical methods: hydrophilic interaction chromatography with fluorescence detection (HILIC-FLD) for released glycans and liquid chromatography tandem mass spectrometry (LC-MS/MS) for glycopeptides. Our analysis included 21 European Union (EU)-Herceptin lots and 14 United States (US)-Herceptin lots. HILIC-FLD detected 25 glycan species, including positional isomers, revealing comparable chromatographic profiles for both EU and US lots. On the other hand, LC-MS/MS identified 26 glycoforms within the glycopeptide EEQYNSTYR. Both methods showed that a subset of glycans dominated the total abundance. Notably, EU-Herceptin lots with an expiration date of October 2022 exhibited increased levels of afucosylated and high mannose N-glycans. Our statistical comparisons showed that the difference in quantitative results between HILIC-FLD and LC-MS/MS is significant, indicating that the absolute quantitative values depend on the choice of the analytical method. However, despite these differences, both methods demonstrated a strong correlation in relative glycan proportions. This study contributes to the comprehensive analysis of Herceptin's glycosylation, offering insights into the influence of analytical methods on glycan quantification and providing valuable information for the biopharmaceutical industry.
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Affiliation(s)
- Navin Rauniyar
- Tanvex BioPharma USA, Inc, 10394 Pacific Center Ct, San Diego, CA 92121, USA.
| | - Joy Khetani
- Tanvex BioPharma USA, Inc, 10394 Pacific Center Ct, San Diego, CA 92121, USA
| | - Xuemei Han
- Tanvex BioPharma USA, Inc, 10394 Pacific Center Ct, San Diego, CA 92121, USA
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4
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Zhang M, Zhao X, Li Y, Ye Q, Wu Y, Niu Q, Zhang Y, Fan G, Chen T, Xia J, Wu Q. Advances in serum-free media for CHO cells: From traditional serum substitutes to microbial-derived substances. Biotechnol J 2024; 19:e2400251. [PMID: 39031790 DOI: 10.1002/biot.202400251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 07/22/2024]
Abstract
The Chinese hamster ovary (CHO) cell is an epithelial-like cell that produces proteins with post-translational modifications similar to human glycosylation. It is widely used in the production of recombinant therapeutic proteins and monoclonal antibodies. Culturing CHO cells typically requires the addition of a certain proportion of fetal bovine serum (FBS) to maintain cell proliferation and passaging. However, serum is characterized by its complex composition, batch-to-batch variability, high cost, and potential risk of exogenous contaminants such as mycoplasma and viruses, which impact the purity and safety of the synthesized proteins. Therefore, search for serum alternatives and development of serum-free media for CHO-based protein biomanufacturing are of great significance. This review systematically summarizes the application advantages of CHO cells and strategies for high-density expression. It highlights the developmental trends of serum substitutes from human platelet lysates to animal-free extracts and microbial-derived substances and elucidates the mechanisms by which these substitutes enhance CHO cell culture performance and recombinant protein production, aiming to provide theoretical guidance for exploring novel serum alternatives and developing serum-free media for CHO cells.
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Affiliation(s)
- Mingcan Zhang
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Zhao
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ying Li
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qinghua Ye
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yuwei Wu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qinya Niu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhang
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guanghan Fan
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Tianxiang Chen
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiarui Xia
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingping Wu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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5
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Makrydaki E, Donini R, Krueger A, Royle K, Moya Ramirez I, Kuntz DA, Rose DR, Haslam SM, Polizzi KM, Kontoravdi C. Immobilized enzyme cascade for targeted glycosylation. Nat Chem Biol 2024; 20:732-741. [PMID: 38321209 PMCID: PMC11142912 DOI: 10.1038/s41589-023-01539-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/21/2023] [Indexed: 02/08/2024]
Abstract
Glycosylation is a critical post-translational protein modification that affects folding, half-life and functionality. Glycosylation is a non-templated and heterogeneous process because of the promiscuity of the enzymes involved. We describe a platform for sequential glycosylation reactions for tailored sugar structures (SUGAR-TARGET) that allows bespoke, controlled N-linked glycosylation in vitro enabled by immobilized enzymes produced with a one-step immobilization/purification method. We reconstruct a reaction cascade mimicking a glycosylation pathway where promiscuity naturally exists to humanize a range of proteins derived from different cellular systems, yielding near-homogeneous glycoforms. Immobilized β-1,4-galactosyltransferase is used to enhance the galactosylation profile of three IgGs, yielding 80.2-96.3% terminal galactosylation. Enzyme recycling is demonstrated for a reaction time greater than 80 h. The platform is easy to implement, modular and reusable and can therefore produce homogeneous glycan structures derived from various hosts for functional and clinical evaluation.
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Affiliation(s)
- Elli Makrydaki
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Roberto Donini
- Department of Life Sciences, Imperial College London, London, UK
| | - Anja Krueger
- Department of Life Sciences, Imperial College London, London, UK
| | - Kate Royle
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Ignacio Moya Ramirez
- Department of Chemical Engineering, Imperial College London, London, UK
- Departamento de Ingeniería Química, Universidad de Granada, Granada, Spain
| | - Douglas A Kuntz
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David R Rose
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London, London, UK.
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London, UK.
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6
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Zhou Y, Priya S, Ong JY. Characterizing Glycosylation of Adeno-Associated Virus Serotype 9 Capsid Proteins Generated from HEK293 Cells through Glycopeptide Mapping and Released Glycan Analysis. Microorganisms 2024; 12:946. [PMID: 38792776 PMCID: PMC11123743 DOI: 10.3390/microorganisms12050946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Recombinant adeno-associated viral (AAV) vectors have emerged as prominent gene delivery vehicles for gene therapy. AAV capsid proteins determine tissue specificity and immunogenicity and play important roles in receptor binding, the escape of the virus from the endosome, and the transport of the viral DNA to the nuclei of target cells. Therefore, the comprehensive characterization of AAV capsid proteins is necessary for a better understanding of the vector assembly, stability, and transduction efficiency of AAV gene therapies. Glycosylation is one of the most common post-translational modifications (PTMs) and may affect the tissue tropism of AAV gene therapy. However, there are few studies on the characterization of the N- and O-glycosylation of AAV capsid proteins. In this study, we identified the N- and O-glycosylation sites and forms of AAV9 capsid proteins generated from HEK293 cells using liquid chromatography-tandem mass spectrometry (LC-MS)-based glycopeptide mapping and identified free N-glycans released from AAV9 capsid proteins by PNGase F using hydrophilic interaction (HILIC) LC-MS and HILIC LC-fluorescence detection (FLD) methods. This study demonstrates that AAV9 capsids are sprinkled with sugars, including N- and O-glycans, albeit at low levels. It may provide valuable information for a better understanding of AAV capsids in supporting AAV-based gene therapy development.
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Affiliation(s)
- Yu Zhou
- Analytical Development & Operations, Novartis Pharmaceuticals, 10210 Campus Point Drive, San Diego, CA 92121, USA
| | - Sonal Priya
- Analytical Development & Operations, Novartis Pharmaceuticals, 10210 Campus Point Drive, San Diego, CA 92121, USA
| | - Joseph Y Ong
- Analytical Development & Operations, Novartis Pharmaceuticals, 10210 Campus Point Drive, San Diego, CA 92121, USA
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7
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Tong Y, Lu X, Shen D, Rao L, Zou L, Lyu S, Hou L, Sun G, Chen L. Identification and characterization of emGalaseE, a β-1,4 galactosidase from Elizabethkingia meningoseptica, and its application on living cell surface. Int J Biol Macromol 2024; 268:131766. [PMID: 38657932 DOI: 10.1016/j.ijbiomac.2024.131766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/18/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
The biological function of terminal galactose on glycoprotein is an open field of research. Although progress had being made on enzymes that can remove the terminal galactose on glycoproteins, there is a lack of report on galactosidases that can work directly on living cells. In this study, a unique beta 1,4 galactosidase was isolated from Elizabethkingia meningoseptica (Em). It exhibited favorable stability at various temperatures (4-37 °C) and pH (5-8) levels and can remove β-1, 4 linked galactoses directly from glycoproteins. Using Alanine scanning, we found that two acidic residues (Glu-468, and Glu-531) in the predicted active pocket are critical for galactosidase activity. In addition, we also demonstrated that it could cleave galactose residues present on living cell surface. As this enzyme has a potential application for living cell glycan editing, we named it emGalaseE or glycan-editing galactosidase I (csgeGalaseI). In summary, our findings lay the groundwork for further investigation by presenting a simple and effective approach for the removal of galactose moieties from cell surface.
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Affiliation(s)
- Yongliang Tong
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xinrong Lu
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Danfeng Shen
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lin Rao
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lin Zou
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Shaoxian Lyu
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Linlin Hou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China.
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang Province, China.
| | - Li Chen
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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8
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Schachner LF, Mullen C, Phung W, Hinkle JD, Beardsley MI, Bentley T, Day P, Tsai C, Sukumaran S, Baginski T, DiCara D, Agard NJ, Masureel M, Gober J, ElSohly AM, Melani R, Syka JEP, Huguet R, Marty MT, Sandoval W. Exposing the molecular heterogeneity of glycosylated biotherapeutics. Nat Commun 2024; 15:3259. [PMID: 38627419 PMCID: PMC11021452 DOI: 10.1038/s41467-024-47693-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
The heterogeneity inherent in today's biotherapeutics, especially as a result of heavy glycosylation, can affect a molecule's safety and efficacy. Characterizing this heterogeneity is crucial for drug development and quality assessment, but existing methods are limited in their ability to analyze intact glycoproteins or other heterogeneous biotherapeutics. Here, we present an approach to the molecular assessment of biotherapeutics that uses proton-transfer charge-reduction with gas-phase fractionation to analyze intact heterogeneous and/or glycosylated proteins by mass spectrometry. The method provides a detailed landscape of the intact molecular weights present in biotherapeutic protein preparations in a single experiment. For glycoproteins in particular, the method may offer insights into glycan composition when coupled with a suitable bioinformatic strategy. We tested the approach on various biotherapeutic molecules, including Fc-fusion, VHH-fusion, and peptide-bound MHC class II complexes to demonstrate efficacy in measuring the proteoform-level diversity of biotherapeutics. Notably, we inferred the glycoform distribution for hundreds of molecular weights for the eight-times glycosylated fusion drug IL22-Fc, enabling correlations between glycoform sub-populations and the drug's pharmacological properties. Our method is broadly applicable and provides a powerful tool to assess the molecular heterogeneity of emerging biotherapeutics.
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Affiliation(s)
- Luis F Schachner
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Christopher Mullen
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Wilson Phung
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Joshua D Hinkle
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | | | - Tracy Bentley
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Peter Day
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Christina Tsai
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
- Protein Analytical Development, Ascendis Pharma, Palo Alto, CA, USA
| | - Siddharth Sukumaran
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
- Translational Pharmacometrics, Janssen, Horsham, PA, USA
| | - Tomasz Baginski
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Danielle DiCara
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Nicholas J Agard
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Matthieu Masureel
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Joshua Gober
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Adel M ElSohly
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Rafael Melani
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - John E P Syka
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Romain Huguet
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA.
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9
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Shah A, Cui W, Harrahy J, Ivanov AR. Characterization of charge variants, including post-translational modifications and proteoforms, of bispecific antigen-binding protein by cation-exchange chromatography coupled to native mass spectrometry. Talanta 2024; 266:125062. [PMID: 37566926 PMCID: PMC10528315 DOI: 10.1016/j.talanta.2023.125062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/29/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023]
Abstract
Charge variant characterization of biologics is critical to ensure that product meets the required quality and regulatory requirements to ensure safety and efficacy of the biotherapeutic. Charge variants arise from post-translation modifications (PTMs) during upstream processing and due to enzymatic and non-enzymatic chemical reactions that occur during downstream processing and storage. Some of these modifications may impact therapeutic potency, efficacy, or immunogenicity of a biotherapeutic. The traditional workflow for characterizing charge variants that involves fraction enrichment is time-consuming and labor-intensive. This approach can be especially challenging if the product is manufactured at low concentrations (e.g., ≤2 mg/mL). Recent advances in pH-based elution for ion-exchange chromatography utilizing volatile buffers have enabled rapid native mass-spectrometry-based identification of PTMs and proteoforms associated with protein therapeutics. In this study, we develop a novel workflow to rapidly and unambiguously characterize modifications associated with a new class of biotherapeutics known as bispecific antigen-binding protein (BsABP), including low-level modifications. A cation-exchange separation was optimized using volatile buffers to provide online hyphenation for native mass spectrometry to profile modifications and proteoforms present at the native level of a biotherapeutic, such as deamidation, O-glycosylation, amino acid substitution, N-linked glycosylation and oxidation. Furthermore, a limited proteolysis method was developed to specifically inform about modifications in the different domains of the bispecific antibody. Using this approach, we could efficiently identify PTMs in unstressed, thermally and photo-stressed samples, and provide information about the impact of downstream purification in clearing out modified BsABP species. Furthermore, peptide mapping was performed to identify and confirm modifications at the amino acid residue level. The developed workflow is less time-consumable and reduces sample processing- and analysis-related artifacts compared to traditional approaches.
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Affiliation(s)
- Arnik Shah
- Amgen Inc, 360 Binney Street, Cambridge, MA, 02141, United States; Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, United States
| | - Weidong Cui
- Amgen Inc, 360 Binney Street, Cambridge, MA, 02141, United States
| | - John Harrahy
- Sanofi, 225 Second Avenue, Waltham, MA 02451, United States
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, United States.
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10
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Reddy JV, Raudenbush K, Papoutsakis ET, Ierapetritou M. Cell-culture process optimization via model-based predictions of metabolism and protein glycosylation. Biotechnol Adv 2023; 67:108179. [PMID: 37257729 DOI: 10.1016/j.biotechadv.2023.108179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/18/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023]
Abstract
In order to meet the rising demand for biologics and become competitive on the developing biosimilar market, there is a need for process intensification of biomanufacturing processes. Process development of biologics has historically relied on extensive experimentation to develop and optimize biopharmaceutical manufacturing. Experimentation to optimize media formulations, feeding schedules, bioreactor operations and bioreactor scale up is expensive, labor intensive and time consuming. Mathematical modeling frameworks have the potential to enable process intensification while reducing the experimental burden. This review focuses on mathematical modeling of cellular metabolism and N-linked glycosylation as applied to upstream manufacturing of biologics. We review developments in the field of modeling cellular metabolism of mammalian cells using kinetic and stoichiometric modeling frameworks along with their applications to simulate, optimize and improve mechanistic understanding of the process. Interest in modeling N-linked glycosylation has led to the creation of various types of parametric and non-parametric models. Most published studies on mammalian cell metabolism have performed experiments in shake flasks where the pH and dissolved oxygen cannot be controlled. Efforts to understand and model the effect of bioreactor-specific parameters such as pH, dissolved oxygen, temperature, and bioreactor heterogeneity are critically reviewed. Most modeling efforts have focused on the Chinese Hamster Ovary (CHO) cells, which are most commonly used to produce monoclonal antibodies (mAbs). However, these modeling approaches can be generalized and applied to any mammalian cell-based manufacturing platform. Current and potential future applications of these models for Vero cell-based vaccine manufacturing, CAR-T cell therapies, and viral vector manufacturing are also discussed. We offer specific recommendations for improving the applicability of these models to industrially relevant processes.
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Affiliation(s)
- Jayanth Venkatarama Reddy
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716-3196, USA
| | - Katherine Raudenbush
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716-3196, USA
| | - Eleftherios Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716-3196, USA; Delaware Biotechnology Institute, Department of Biological Sciences, University of Delaware, USA.
| | - Marianthi Ierapetritou
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716-3196, USA.
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11
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Mao L, Schneider JW, Robinson AS. Use of single analytic tool to quantify both absolute N-glycosylation and glycan distribution in monoclonal antibodies. Biotechnol Prog 2023; 39:e3365. [PMID: 37221987 DOI: 10.1002/btpr.3365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/22/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023]
Abstract
Recombinant proteins represent almost half of the top selling therapeutics-with over a hundred billion dollars in global sales-and their efficacy and safety strongly depend on glycosylation. In this study, we showcase a simple method to simultaneously analyze N-glycan micro- and macroheterogeneity of an immunoglobulin G (IgG) by quantifying glycan occupancy and distribution. Our approach is linear over a wide range of glycan and glycoprotein concentrations down to 25 ng/mL. Additionally, we present a case study demonstrating the effect of small molecule metabolic regulators on glycan heterogeneity using this approach. In particular, sodium oxamate (SOD) decreased Chinese hamster ovary (CHO) glucose metabolism and reduced IgG glycosylation by 40% through upregulating reactive oxygen species (ROS) and reducing the UDP-GlcNAc pool, while maintaining a similar glycan profile to control cultures. Here, we suggest glycan macroheterogeneity as an attribute should be included in bioprocess screening to identify process parameters that optimize culture performance without compromising antibody quality.
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Affiliation(s)
- Leran Mao
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - James W Schneider
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Anne S Robinson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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12
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Srila W, Baumann M, Riedl M, Rangnoi K, Borth N, Yamabhai M. Glutamine synthetase (GS) knockout (KO) using CRISPR/Cpf1 diversely enhances selection efficiency of CHO cells expressing therapeutic antibodies. Sci Rep 2023; 13:10473. [PMID: 37380701 DOI: 10.1038/s41598-023-37288-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
The glutamine synthetase (GS)-based Chinese hamster ovary (CHO) selection system is an attractive approach to efficiently identify suitable clones in the cell line generation process for biologics manufacture, for which GS-knockout (GS-KO) CHO cell lines are commonly used. Since genome analysis indicated that there are two GS genes in CHO cells, deleting only 1 GS gene could potentially result in the activation of other GS genes, consequently reducing the selection efficiency. Therefore, in this study, both GS genes identified on chromosome 5 (GS5) and 1 (GS1) of CHO-S and CHO-K1, were deleted using CRISPR/Cpf1. Both single and double GS-KO CHO-S and K1 showed robust glutamine-dependent growth. Next, the engineered CHO cells were tested for their efficiency of selection of stable producers of two therapeutic antibodies. Analysis of pool cultures and subclones after a single round of 25 µM methionine sulfoxinime (MSX) selection indicated that for CHO-K1 the double GS5,1-KO was more efficient as in the case of a single GS5-KO the GS1 gene was upregulated. In CHO-S, on the other hand, with an autologously lower level of expression of both variants of GS, a single GS5-KO was more robust and already enabled selection of high producers. In conclusion, CRISPR/Cpf1 can be efficiently used to knock out GS genes from CHO cells. The study also indicates that for the generation of host cell lines for efficient selection, the initial characterisation of expression levels of the target gene as well as the identification of potential escape mechanisms is important.
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Affiliation(s)
- Witsanu Srila
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Markus Riedl
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Kuntalee Rangnoi
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria.
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
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13
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Shivatare VS, Chuang PK, Tseng TH, Zeng YF, Huang HW, Veeranjaneyulu G, Wu HC, Wong CH. Study on antibody Fc-glycosylation for optimal effector functions. Chem Commun (Camb) 2023; 59:5555-5558. [PMID: 37071468 PMCID: PMC10259620 DOI: 10.1039/d3cc00672g] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
A comprehensive structure-activity relationship study on antibody Fc-glycosylation has been performed using the chimeric anti-SSEA4 antibody chMC813-70 as a model. The α-2,6 sialylated biantennary complex type glycan was identified as the optimal Fc-glycan with significant enhancement in antibody effector functions, including binding to different Fc receptors and ADCC.
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Affiliation(s)
- Vidya S Shivatare
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.
| | - Po-Kai Chuang
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.
| | - Tzu-Hao Tseng
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.
| | - Yi-Fang Zeng
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.
| | - Han-Wen Huang
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.
| | - Gannedi Veeranjaneyulu
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA.
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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14
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Liang C, Chiang AWT, Lewis NE. GlycoMME, a Markov modeling platform for studying N-glycosylation biosynthesis from glycomics data. STAR Protoc 2023; 4:102244. [PMID: 37086409 PMCID: PMC10160804 DOI: 10.1016/j.xpro.2023.102244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/07/2023] [Accepted: 03/24/2023] [Indexed: 04/23/2023] Open
Abstract
Variations in N-glycosylation, which is crucial to glycoprotein functions, impact many diseases and the safety and efficacy of biotherapeutic drugs. Here, we present a protocol for using GlycoMME (Glycosylation Markov Model Evaluator) to study N-glycosylation biosynthesis from glycomics data. We describe steps for annotating glycomics data and quantifying perturbations to N-glycan biosynthesis with interpretable models. We then detail procedures to predict the impact of mutations in disease or potential glycoengineering strategies in drug development. For complete details on the use and execution of this protocol, please refer to Liang et al. (2020).1.
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Affiliation(s)
- Chenguang Liang
- Department of Pediatrics, University of California, San Diego, La Jolla, San Diego, CA 92130, USA; Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92130, USA
| | - Austin W T Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, San Diego, CA 92130, USA.
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, San Diego, CA 92130, USA; Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92130, USA.
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15
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Chia S, Tay SJ, Song Z, Yang Y, Walsh I, Pang KT. Enhancing pharmacokinetic and pharmacodynamic properties of recombinant therapeutic proteins by manipulation of sialic acid content. Biomed Pharmacother 2023; 163:114757. [PMID: 37087980 DOI: 10.1016/j.biopha.2023.114757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/13/2023] [Accepted: 04/20/2023] [Indexed: 04/25/2023] Open
Abstract
The circulatory half-life of recombinant therapeutic proteins is an important pharmacokinetic attribute because it determines the dosing frequency of these drugs, translating directly to treatment cost. Thus, recombinant therapeutic glycoproteins such as monoclonal antibodies have been chemically modified by various means to enhance their circulatory half-life. One approach is to manipulate the N-glycan composition of these agents. Among the many glycan constituents, sialic acid (specifically, N-acetylneuraminic acid) plays a critical role in extending circulatory half-life by masking the terminal galactose that would otherwise be recognised by the hepatic asialoglycoprotein receptor (ASGPR), resulting in clearance of the biotherapeutic from the circulation. This review aims to provide an illustrative overview of various strategies to enhance the pharmacokinetic/pharmacodynamic properties of recombinant therapeutic proteins through manipulation of their sialic acid content.
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Affiliation(s)
- Sean Chia
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Shi Jie Tay
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Zhiwei Song
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Yuansheng Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Ian Walsh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore.
| | - Kuin Tian Pang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A⁎STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore; School of Chemistry, Chemical Engineering, and Biotechnology, Nanyang Technology University, 62 Nanyang Drive, N1.2-B3, 637459, Singapore.
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16
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Burock R, Cajic S, Hennig R, Buettner FFR, Reichl U, Rapp E. Reliable N-Glycan Analysis-Removal of Frequently Occurring Oligosaccharide Impurities by Enzymatic Degradation. Molecules 2023; 28:molecules28041843. [PMID: 36838829 PMCID: PMC9967028 DOI: 10.3390/molecules28041843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Glycosylation, especially N-glycosylation, is one of the most common protein modifications, with immense importance at the molecular, cellular, and organismal level. Thus, accurate and reliable N-glycan analysis is essential in many areas of pharmaceutical and food industry, medicine, and science. However, due to the complexity of the cellular glycosylation process, in-depth glycoanalysis is still a highly challenging endeavor. Contamination of samples with oligosaccharide impurities (OSIs), typically linear glucose homo-oligomers, can cause further complications. Due to their physicochemical similarity to N-glycans, OSIs produce potentially overlapping signals, which can remain unnoticed. If recognized, suspected OSI signals are usually excluded in data evaluation. However, in both cases, interpretation of results can be impaired. Alternatively, sample preparation can be repeated to include an OSI removal step from samples. However, this significantly increases sample amount, time, and effort necessary. To overcome these issues, we investigated the option to enzymatically degrade and thereby remove interfering OSIs as a final sample preparation step. Therefore, we screened ten commercially available enzymes concerning their potential to efficiently degrade maltodextrins and dextrans as most frequently found OSIs. Of these enzymes, only dextranase from Chaetomium erraticum and glucoamylase P from Hormoconis resinae enabled a degradation of OSIs within only 30 min that is free of side reactions with N-glycans. Finally, we applied the straightforward enzymatic degradation of OSIs to N-glycan samples derived from different standard glycoproteins and various stem cell lysates.
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Affiliation(s)
- Robert Burock
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
| | - Samanta Cajic
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
| | - René Hennig
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
- Correspondence:
| | - Falk F. R. Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Udo Reichl
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Erdmann Rapp
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
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17
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Saldanha M, Shelar A, Patil V, Warke VG, Dandekar P, Jain R. A case study: Correlation of the nutrient composition in Chinese Hamster Ovary cultures with cell growth, antibody titre and quality attributes using multivariate analyses for guiding medium and feed optimization in early upstream process development. Cytotechnology 2023; 75:77-91. [PMID: 36713064 PMCID: PMC9880107 DOI: 10.1007/s10616-022-00561-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/12/2022] [Indexed: 11/25/2022] Open
Abstract
In this case-study, we demonstrate an approach for identifying correlations between nutrients/metabolites in the spent medium of CHO cell cultures and cell growth, mAb titre and critical quality attributes, using multivariate analyses, which can aid in selection of targets for medium and feed optimization. An extensive LC-MS-based method was used to analyse the spent medium composition. Partial least squares (PLS) model was used to identify correlations between nutrient composition and cell growth and mAb titre and orthogonal projections to latent structures (OPLS) model was used to determine the effect of the changing nutrient composition during the culture on critical quality attributes. The PLS model revealed that the initial concentrations of several amino acids as well as pyruvic acid and pyridoxine, governed the early cell growth, while the concentrations of TCA cycle intermediates and several vitamins highly influenced the stationary phase, in which mAb production was maximum. For the first time, with the help of the OPLS model, we were able to draw correlations between nutrients/metabolites during the culture and critical quality attributes, for example, optimizing the supply of certain amino acids and vitamins could reduce impurities while simultaneously increasing desirable glycoforms. The unique correlations obtained from such an exploratory analysis, utilizing conditions that are commonly adopted in early process development, present opportunities for optimizing the compositions of the growth media and the feed media for enhancing cell growth, mAb production and quality, thereby proving to be a useful preliminary step in bioprocess optimization. Supplementary Information The online version contains supplementary material available at 10.1007/s10616-022-00561-z.
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Affiliation(s)
- Marianne Saldanha
- Department of Biological Sciences and Biotechnology, Institute of Chemical Technology, Matunga, Mumbai, 400019 India
| | - Ashutosh Shelar
- Shimadzu Analytical (India) Private Limited, Rushabh Chambers, Marol, Andheri East, Mumbai, 400059 India
| | - Vaibhav Patil
- Sartorius Stedim India Private Limited, No. 69/2 & 69/3, Jakkasandra, Nelamangala, Bangalore, 562123 India
| | - Vishal G. Warke
- Himedia Laboratories Private Limited, Plot No. C40, MIDC, Wagle Industrial Area, Thane, 400604 India
| | - Prajakta Dandekar
- Department of Pharmaceutical Science and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019 India
| | - Ratnesh Jain
- Department of Biological Sciences and Biotechnology, Institute of Chemical Technology, Matunga, Mumbai, 400019 India
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18
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Puranik A, Goswami R, Sutar P, Tupe D, Rasam P, Dandekar P, Jain R. Mass spectrometry-based glycoprofiling of biopharmaceuticals by using an automated data processing tool: SimGlycan ®. J Sep Sci 2023; 46:e2200521. [PMID: 36463509 DOI: 10.1002/jssc.202200521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/15/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
The therapeutic and immunological properties of biopharmaceuticals are governed by the glycoforms contained in them. Thus, bioinformatics tools capable of performing comprehensive characterization of glycans are significantly important to the biopharma industry. The primary structural elucidation of glycans using mass spectrometry is tricky and tedious in terms of spectral interpretation. In this study, the biosimilars of a therapeutic monoclonal antibody and an Fc-fusion protein with moderate and heavy glycosylation, respectively, were employed as representative biopharmaceuticals for released glycan analysis using liquid chromatography-tandem mass spectrometry instead of conventional mass spectrometry-based analysis. SimGlycan® is a software with proven ability to process tandem MS data for released glycans could identify eight additional glycoforms in Fc-fusion protein biosimilar, which were not detected during mass spectrometry analysis of released glycans or glyco-peptide mapping of the same molecule. Thus, liquid chromatography-tandem mass spectrometry analysis of released glycans not only complements conventional liquid chromatography-mass spectrometry-based glycan profiling but can also identify additional glycan structures that may otherwise be omitted during conventional liquid chromatography-tandem mass spectrometry based analysis of mAbs. The mass spectrometry data processing tools, such as PMI Byos™, SimGlycan® , etc., can display pivotal analytical capabilities in automated liquid chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry-based glycan analysis workflows, especially for high-throughput structural characterization of glycoforms in biopharmaceuticals.
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Affiliation(s)
- Amita Puranik
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
| | | | | | - Devika Tupe
- Shimadzu Analytical (India) Private Limited, Mumbai, India
| | - Pratap Rasam
- Shimadzu Analytical (India) Private Limited, Mumbai, India
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
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19
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Simplifying the detection and monitoring of protein glycosylation during in vitro glycoengineering. Sci Rep 2023; 13:567. [PMID: 36631484 PMCID: PMC9834283 DOI: 10.1038/s41598-023-27634-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
The majority of mammalian proteins are glycosylated, with the glycans serving to modulate a wide range of biological activities. Variations in protein glycosylation can have dramatic effects on protein stability, immunogenicity, antibody effector function, pharmacological safety and potency, as well as serum half-life. The glycosylation of therapeutic biologicals is a critical quality attribute (CQA) that must be carefully monitored to ensure batch-to-batch consistency. Notably, many factors can affect the composition of the glycans during glycoprotein production, and variations in glycosylation are among the leading causes of pharmaceutical batch rejection. Currently, the characterization of protein glycosylation relies heavily on methods that employ chromatography and/or mass spectrometry, which require a high level of expertise, are time-consuming and costly and, because they are challenging to implement during in-process biologics production or during in vitro glycan modification, are generally performed only post-production. Here we report a simplified approach to assist in monitoring glycosylation features during glycoprotein engineering, that employs flow cytometry using fluorescent microspheres chemically coupled to high-specificity glycan binding reagents. In our GlycoSense method, a range of carbohydrate-sensing microspheres with distinct optical properties may be combined into a multiplex suspension array capable of detecting multiple orthogonal glycosylation features simultaneously, using commonplace instrumentation, without the need for glycan release. The GlycoSense method is not intended to replace more detailed post-production glycan profiling, but instead, to complement them by potentially providing a cost-effective, rapid, yet robust method for use at-line as a process analytic technology (PAT) in a biopharmaceutical workflow or at the research bench. The growing interest in using in vitro glycoengineering to generate glycoproteins with well-defined glycosylation, provides motivation to demonstrate the capabilities of the GlycoSense method, which we apply here to monitor changes in the protein glycosylation pattern (GlycoPrint) during the in vitro enzymatic modification of the glycans in model glycoproteins.
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20
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Hatfield G, Tepliakova L, Tran J, Lu H, Gilbert M, Tam RY. Bivalent non-human gal-α1-3-gal glycan epitopes in the Fc region of a monoclonal antibody model can be recognized by anti-Gal-α1-3-Gal IgE antibodies. MAbs 2023; 15:2239405. [PMID: 37497986 PMCID: PMC10376915 DOI: 10.1080/19420862.2023.2239405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/28/2023] Open
Abstract
Monoclonal antibody (mAb) production using non-human cells can introduce non-human glycan epitopes including terminal galactosyl-α1-3-galactose (α1-3-Gal) moieties. Cetuximab is a commercial mAb associated with causing anaphylaxis in some patients due to the binding of endogenous anti-α1-3-Gal IgE to the Fab (containing bi-α1-3-galactosylated glycans) but not to the Fc region (containing mono-α1-3-galactosylated glycans). Despite being low in abundance in typical commercial mAbs, the inherent sensitivity of cell culture conditions on glycosylation profiles, and the development of novel glycoengineering strategies, novel antibody-based modalities, and biosimilars by various manufacturers with varying procedures, necessitates a better understanding of the structural requirements for anti-α1-3-Gal IgE binding to the Fc region. Herein, we synthesized mAb glycoforms with varying degrees and regioisomers of α1-3-galactosylation and tested their binding to two commercial anti-α1-3-Gal human IgE antibodies derived from a human patient with allergies to red meat (comprising α1-3-Gal epitopes), as well as to the FcγRIIIA receptor. Our results demonstrate that unexpectedly, anti-α1-3-Gal human IgE antibodies can bind to Fc glycans, with bi-α1-3-galactosylation being the most important factor, highlighting that their presence in the Fc region may be considered as a potential critical quality attribute, particularly when using novel platforms in mAb-based biotherapeutics.
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Affiliation(s)
- Grayson Hatfield
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Lioudmila Tepliakova
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Jessica Tran
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Huixin Lu
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Michel Gilbert
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Roger Y. Tam
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario, Canada
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21
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Lim SY, Lim FLS, Criado-Navarro I, Yeo XH, Dayal H, Vemulapalli SD, Seah SJ, Laserna AKC, Yang X, Tan SH, Chan MY, Li SFY. Multi-Omics Investigation into Acute Myocardial Infarction: An Integrative Method Revealing Interconnections amongst the Metabolome, Lipidome, Glycome, and Metallome. Metabolites 2022; 12:metabo12111080. [PMID: 36355163 PMCID: PMC9693522 DOI: 10.3390/metabo12111080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Acute myocardial infarction (AMI) is a leading cause of mortality and morbidity worldwide. This work aims to investigate the translational potential of a multi-omics study (comprising metabolomics, lipidomics, glycomics, and metallomics) in revealing biomechanistic insights into AMI. Following the N-glycomics and metallomics studies performed by our group previously, untargeted metabolomic and lipidomic profiles were generated and analysed in this work via the use of a simultaneous metabolite/lipid extraction and liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis workflow. The workflow was applied to blood plasma samples from AMI cases (n = 101) and age-matched healthy controls (n = 66). The annotated metabolomic (number of features, n = 27) and lipidomic (n = 48) profiles, along with the glycomic (n = 37) and metallomic (n = 30) profiles of the same set of AMI and healthy samples were integrated and analysed. The integration method used here works by identifying a linear combination of maximally correlated features across the four omics datasets, via utilising both block-partial least squares-discriminant analysis (block-PLS-DA) based on sparse generalised canonical correlation analysis. Based on the multi-omics mapping of biomolecular interconnections, several postulations were derived. These include the potential roles of glycerophospholipids in N-glycan-modulated immunoregulatory effects, as well as the augmentation of the importance of Ca–ATPases in cardiovascular conditions, while also suggesting contributions of phosphatidylethanolamine in their functions. Moreover, it was shown that combining the four omics datasets synergistically enhanced the classifier performance in discriminating between AMI and healthy subjects. Fresh and intriguing insights into AMI, otherwise undetected via single-omics analysis, were revealed in this multi-omics study. Taken together, we provide evidence that a multi-omics strategy may synergistically reinforce and enhance our understanding of diseases.
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Affiliation(s)
- Si Ying Lim
- NUS Graduate School’s Integrative Sciences & Engineering Programme (ISEP), National University of Singapore, Singapore 119077, Singapore
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Felicia Li Shea Lim
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | | | - Xin Hao Yeo
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Hiranya Dayal
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | | | - Song Jie Seah
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Anna Karen Carrasco Laserna
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- Central Instrumentation Facility (Laguna Campus), Office of the Vice President for Research and Innovation, De La Salle University, Manila 1004, Philippines
| | - Xiaoxun Yang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Sock Hwee Tan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Mark Y. Chan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Sam Fong Yau Li
- NUS Graduate School’s Integrative Sciences & Engineering Programme (ISEP), National University of Singapore, Singapore 119077, Singapore
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- Correspondence: ; Tel.: +65-6516-2681; Fax: +65-6779-1691
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22
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Hatfield G, Tepliakova L, Gingras G, Stalker A, Li X, Aubin Y, Tam RY. Specific location of galactosylation in an afucosylated antiviral monoclonal antibody affects its FcγRIIIA binding affinity. Front Immunol 2022; 13:972168. [PMID: 36304448 PMCID: PMC9596277 DOI: 10.3389/fimmu.2022.972168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Monoclonal antibodies (mAbs) comprise an essential type of biologic therapeutics and are used to treat diseases because of their anti-cancer and anti-inflammatory properties, and their ability to protect against respiratory infections. Its production involves post-translational glycosylation, a biosynthetic process that conjugates glycans to proteins, which plays crucial roles in mAb bioactivities including effector functions and pharmacokinetics. These glycans are heterogeneous and have diverse chemical structures whose composition is sensitive to manufacturing conditions, rendering the understanding of how specific glycan structures affect mAb bioactivity challenging. There is a need to delineate the effects of specific glycans on mAb bioactivity to determine whether changes in certain glycosylation profiles (that can occur during manufacturing) will significantly affect product quality. Using enzymatic transglycosylation with chemically-defined N-glycans, we show that galactosylation at a specific location of N-glycans in an afucosylated anti-viral mAb is responsible for FcγRIIIA binding and antibody-dependent cell-mediated cytotoxicity (ADCC) activity. We report a facile method to obtain purified asymmetric mono-galactosylated biantennary complex N-glycans, and their influence on bioactivity upon incorporation into an afucosylated mAb. Using ELISA, surface plasmon resonance and flow cytometry, we show that galactosylation of the α6 antenna, but not the α3 antenna, consistently increases FcγRIIIA binding affinity. We confirm its relevance in an anti-viral model of respiratory syncytial virus (RSV) using an adapted ADCC reporter assay. We further correlate this structure-function relationship to the interaction of the galactose residue of the α6 antenna with the protein backbone using 2D-1H-15N-NMR, which showed that galactosylation of at this location exhibited chemical shift perturbations compared to glycoforms lacking this galactose residue. Our results highlight the importance of identifying and quantifying specific glycan isomers to ensure adequate quality control in batch-to-batch and biosimilar comparisons.
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23
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Highly sensitive characterization of non-human glycan structures of monoclonal antibody drugs utilizing tandem mass spectrometry. Sci Rep 2022; 12:15109. [PMID: 36068283 PMCID: PMC9448817 DOI: 10.1038/s41598-022-19488-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
Glycosylation is an important attribute of monoclonal antibodies (mAbs) for assessing manufacturing quality. Analysis of non-human glycans containing terminal galactose-α1,3-galactose and N-glycolylneuraminic acid is essential due to the potential immunogenicity and insufficient efficacy caused by mAb expression in non-human mammalian cells. Using parallel sequencing of isobaric glycopeptides and isomeric glycans that were separated by reversed-phase and porous graphitic carbon LC, we report a highly sensitive LC MS/MS method for the comprehensive characterization of low-abundance non-human glycans and their closely related structural isomers. We demonstrate that the straightforward use of high-abundance diagnostic ions and complementary fragments under the positive ionization low-energy collision-induced dissociation is a universal approach to rapidly discriminate branch-linkage structures of biantennary glycans. Our findings reveal the structural diversity of non-human glycans and sulfation of α-galactosylated glycans, providing both an analytical method and candidate structures that could potentially be used in the crucial quality control of therapeutic mAb products.
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24
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Yang B, Mai TD, Tran NT, Taverna M. In capillary labeling and online electrophoretic separation of N-glycans from glycoproteins. J Sep Sci 2022; 45:3594-3603. [PMID: 35820058 PMCID: PMC9796131 DOI: 10.1002/jssc.202200340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/16/2022] [Accepted: 07/07/2022] [Indexed: 01/01/2023]
Abstract
In this study, we present a new approach for in-capillary fluorescent labeling of N-glycans prior to their analysis with CE coupled with laser-induced fluorescent detection. This integrated approach allows using a CE capillary as a microreactor to perform several steps required for labeling glycans with 8-aminopyrene-1,3,6 trisulfonic acid and at the same time as a separation channel for CE of fluorescently labeled glycans. This could be achieved through careful optimization of all different steps, including sequential injections of fluorescent dye and glycan plugs, mixing by transverse diffusion of laminar flow profiles, incubation in a thermostatic zone, and finally separation and detection with CE. Such a complex sample treatment protocol for glycan labeling that is feasible thus far only in batchwise mode can now be converted into an automated and integrated protocol. Our approach was applied successfully to analyze fluorescently labeled N-linked oligosaccharides released from human immunoglobulin G and rituximab, a monoclonal antibody used for cancer treatment. We demonstrated the superiority of this in-capillary approach over the conventional in-tube protocol, with fourfold less reagent consumption and full automation without remarkable degradation of the glycan separation profile obtained by capillary electrophoresis.
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Affiliation(s)
- Bin Yang
- Université Paris‐Saclay, CNRS, Faculté de PharmacieInstitut Galien Paris‐SaclayBâtiment Henri Moissan, 17 Avenue des SciencesOrsay91400France
| | - Thanh Duc Mai
- Université Paris‐Saclay, CNRS, Faculté de PharmacieInstitut Galien Paris‐SaclayBâtiment Henri Moissan, 17 Avenue des SciencesOrsay91400France
| | - Nguyet Thuy Tran
- Université Paris‐Saclay, CNRS, Faculté de PharmacieInstitut Galien Paris‐SaclayBâtiment Henri Moissan, 17 Avenue des SciencesOrsay91400France
| | - Myriam Taverna
- Université Paris‐Saclay, CNRS, Faculté de PharmacieInstitut Galien Paris‐SaclayBâtiment Henri Moissan, 17 Avenue des SciencesOrsay91400France,Institut Universitaire de France (IUF)ParisFrance
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25
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Liénard--Mayor T, Bricteux C, Bendali A, Tran NT, Bruneel A, Taverna M, Mai TD. Lab-in-droplet: From glycan sample treatment toward diagnostic screening of congenital disorders of glycosylation. Anal Chim Acta 2022; 1221:340150. [DOI: 10.1016/j.aca.2022.340150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/09/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022]
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26
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Orr CM, Fisher H, Yu X, Chan CHT, Gao Y, Duriez PJ, Booth SG, Elliott I, Inzhelevskaya T, Mockridge I, Penfold CA, Wagner A, Glennie MJ, White AL, Essex JW, Pearson AR, Cragg MS, Tews I. Hinge disulfides in human IgG2 CD40 antibodies modulate receptor signaling by regulation of conformation and flexibility. Sci Immunol 2022; 7:eabm3723. [PMID: 35857577 DOI: 10.1126/sciimmunol.abm3723] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Antibodies protect from infection, underpin successful vaccines and elicit therapeutic responses in otherwise untreatable cancers and autoimmune conditions. The human IgG2 isotype displays a unique capacity to undergo disulfide shuffling in the hinge region, leading to modulation of its ability to drive target receptor signaling (agonism) in a variety of important immune receptors, through hitherto unexplained molecular mechanisms. To address the underlying process and reveal how hinge disulfide orientation affects agonistic activity, we generated a series of cysteine to serine exchange variants in the hinge region of the clinically relevant monoclonal antibody ChiLob7/4, directed against the key immune receptor CD40. We report how agonistic activity varies with disulfide pattern and is afforded by the presence of a disulfide crossover between F(ab) arms in the agonistic forms, independently of epitope, as observed in the determined crystallographic structures. This structural "switch" affects directly on antibody conformation and flexibility. Small-angle x-ray scattering and ensemble modeling demonstrated that the least flexible variants adopt the fewest conformations and evoke the highest levels of receptor agonism. This covalent change may be amenable for broad implementation to modulate receptor signaling in an epitope-independent manner in future therapeutics.
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Affiliation(s)
- Christian M Orr
- University of Southampton, Biological Sciences, Southampton SO17 1BJ, UK
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
- Hamburg Centre for Ultrafast Imaging CFEL, Hamburg 22761, Germany
- Diamond Light Source, Didcot OX11 0FA, UK
| | - Hayden Fisher
- University of Southampton, Biological Sciences, Southampton SO17 1BJ, UK
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
| | - Xiaojie Yu
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
| | - Claude H-T Chan
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
| | - Yunyun Gao
- Hamburg Centre for Ultrafast Imaging CFEL, Hamburg 22761, Germany
- Institute for Nanostructure and Solid State Physics, Hamburg 22761, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg 22761, Germany
| | - Patrick J Duriez
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
- University of Southampton, CRUK Protein Core Facility, Southampton, SO16 6YD, UK
| | - Steven G Booth
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
| | - Isabel Elliott
- University of Southampton, Biological Sciences, Southampton SO17 1BJ, UK
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
- University of Southampton, School of Chemistry, Southampton SO17 1BJ, UK
| | | | - Ian Mockridge
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
| | - Christine A Penfold
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
| | | | - Martin J Glennie
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
| | - Ann L White
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
- UCB Pharma, Slough SL1 3WE, UK
| | - Jonathan W Essex
- University of Southampton, School of Chemistry, Southampton SO17 1BJ, UK
- University of Southampton, Institute for Life Sciences, Southampton SO17 1BJ, UK
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging CFEL, Hamburg 22761, Germany
- Institute for Nanostructure and Solid State Physics, Hamburg 22761, Germany
| | - Mark S Cragg
- University of Southampton, Centre for Cancer Immunology, Southampton SO16 6YD, UK
- University of Southampton, Institute for Life Sciences, Southampton SO17 1BJ, UK
| | - Ivo Tews
- University of Southampton, Biological Sciences, Southampton SO17 1BJ, UK
- University of Southampton, Institute for Life Sciences, Southampton SO17 1BJ, UK
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27
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Poudel PB, Pandey RP, Dhakal D, Kim TS, Nguyen TTH, Jung HJ, Shin HJ, Timalsina B, Sohng JK. Functional Characterization of a Regiospecific Sugar- O-Methyltransferase from Nocardia. Appl Environ Microbiol 2022; 88:e0075422. [PMID: 35703553 PMCID: PMC9275233 DOI: 10.1128/aem.00754-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Methyltransferases transfer a methyl group to a diverse group of natural products, thus providing structural diversity, stability, and altered pharmacological properties to the molecules. A limited number of regiospecific sugar-O-methyltransferases are functionally characterized. Thus, discovery of such an enzyme could solve the difficulties of biological production of methoxy derivatives of glycosylated molecules. In the current study, a regiospecific sugar-O-methyltransferase, ThnM1, belonging to the biosynthetic gene cluster (BGC) of 1-(α-L-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene produced by Nocardia sp. strain CS682, was analyzed and functionally characterized. ThnM1 demonstrated promiscuity to diverse chemical structures such as rhamnose-containing anthraquinones and flavonoids with regiospecific methylation at the 2'-hydroxyl group of the sugar moiety. Compared with other compounds, anthraquinone rhamnosides were found to be the preferred substrates for methylation. Thus, the enzyme was further employed for whole-cell biotransformation using engineered Escherichia coli to produce a methoxy-rhamnosyl derivative of quinizarin, an anthraquinone derivative. The structure of the newly generated derivative from Escherichia coli fermentation was elucidated by liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopic analyses and identified as quinizarin-4-O-α-l-2-O-methylrhamnoside (QRM). Further, the biological impact of methylation was studied by comparing the cytotoxicity of QRM with that of quinizarin against the U87MG, SNU-1, and A375SM cancer cell lines. IMPORTANCE ThnM1 is a putative sugar-O-methyltransferase produced by the Nocardia sp. strain CS682 and is encoded by a gene belonging to the biosynthetic gene cluster (BGC) of 1-(α-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene. We demonstrated that ThnM1 is a promiscuous enzyme with regiospecific activity at the 2'-OH of rhamnose. As regiospecific methylation of sugars by chemical synthesis is a challenging step, ThnM1 may fill the gap in the potential diversification of natural products by methylating the rhamnose moiety attached to them.
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Affiliation(s)
- Purna Bahadur Poudel
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Ramesh Prasad Pandey
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Dipesh Dhakal
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Tae-Su Kim
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Trang Thi Huyen Nguyen
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Hye Jin Jung
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
- Department of Biotechnology and Pharmaceutical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Hee Jeong Shin
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Binod Timalsina
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
- Department of Biotechnology and Pharmaceutical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
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28
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Puranik A, Saldanha M, Chirmule N, Dandekar P, Jain R. Advanced strategies in glycosylation prediction and control during biopharmaceutical development: Avenues toward Industry 4.0. Biotechnol Prog 2022; 38:e3283. [PMID: 35752935 DOI: 10.1002/btpr.3283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/31/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
Glycosylation has been shown to define the safety and efficacy of biopharmaceuticals, thus classified as a critical quality attribute. However, controlling glycan heterogeneity has always been a major challenge owing to the multi-variate factors that govern the glycosylation process. Conventional approaches for controlling glycosylation such as gene editing and metabolic control have succeeded in obtaining desired glycan profiles in accordance with the Quality by Design paradigm. Nonetheless, the development of smart algorithms and omics-enabled complete cell characterization have made it possible to predict glycan profiles beforehand, and manipulate process variables accordingly. This review thus discusses the various approaches available for control and prediction of glycosylation in biopharmaceuticals. Further, the futuristic goal of integrating such technologies is discussed in order to attain an automated and digitized continuous bioprocess for control of glycosylation. Given, control of a process as complex as glycosylation requires intense monitoring intervention, we examine the current technologies that enable automation. Finally, we discuss the challenges and the technological gap that currently limits incorporation of an automated process in routine bio-manufacturing, with a glimpse into the economic bearing. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Amita Puranik
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, India
| | - Marianne Saldanha
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, India
| | | | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, India
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, India
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29
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Glinšek K, Kramer L, Krajnc A, Kranjc E, Pirher N, Marušič J, Hellmann L, Podobnik B, Štrukelj B, Ausländer D, Gaber R. Coupling CRISPR interference with FACS enrichment: New approach in glycoengineering of CHO cell lines for therapeutic glycoprotein production. Biotechnol J 2022; 17:e2100499. [PMID: 35481906 DOI: 10.1002/biot.202100499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/10/2022] [Accepted: 04/23/2022] [Indexed: 11/05/2022]
Abstract
Difficulties in obtaining and maintaining the desired level of the critical quality attributes (CQAs) of therapeutic proteins as well as the pace of the development are major challenges of current biopharmaceutical development. Therapeutic proteins, both innovative and biosimilars, are mostly glycosylated. Glycans directly influence the stability, potency, plasma half-life, immunogenicity, and effector functions of the therapeutic. Hence, glycosylation is widely recognized as a process-dependent CQA of therapeutic glycoproteins. Due to the typically high heterogeneity of glycoforms attached to the proteins, control of glycosylation represents one of the most challenging aspects of biopharmaceutical development. Here, we explored a new glycoengineering approach in therapeutic glycoproteins development, which enabled us to achieve the targeted glycoprofile of the Fc-fusion protein in a fast manner. Coupling CRISPRi technology with lectin-FACS sorting enabled downregulation of the endogenous gene involved in fucosylation and further enrichment of CHO cells producing Fc-fusion proteins with reduced fucosylation levels. Enrichment of cells with targeted glycoprofile can lead to time-optimized clone screening and speed up cell line development. Moreover, the presented approach allows isolation of clones with varying levels of fucosylation, which makes it applicable to a broad range of glycoproteins differing in target fucosylation level. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Katja Glinšek
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, Ljubljana, SI-1000, Slovenia
| | - Lovro Kramer
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Aleksander Krajnc
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Eva Kranjc
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, Ljubljana, SI-1000, Slovenia
| | - Nina Pirher
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Jaka Marušič
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Leon Hellmann
- Novartis Institutes for Biomedical Research, Klybeckstrasse 141, Basel, CH-4057, Switzerland
| | - Barbara Podobnik
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Borut Štrukelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, Ljubljana, SI-1000, Slovenia
| | - David Ausländer
- Novartis Institutes for Biomedical Research, Klybeckstrasse 141, Basel, CH-4057, Switzerland
| | - Rok Gaber
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
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30
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N-Glycosylation of monoclonal antibody therapeutics: A comprehensive review on significance and characterization. Anal Chim Acta 2022; 1209:339828. [DOI: 10.1016/j.aca.2022.339828] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 01/02/2023]
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31
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Wang T, Liu L, Voglmeir J. mAbs N-glycosylation: Implications for biotechnology and analytics. Carbohydr Res 2022; 514:108541. [DOI: 10.1016/j.carres.2022.108541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 12/29/2022]
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32
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Correlative N-Glycan and Charge Variant Analysis of Cetuximab Expressed in Murine, Chinese Hamster and Human Expression Systems. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1194:123186. [DOI: 10.1016/j.jchromb.2022.123186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/14/2022] [Accepted: 02/15/2022] [Indexed: 11/19/2022]
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Establishment of a glycoengineered CHO cell line for enhancing the antennary structure and sialylation of CTLA4-Ig. Enzyme Microb Technol 2022; 157:110007. [DOI: 10.1016/j.enzmictec.2022.110007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 11/23/2022]
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Mimura Y, Mimura-Kimura Y, Saldova R, Rudd PM, Jefferis R. Enhanced Immunomodulatory Effect of Intravenous Immunoglobulin by Fc Galactosylation and Nonfucosylation. Front Immunol 2022; 13:818382. [PMID: 35154135 PMCID: PMC8831331 DOI: 10.3389/fimmu.2022.818382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/10/2022] [Indexed: 11/30/2022] Open
Abstract
Intravenous immunoglobulin (IVIG) is used as an immunomodulatory agent in the treatment of various autoimmune/inflammatory diseases although its mechanism of action remains elusive. Recently, nonfucosylated IgG has been shown to be preferentially bound to Fcγ receptor IIIa (FcγRIIIa) on circulating natural killer cells; therefore, we hypothesized that nonfucosylated IVIG may modulate immune responses through FcγRIIIa blockade. Here, homogeneous fucosylated or nonfucosylated glycoforms of normal polyclonal IgG bearing sialylated, galactosylated or nongalactosylated Fc oligosaccharides were generated by chemoenzymatic glycoengineering to investigate whether the IgG glycoforms can inhibit antibody-dependent cellular cytotoxicity (ADCC). Among the six IgG glycoforms, galactosylated, nonfucosylated IgG [(G2)2] had the highest affinity to FcγRIIIa and 20 times higher potency to inhibit ADCC than native IgG. A pilot study of IVIG treatment in mice with collagen antibody-induced arthritis highlighted the low-dose (G2)2 glycoform of IVIG (0.1 g/kg) as an effective immunomodulatory agent as the 10-fold higher dose of native IVIG. These preliminary results suggest that the anti-inflammatory activity of IVIG is in part mediated via activating FcγR blockade by galactosylated, nonfucosylated IgG and that such nonfucosylated IgG glycoforms bound to FcγRs on immune cells play immunomodulatory roles in health and disease. This study provides insights into improved therapeutic strategies for autoimmune/inflammatory diseases using glycoengineered IVIG and recombinant Fc.
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Affiliation(s)
- Yusuke Mimura
- Department of Clinical Research, National Hospital Organization Yamaguchi Ube Medical Center, Ube, Japan
- *Correspondence: Yusuke Mimura,
| | - Yuka Mimura-Kimura
- Department of Clinical Research, National Hospital Organization Yamaguchi Ube Medical Center, Ube, Japan
| | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Dublin, Ireland
- UCD School of Medicine, College of Health and Agricultural Science, University College Dublin, Dublin, Ireland
| | - Pauline M. Rudd
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Dublin, Ireland
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Centros, Singapore
| | - Roy Jefferis
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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Engineering an Enhanced EGFR Engager: Humanization of Cetuximab for Improved Developability. Antibodies (Basel) 2022; 11:antib11010006. [PMID: 35076451 PMCID: PMC8788544 DOI: 10.3390/antib11010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/12/2021] [Accepted: 01/05/2022] [Indexed: 01/05/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase whose proliferative effects can contribute to the development of many types of solid tumors when overexpressed. For this reason, EGFR inhibitors such as cetuximab can play an important role in treating cancers such as colorectal cancer and head and neck cancer. Cetuximab is a chimeric monoclonal antibody containing mouse variable regions that bind to EGFR and prevent it from signaling. Although cetuximab has been used clinically since 2004 to successfully control solid tumors, advances in protein engineering have created the opportunity to address some of its shortcomings. In particular, the presence of mouse sequences could contribute to immunogenicity in the form of anti-cetuximab antibodies, and an occupied glycosylation site in FR3 can contribute to hypersensitivity reactions and product heterogeneity. Using simple framework graft or sequence-/structure-guided approaches, cetuximab was humanized onto 11 new frameworks. In addition to increasing humanness and removing the VH glycosylation site, dynamic light scattering revealed increases in stability, and bio-layer interferometry confirmed minimal changes in binding affinity, with patterns emerging across the humanization method. This work demonstrates the potential to improve the biophysical and clinical properties of first-generation protein therapeutics and highlights the advantages of computationally guided engineering.
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Murray TV, Kozakowska-McDonnell K, Tibbles A, Taylor A, Higazi D, Rossy E, Rossi A, Genapathy S, Tamburrino G, Rath N, Tigue N, Lindo V, Vaughan T, Papworth MA. An efficient system for bioconjugation based on a widely applicable engineered O-glycosylation tag. MAbs 2021; 13:1992068. [PMID: 34781832 PMCID: PMC8604393 DOI: 10.1080/19420862.2021.1992068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Bioconjugates are an important class of therapeutic molecules. To date, O-glycan-based metabolic glycoengineering has had limited use in this field, due to the complexities of the endogenous O-glycosylation pathway and the lack of an O-glycosylation consensus sequence. Here, we describe the development of a versatile on-demand O-glycosylation system that uses a novel, widely applicable 5 amino acid O-glycosylation tag, and a metabolically engineered UDP-galactose-4-eperimase (GALE) knock-out cell line. Optimization of the primary sequence of the tag enables the production of Fc-based proteins with either single or multiple O-glycans with complexity fully controlled by media supplementation. We demonstrate how the uniformly labeled proteins containing exclusively N-azido-acetylgalactosamine are used for CLICK chemistry-based bioconjugation to generate site-specifically fluorochrome-labeled antibodies, dual-payload molecules, and bioactive Fc-peptides for applications in basic research and drug discovery. To our knowledge, this is the first description of generating a site-specific O-glycosylation system by combining an O-glycosylation tag and a metabolically engineered cell line.
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Affiliation(s)
| | | | - Adam Tibbles
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | - Annabel Taylor
- Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Daniel Higazi
- Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Emmanuel Rossy
- Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Alessandra Rossi
- Cardiovascular Renal and Metabolism, R&D, AstraZeneca, Cambridge, UK
| | | | | | | | | | - Vivian Lindo
- Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
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Liénard-Mayor T, Yang B, Tran NT, Bruneel A, Guttman A, Taverna M, Mai TD. High sensitivity capillary electrophoresis with fluorescent detection for glycan mapping. J Chromatogr A 2021; 1657:462593. [PMID: 34689907 DOI: 10.1016/j.chroma.2021.462593] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022]
Abstract
We present in this study a novel strategy to drastically improve the detection sensitivity and peak capacity for capillary electrophoresis with laser induced fluorescent detection (CE-LIF) of glucose oligomers and released glycans. This is based on a new approach exploiting a polymer-free background electrolyte (BGE) for CE-LIF of glycans. The best performance in terms of sample stacking and suppression of electroosmotic flow (EOF) was found for a BGE composed of triethanolamine/citric acid and triethanolamine/acetic acid at elevated ionic strengths (IS up to 200 mM). Compared to the conventional protocols for CE-LIF of glucose-oligosaccharides and released glycans, our polymer-free strategy offered up to 5-fold improvement of detection sensitivity and visualization of higher degree of polymerization (DP) of glucose oligomers (18 vs 15). To further improve the detection sensitivity, a new electrokinetic preconcentration strategy via large volume sample stacking with electroosmotic modulation without having recourse to neutrally coated capillaries is proposed, offering a 200-fold signal enhancement. This approach is based on variation of the buffer's IS, rather than pH adjustment as in conventional methods, for EOF modulation or quasi-total reduction. This strategy allows selecting with high flexibility the best pH conditions to perform efficient preconcentration and separation. The new approach was demonstrated to be applicable for the analysis of N-linked oligosaccharides released from a model glycoprotein (Human Immunoglobulin G) and applied to map N-glycans from human serum for congenital disorders of glycosylation (CDG) diagnosis.
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Affiliation(s)
- Théo Liénard-Mayor
- Institut Galien Paris Sud, UMR 8612, Protein and Nanotechnology in Analytical Science (PNAS), CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, 5 rue Jean Baptiste Clément, 92290 Châtenay-Malabry, France
| | - Bin Yang
- Institut Galien Paris Sud, UMR 8612, Protein and Nanotechnology in Analytical Science (PNAS), CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, 5 rue Jean Baptiste Clément, 92290 Châtenay-Malabry, France
| | - Nguyet Thuy Tran
- Institut Galien Paris Sud, UMR 8612, Protein and Nanotechnology in Analytical Science (PNAS), CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, 5 rue Jean Baptiste Clément, 92290 Châtenay-Malabry, France
| | - Arnaud Bruneel
- Université Paris-Saclay, INSERM UMR1193, Mécanismes cellulaires et moléculaires de l'adaptation au stress et cancérogenèse, Châtenay-Malabry, France; AP-HP, Biochimie Métabolique et Cellulaire, Hôpital Bichat-Claude Bernard, Paris, France
| | - Andras Guttman
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprem 8200, Hungary; Horváth Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei Krt, Debrecen, 4032, Hungary
| | - Myriam Taverna
- Institut Galien Paris Sud, UMR 8612, Protein and Nanotechnology in Analytical Science (PNAS), CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, 5 rue Jean Baptiste Clément, 92290 Châtenay-Malabry, France; Institut Universitaire de France (IUF)
| | - Thanh Duc Mai
- Institut Galien Paris Sud, UMR 8612, Protein and Nanotechnology in Analytical Science (PNAS), CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, 5 rue Jean Baptiste Clément, 92290 Châtenay-Malabry, France.
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Jakes C, Füssl F, Zaborowska I, Bones J. Rapid Analysis of Biotherapeutics Using Protein A Chromatography Coupled to Orbitrap Mass Spectrometry. Anal Chem 2021; 93:13505-13512. [PMID: 34585915 PMCID: PMC8515350 DOI: 10.1021/acs.analchem.1c02365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Monoclonal antibodies
(mAbs) and related products undergo a wide
range of modifications, many of which can often be directly associated
to culture conditions during upstream processing. Ideally, such conditions
should be monitored and fine-tuned based on real-time or close to
real-time information obtained by the assessment of the product quality
attribute (PQA) profile of the biopharmaceutical produced, which is
the fundamental idea of process analytical technology. Therefore,
methods that are simple, quick and robust, but sufficiently powerful,
to allow for the generation of a comprehensive picture of the PQA
profile of the protein of interest are required. A major obstacle
for the analysis of proteins directly from cultures is the presence
of impurities such as cell debris, host cell DNA, proteins and small-molecule
compounds, which usually requires a series of capture and polishing
steps using affinity and ion-exchange chromatography before characterization
can be attempted. In the current study, we demonstrate direct coupling
of protein A affinity chromatography with native mass spectrometry
(ProA-MS) for development of a robust method that can be used to generate
information on the PQA profile of mAbs and related products in as
little as 5 min. The developed method was applied to several samples
ranging in complexity and stability, such as simple and more complex
monoclonal antibodies, as well as cysteine-conjugated antibody–drug
conjugate mimics. Moreover, the method demonstrated suitability for
the analysis of protein amounts of <1 μg, which suggests
applicability during early-stage development activities.
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Affiliation(s)
- Craig Jakes
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, County Dublin A94 X099, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - Florian Füssl
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, County Dublin A94 X099, Ireland
| | - Izabela Zaborowska
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, County Dublin A94 X099, Ireland
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, County Dublin A94 X099, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
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Abstract
The aggregation of therapeutic antibodies is a major issue for the pharmaceutical industry leading to loss of drug quality, increased dosage, and unwanted immune responses such as the production of anti-drug antibodies (ADA). As aggregation can occur at various stages of development and storage, much work has been performed to reduce or eliminate it. In this report we analyzed four antibodies available in the PDB (1IGT, 1IGY, 1HZH, and 5DK3) using the online software UCSF Chimera to study the structural features of the proteins and the associated N-linked glycans in the CH2 domains of the Fc region. To study antibody aggregation in silico we used the online software TANGO and AGGRESCAN to identify aggregation prone regions (APR) in the antibodies and the influence of the Fc glycans on hydrophobic and aromatic residues present in the APRs. In the 3D structures of 1IGT and 1IGY the glycan chains are in close enough proximity to influence and protect these hydrophobic regions. However, in the 3D structures of 1HZH and 5DK3 the glycans do not appear to influence the likely APRs of the antibodies. Therefore, in these structures we modified the Fc glycan regions by adjusting the glycosylated asparagine side chains and glycosidic bonds. We successfully adjusted the glycan chains of 1HZH and 5DK3 and reduced the distance between them and the APRs to show potential influence on aggregation. However, similar to 5DK3, the influence of glycosylation on the APRs of the antibody was limited due to the size of the glycans present in the 3D structure. This report is based on in silico studies to show how antibody glycans can influence aggregation.
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40
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Mastrangeli R, Audino MC, Palinsky W, Broly H, Bierau H. Current views on N-glycolylneuraminic acid in therapeutic recombinant proteins. Trends Pharmacol Sci 2021; 42:943-956. [PMID: 34544608 DOI: 10.1016/j.tips.2021.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
The incorporation of the non-human N-glycolylneuraminic acid (Neu5Gc) in therapeutic recombinant proteins raises clinical concerns due to its immunogenic potential and the high prevalence of pre-existing anti-Neu5Gc antibodies in humans. The scientific literature is ambiguous regarding the actual impact of Neu5Gc-containing biotherapeutics as no severe adverse clinical manifestations were unequivocally attributed to Neu5Gc for currently marketed biotherapeutics. This review discusses structural and functional considerations of Neu5Gc-containing glycans regarding the potential impact on drug clearance, their recognition by pre-existing antibodies, and recent hypotheses regarding the tolerance to low Neu5Gc levels. Furthermore, it provides recommendations regarding the standardization of analysis and reporting, analytical aspects relevant for assessing risks associated with Neu5Gc-containing biotherapeutics, and approaches to minimize Neu5Gc incorporation in recombinant protein manufacturing.
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Affiliation(s)
- Renato Mastrangeli
- Technology & Innovation, CMC Science & Intelligence, Merck Serono SpA (an affiliate of Merck KgaA, Darmstadt, Germany), Guidonia Montecelio (Rome), Italy
| | - Maria Concetta Audino
- Technology & Innovation, CMC Science & Intelligence, Merck Serono SpA (an affiliate of Merck KgaA, Darmstadt, Germany), Guidonia Montecelio (Rome), Italy
| | - Wolf Palinsky
- Biotech Development Programme, Merck Biopharma (an affiliate of Merck KgaA, Darmstadt, Germany), Aubonne, Switzerland
| | - Hervé Broly
- Biotech Process Sciences, Merck Serono S.A. (an affiliate of Merck KgaA, Darmstadt, Germany), Corsier-sur-Vevey, Switzerland
| | - Horst Bierau
- Technology & Innovation, CMC Science & Intelligence, Merck Serono SpA (an affiliate of Merck KgaA, Darmstadt, Germany), Guidonia Montecelio (Rome), Italy.
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41
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Rathore A, Malani H. Need for a risk-based control strategy for managing glycosylation profile for biosimilar products. Expert Opin Biol Ther 2021; 22:123-131. [PMID: 34431439 DOI: 10.1080/14712598.2021.1973425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Monoclonal antibodies, though a popular class of therapeutics, are complex molecules that are manufactured using complex processes, making it nontrivial to maintain high level of batch-to-batch consistency in product quality. Glycosylation is a posttranslation modification that is widely considered a critical quality attribute (CQA) as its variations are known to impact the Fc effector functions of mAbs. With continuing rise of biosimilars, comparability of these products to the reference product with respect to glycosylation is a topic of immense interest. AREAS COVERED In this article, we focus on the various aspects related to this topic including criticality of the various glycosylated forms, as well as comparability of biosimilars with respect to glycosylation. EXPERT OPINION We propose that manufacturers should focus on those glycoforms that are present in larger amounts and are known to be critical with respect to the biotherapeutic's safety and efficacy. Such risk-based evaluation of glycoforms and their control would offer an optimal route to biosimilar manufacturers for a cost-effective approach toward product development without compromising on the safety and efficacy characteristics of the therapeutic. For mAbs lacking Fc effector function, devising stringent glycosylation control strategies can be bypassed, thereby simplifying process and product development.
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Affiliation(s)
- Anurag Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Himanshu Malani
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
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42
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Oliveira T, Thaysen-Andersen M, Packer NH, Kolarich D. The Hitchhiker's guide to glycoproteomics. Biochem Soc Trans 2021; 49:1643-1662. [PMID: 34282822 PMCID: PMC8421054 DOI: 10.1042/bst20200879] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
Protein glycosylation is one of the most common post-translational modifications that are essential for cell function across all domains of life. Changes in glycosylation are considered a hallmark of many diseases, thus making glycoproteins important diagnostic and prognostic biomarker candidates and therapeutic targets. Glycoproteomics, the study of glycans and their carrier proteins in a system-wide context, is becoming a powerful tool in glycobiology that enables the functional analysis of protein glycosylation. This 'Hitchhiker's guide to glycoproteomics' is intended as a starting point for anyone who wants to explore the emerging world of glycoproteomics. The review moves from the techniques that have been developed for the characterisation of single glycoproteins to technologies that may be used for a successful complex glycoproteome characterisation. Examples of the variety of approaches, methodologies, and technologies currently used in the field are given. This review introduces the common strategies to capture glycoprotein-specific and system-wide glycoproteome data from tissues, body fluids, or cells, and a perspective on how integration into a multi-omics workflow enables a deep identification and characterisation of glycoproteins - a class of biomolecules essential in regulating cell function.
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Affiliation(s)
- Tiago Oliveira
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | | | - Nicolle H. Packer
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
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43
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Chuzel L, Fossa SL, Boisvert ML, Cajic S, Hennig R, Ganatra MB, Reichl U, Rapp E, Taron CH. Combining functional metagenomics and glycoanalytics to identify enzymes that facilitate structural characterization of sulfated N-glycans. Microb Cell Fact 2021; 20:162. [PMID: 34419057 PMCID: PMC8379841 DOI: 10.1186/s12934-021-01652-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sulfate modification of N-glycans is important for several biological functions such as clearance of pituitary hormones or immunoregulation. Yet, the prevalence of this N-glycan modification and its functions remain largely unexplored. Characterization of N-glycans bearing sulfate modifications is hampered in part by a lack of enzymes that enable site-specific detection of N-glycan sulfation. In this study, we used functional metagenomic screening to identify enzymes that act upon sulfated N-acetylglucosamine (GlcNAc). Using multiplexed capillary gel electrophoresis with laser-induced fluorescence detection (xCGE-LIF) -based glycoanalysis we proved their ability to act upon GlcNAc-6-SO4 on N-glycans. RESULTS Our screen identified a sugar-specific sulfatase that specifically removes sulfate from GlcNAc-6-SO4 when it is in a terminal position on an N-glycan. Additionally, in the absence of calcium, this sulfatase binds to the sulfated glycan but does not remove the sulfate group, suggesting it could be used for selective isolation of sulfated N-glycans. Further, we describe isolation of a sulfate-dependent hexosaminidase that removes intact GlcNAc-6-SO4 (but not asulfated GlcNAc) from a terminal position on N-glycans. Finally, the use of these enzymes to detect the presence of sulfated N-glycans by xCGE-LIF is demonstrated. CONCLUSION The present study demonstrates the feasibility of using functional metagenomic screening combined with glycoanalytics to discover enzymes that act upon chemical modifications of glycans. The discovered enzymes represent new specificities that can help resolve the presence of GlcNAc-6-SO4 in N-glycan structural analyses.
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Affiliation(s)
- Léa Chuzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- New England Biolabs, Ipswich, MA, 01938, USA
| | | | | | - Samanta Cajic
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | | | | | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- Chair of Bioprocess Engineering, Otto-von-Guericke University, 39106, Magdeburg, Germany
| | - Erdmann Rapp
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- glyXera GmbH, 39120, Magdeburg, Germany
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Sánchez-Trasviña C, Flores-Gatica M, Enriquez-Ochoa D, Rito-Palomares M, Mayolo-Deloisa K. Purification of Modified Therapeutic Proteins Available on the Market: An Analysis of Chromatography-Based Strategies. Front Bioeng Biotechnol 2021; 9:717326. [PMID: 34490225 PMCID: PMC8417561 DOI: 10.3389/fbioe.2021.717326] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/09/2021] [Indexed: 02/02/2023] Open
Abstract
Proteins, which have inherent biorecognition properties, have long been used as therapeutic agents for the treatment of a wide variety of clinical indications. Protein modification through covalent attachment to different moieties improves the therapeutic's pharmacokinetic properties, affinity, stability, confers protection against proteolytic degradation, and increases circulation half-life. Nowadays, several modified therapeutic proteins, including PEGylated, Fc-fused, lipidated, albumin-fused, and glycosylated proteins have obtained regulatory approval for commercialization. During its manufacturing, the purification steps of the therapeutic agent are decisive to ensure the quality, effectiveness, potency, and safety of the final product. Due to the robustness, selectivity, and high resolution of chromatographic methods, these are recognized as the gold standard in the downstream processing of therapeutic proteins. Moreover, depending on the modification strategy, the protein will suffer different physicochemical changes, which must be considered to define a purification approach. This review aims to deeply analyze the purification methods employed for modified therapeutic proteins that are currently available on the market, to understand why the selected strategies were successful. Emphasis is placed on chromatographic methods since they govern the purification processes within the pharmaceutical industry. Furthermore, to discuss how the modification type strongly influences the purification strategy, the purification processes of three different modified versions of coagulation factor IX are contrasted.
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Affiliation(s)
- Calef Sánchez-Trasviña
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
| | - Miguel Flores-Gatica
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
| | - Daniela Enriquez-Ochoa
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
| | - Marco Rito-Palomares
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Karla Mayolo-Deloisa
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
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Čaval T, Buettner A, Haberger M, Reusch D, Heck AJ. Discrepancies between High-Resolution Native and Glycopeptide-Centric Mass Spectrometric Approaches: A Case Study into the Glycosylation of Erythropoietin Variants. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2099-2104. [PMID: 33856811 PMCID: PMC8343523 DOI: 10.1021/jasms.1c00060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 05/04/2023]
Abstract
Glycosylation represents a critical quality attribute modulating a myriad of physiochemical properties and effector functions of biotherapeutics. Furthermore, a rising landscape of glycosylated biotherapeutics including biosimilars, biobetters, and fusion proteins harboring complicated and dynamic glycosylation profiles requires tailored analytical approaches capable of characterizing their heterogeneous nature. In this work, we perform in-depth evaluation of the glycosylation profiles of three glycoengineered variants of the widely used biotherapeutic erythropoietin. We analyzed these samples in parallel using a glycopeptide-centric liquid chromatography/mass spectrometry approach and high-resolution native mass spectrometry. Although for all of the studied variants the glycopeptide and native mass spectrometry data were in good qualitative agreement, we observed substantial quantitative differences arising from ionization deficiencies and unwanted neutral losses, in particular, for sialylated glycopeptides in the glycoproteomics approach. However, the latter provides direct information about glycosite localization. We conclude that the combined parallel use of native mass spectrometry and bottom-up glycoproteomics offers superior characterization of glycosylated biotherapeutics and thus provides a valuable attribute in the characterization of glycoengineered proteins and other complex biotherapeutics.
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Affiliation(s)
- Tomislav Čaval
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
| | - Alexander Buettner
- Pharma
Technical Development, Roche Diagnostics
GmbH, Penzberg 82377, Germany
| | - Markus Haberger
- Pharma
Technical Development, Roche Diagnostics
GmbH, Penzberg 82377, Germany
| | - Dietmar Reusch
- Pharma
Technical Development, Roche Diagnostics
GmbH, Penzberg 82377, Germany
| | - Albert J.R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
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46
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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47
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Anyaogu DC, Hansen AH, Hoof JB, Majewska NI, Contesini FJ, Paul JT, Nielsen KF, Hobley TJ, Yang S, Zhang H, Betenbaugh M, Mortensen UH. Glycoengineering of Aspergillus nidulans to produce precursors for humanized N-glycan structures. Metab Eng 2021; 67:153-163. [PMID: 34174425 DOI: 10.1016/j.ymben.2021.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 04/15/2021] [Accepted: 06/14/2021] [Indexed: 02/08/2023]
Abstract
Filamentous fungi secrete protein with a very high efficiency, and this potential can be exploited advantageously to produce therapeutic proteins at low costs. A significant barrier to this goal is posed by the fact that fungal N-glycosylation varies substantially from that of humans. Inappropriate N-glycosylation of therapeutics results in reduced product quality, including poor efficacy, decreased serum half-life, and undesirable immune reactions. One solution to this problem is to reprogram the glycosylation pathway of filamentous fungi to decorate proteins with glycans that match, or can be remodeled into, those that are accepted by humans. In yeast, deletion of ALG3 leads to the accumulation of Man5GlcNAc2 glycan structures that can act as a precursor for remodeling. However, in Aspergilli, deletion of the ALG3 homolog algC leads to an N-glycan pool where the majority of the structures contain more hexose residues than the Man3-5GlcNAc2 species that can serve as substrates for humanized glycan structures. Hence, additional strain optimization is required. In this report, we have used gene deletions in combination with enzymatic and chemical glycan treatments to investigate N-glycosylation in the model fungus Aspergillus nidulans. In vitro analyses showed that only some of the N-glycan structures produced by a mutant A. nidulans strain, which is devoid of any of the known ER mannose transferases, can be trimmed into desirable Man3GlcNAc2 glycan structures, as substantial amounts of glycan structures appear to be capped by glucose residues. In agreement with this view, deletion of the ALG6 homolog algF, which encodes the putative α-1,3- glucosyltransferase that adds the first glucose residue to the growing ER glycan structure, dramatically reduces the amounts of Hex6-7HexNAc2 structures. Similarly, these structures are also sensitive to overexpression of the genes encoding the heterodimeric α-glucosidase II complex. Without the glucose caps, a new set of large N-glycan structures was formed. Formation of this set is mostly, perhaps entirely, due to mannosylation, as overexpression of the gene encoding mannosidase activity led to their elimination. Based on our new insights into the N-glycan processing in A. nidulans, an A. nidulans mutant strain was constructed in which more than 70% of the glycoforms appear to be Man3-5GlcNAc2 species, which may serve as precursors for further engineering in order to create more complex human-like N-glycan structures.
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Affiliation(s)
- Diana Chinyere Anyaogu
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 kgs, Lyngby, Denmark
| | - Anders Holmgaard Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Lyngby, Denmark
| | - Jakob Blæsbjerg Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 kgs, Lyngby, Denmark
| | - Natalia I Majewska
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Fabiano Jares Contesini
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 kgs, Lyngby, Denmark
| | - Jackson T Paul
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kristian Fog Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 kgs, Lyngby, Denmark
| | - Timothy John Hobley
- National Food Institute, Technical University of Denmark, Søltofts Plads, Building 222, 2800 Kgs, Lyngby, Denmark
| | - Shuang Yang
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Uffe Hasbro Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 kgs, Lyngby, Denmark.
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48
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Kudelka MR, Li Z, Chernova TA, Smith DF, Song X, Cummings RD, Ju T. Cellular O-Glycome Reporter/Amplification (CORA): Analytical and Preparative Tools to Study Mucin-Type O-Glycans of Living Cells. Curr Protoc 2021; 1:e142. [PMID: 34101390 DOI: 10.1002/cpz1.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mucin-type O-glycosylation (O-glycans, O-glycome) is among the most biologically important post-translational modification in glycoproteins but O-glycan structural diversity and expression are poorly understood due to the inadequacy of current analytical methods. We recently developed a new tool termed cellular O-glycome reporter/amplification (CORA), which uses O-glycan precursors, benzyl-α-GalNAc (Bn-α-GalNAc) or azido-Bn-α-GalNAc (N3 -Bn-α-GalNAc), as surrogates of protein O-glycosylation. Living cells metabolically convert these precursors to all types of O-GalNAc glycans representative of the cells' capabilities. The amplification and secretion of the O-glycome products greatly facilitates their analysis and functional studies. Here we describe protocols for analytical and preparative applications. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. This article is a U.S. Government work and is in the public domain in the USA. Basic Protocol 1: Cellular O-glycome reporter/amplification for the analysis of mucin-type O-glycans from living cells Basic Protocol 2: Preparation of cellular O-glycans from living cells for functional glycomics and glycan microarrays Basic Protocol 3: Conjugation of cellular O-glycans with a bifunctional fluorescent tag Basic Protocol 4: 2D-HPLC purification and MALDI-TOF/MS identification of individual PYAB-Bn-O-glycan.
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Affiliation(s)
| | - Zhonghua Li
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia.,NHC Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - David F Smith
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Xuezheng Song
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Tongzhong Ju
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
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49
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Pang KT, Tay SJ, Wan C, Walsh I, Choo MSF, Yang YS, Choo A, Ho YS, Nguyen-Khuong T. Semi-Automated Glycoproteomic Data Analysis of LC-MS Data Using GlycopeptideGraphMS in Process Development of Monoclonal Antibody Biologics. Front Chem 2021; 9:661406. [PMID: 34084765 PMCID: PMC8167043 DOI: 10.3389/fchem.2021.661406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
The glycosylation of antibody-based proteins is vital in translating the right therapeutic outcomes of the patient. Despite this, significant infrastructure is required to analyse biologic glycosylation in various unit operations from biologic development, process development to QA/QC in bio-manufacturing. Simplified mass spectrometers offer ease of operation as well as the portability of method development across various operations. Furthermore, data analysis would need to have a degree of automation to relay information back to the manufacturing line. We set out to investigate the applicability of using a semiautomated data analysis workflow to investigate glycosylation in different biologic development test cases. The workflow involves data acquisition using a BioAccord LC-MS system with a data-analytical tool called GlycopeptideGraphMS along with Progenesis QI to semi-automate glycoproteomic characterisation and quantitation with a LC-MS1 dataset of a glycopeptides and peptides. Data analysis which involved identifying glycopeptides and their quantitative glycosylation was performed in 30 min with minimal user intervention. To demonstrate the effectiveness of the antibody and biologic glycopeptide assignment in various scenarios akin to biologic development activities, we demonstrate the effectiveness in the filtering of IgG1 and IgG2 subclasses from human serum IgG as well as innovator drugs trastuzumab and adalimumab and glycoforms by virtue of their glycosylation pattern. We demonstrate a high correlation between conventional released glycan analysis with fluorescent tagging and glycopeptide assignment derived from GraphMS. GraphMS workflow was then used to monitor the glycoform of our in-house trastuzumab biosimilar produced in fed-batch cultures. The demonstrated utility of GraphMS to semi-automate quantitation and qualitative identification of glycopeptides proves to be an easy data analysis method that can complement emerging multi-attribute monitoring (MAM) analytical toolsets in bioprocess environments.
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Affiliation(s)
- Kuin Tian Pang
- Bioprocessing Technology Institute, Agency for Science Technology and Research (ASTAR), Queenstown, Singapore
| | - Shi Jie Tay
- Bioprocessing Technology Institute, Agency for Science Technology and Research (ASTAR), Queenstown, Singapore
| | - Corrine Wan
- Bioprocessing Technology Institute, Agency for Science Technology and Research (ASTAR), Queenstown, Singapore
| | - Ian Walsh
- Bioprocessing Technology Institute, Agency for Science Technology and Research (ASTAR), Queenstown, Singapore
| | - Matthew S F Choo
- Bioprocessing Technology Institute, Agency for Science Technology and Research (ASTAR), Queenstown, Singapore
| | - Yuan Sheng Yang
- Bioprocessing Technology Institute, Agency for Science Technology and Research (ASTAR), Queenstown, Singapore
| | - Andre Choo
- Bioprocessing Technology Institute, Agency for Science Technology and Research (ASTAR), Queenstown, Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science Technology and Research (ASTAR), Queenstown, Singapore
| | - Terry Nguyen-Khuong
- Bioprocessing Technology Institute, Agency for Science Technology and Research (ASTAR), Queenstown, Singapore
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50
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Štor J, Ruckerbauer DE, Széliová D, Zanghellini J, Borth N. Towards rational glyco-engineering in CHO: from data to predictive models. Curr Opin Biotechnol 2021; 71:9-17. [PMID: 34048995 DOI: 10.1016/j.copbio.2021.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/26/2021] [Accepted: 05/07/2021] [Indexed: 12/22/2022]
Abstract
Metabolic modelling strives to develop modelling approaches that are robust and highly predictive. To achieve this, various modelling designs, including hybrid models, and parameter estimation methods that define the type and number of parameters used in the model, are adapted. Accurate input data play an important role so that the selection of experimental methods that provide input data of the required precision with low measurement errors is crucial. For the biopharmaceutically relevant protein glycosylation, the most prominent available models are kinetic models which are able to capture the dynamic nature of protein N-glycosylation. In this review we focus on how to choose the most suitable model for a specific research question, as well as on parameters and considerations to take into account before planning relevant experiments.
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Affiliation(s)
- Jerneja Štor
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - David E Ruckerbauer
- acib - Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria; Department of Analytical Chemistry, University of Vienna, A-1090 Vienna, Austria
| | - Diana Széliová
- acib - Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria; Department of Analytical Chemistry, University of Vienna, A-1090 Vienna, Austria
| | - Jürgen Zanghellini
- acib - Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria; Department of Analytical Chemistry, University of Vienna, A-1090 Vienna, Austria.
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria; acib - Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria.
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