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López-Cortés R, Muinelo-Romay L, Fernández-Briera A, Gil Martín E. High-Throughput Mass Spectrometry Analysis of N-Glycans and Protein Markers after FUT8 Knockdown in the Syngeneic SW480/SW620 Colorectal Cancer Cell Model. J Proteome Res 2024; 23:1379-1398. [PMID: 38507902 PMCID: PMC11002942 DOI: 10.1021/acs.jproteome.3c00833] [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: 12/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Disruption of the glycosylation machinery is a common feature in many types of cancer, and colorectal cancer (CRC) is no exception. Core fucosylation is mediated by the enzyme fucosyltransferase 8 (FucT-8), which catalyzes the addition of α1,6-l-fucose to the innermost GlcNAc residue of N-glycans. We and others have documented the involvement of FucT-8 and core-fucosylated proteins in CRC progression, in which we addressed core fucosylation in the syngeneic CRC model formed by SW480 and SW620 tumor cell lines from the perspective of alterations in their N-glycosylation profile and protein expression as an effect of the knockdown of the FUT8 gene that encodes FucT-8. Using label-free, semiquantitative mass spectrometry (MS) analysis, we found noticeable differences in N-glycosylation patterns in FUT8-knockdown cells, affecting core fucosylation and sialylation, the Hex/HexNAc ratio, and antennarity. Furthermore, stable isotopic labeling of amino acids in cell culture (SILAC)-based proteomic screening detected the alteration of species involved in protein folding, endoplasmic reticulum (ER) and Golgi post-translational stabilization, epithelial polarity, and cellular response to damage and therapy. This data is available via ProteomeXchange with identifier PXD050012. Overall, the results obtained merit further investigation to validate their feasibility as biomarkers of progression and malignization in CRC, as well as their potential usefulness in clinical practice.
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Affiliation(s)
- Rubén López-Cortés
- Doctoral
Program in Methods and Applications in Life Sciences, Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Laura Muinelo-Romay
- Liquid
Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela
(IDIS), CIBERONC, Travesía da Choupana, 15706 Santiago de Compostela, A Coruña
(Galicia), Spain
| | - Almudena Fernández-Briera
- Molecular
Biomarkers, Biomedical Research Centre (CINBIO), Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Emilio Gil Martín
- Nutrition
and Food Science Group, Department of Biochemistry, Genetics and Immunology,
Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
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2
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Trbojević-Akmačić I, Lageveen-Kammeijer GSM, Heijs B, Petrović T, Deriš H, Wuhrer M, Lauc G. High-Throughput Glycomic Methods. Chem Rev 2022; 122:15865-15913. [PMID: 35797639 PMCID: PMC9614987 DOI: 10.1021/acs.chemrev.1c01031] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Glycomics aims to identify the structure and function of the glycome, the complete set of oligosaccharides (glycans), produced in a given cell or organism, as well as to identify genes and other factors that govern glycosylation. This challenging endeavor requires highly robust, sensitive, and potentially automatable analytical technologies for the analysis of hundreds or thousands of glycomes in a timely manner (termed high-throughput glycomics). This review provides a historic overview as well as highlights recent developments and challenges of glycomic profiling by the most prominent high-throughput glycomic approaches, with N-glycosylation analysis as the focal point. It describes the current state-of-the-art regarding levels of characterization and most widely used technologies, selected applications of high-throughput glycomics in deciphering glycosylation process in healthy and disease states, as well as future perspectives.
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Affiliation(s)
| | | | - Bram Heijs
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Tea Petrović
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
| | - Helena Deriš
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Gordan Lauc
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
- Faculty
of Pharmacy and Biochemistry, University
of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia
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3
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Li M, Zhu W, Zheng H, Zhang J. Efficient HCD-pd-EThcD approach for N-glycan mapping of therapeutic antibodies at intact glycopeptide level. Anal Chim Acta 2022; 1189:339232. [PMID: 34815030 DOI: 10.1016/j.aca.2021.339232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 09/30/2021] [Accepted: 10/28/2021] [Indexed: 11/28/2022]
Abstract
N-glycosylation is a critical quality attribute for monoclonal antibody (mAb)-based therapeutics due to its significant impact on drug efficacy and safety. Extensive glycosylation mapping is therefore necessary for mAb drug development and quality control. We utilized a higher-energy dissociation product ions-triggered electron-transfer/higher-energy collision dissociation (HCD-pd-EThcD) approach to mapping N-glycosylation in therapeutic mAbs. Due to the improved duty cycle and targeted ability, HCD-pd-EThcD could provide extensive N-glycan identifications as well as higher quality spectra than EThcD mode. On average, ten types of N-glycan were uncovered in two different lots of trastuzumab, demonstrating a significant increment in N-glycan species compared to only four types identified by EThcD. After integrating pre-enrichment of glycopeptides, up to 16 N-glycans were recognized. Significantly, this strategy facilitated the identification of glycopeptides containing fucosylated and sialylated glycans, meanwhile enabled the recognition of different N-glycan classes (high mannose, hybrid, and complex). Further application in the glycosylation analysis of adalimumab and bevacizumab resulted in 19 and 8 N-glycans species, providing a more comprehensive insight into their glycosylation modification status. We demonstrated the benefits of an integrated strategy in characterizing various N-glycans of mAb therapeutics and offer an alternative approach for their quality control at the intact glycopeptides level.
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Affiliation(s)
- Menglin Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Wenwen Zhu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Hao Zheng
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Jinlan Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
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4
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Kinoshita M, Nakajima K, Yamamoto S, Suzuki S. High-throughput N-glycan screening method for therapeutic antibodies using a microchip-based DNA analyzer: a promising methodology for monitoring monoclonal antibody N-glycosylation. Anal Bioanal Chem 2021; 413:4727-4738. [PMID: 34080034 DOI: 10.1007/s00216-021-03434-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/11/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
N-Glycosylation of therapeutic antibodies is a critical quality attribute (CQA), and the micro-heterogeneity affects the biological and physicochemical properties of antibodies. Therefore, the profiling of N-glycans on antibodies is essential for controlling the manufacturing process and ensuring the efficacy and safety of the therapeutic antibodies. To monitor N-glycosylation in recombinant proteins, a high-throughput (HTP) methodology for glycan analysis is required to handle bulk samples in various stages of the manufacturing process. In this study, we focused on the HTP methodology for N-glycan analysis using a commercial microchip electrophoresis-based DNA analyzer and demonstrated the feasibility of the workflow consisting of sample preparation and electrophoretic separation. Even if there is a demand to analyze up to 96 samples, the present workflow can be completed in a day without expensive instruments and reagent kits for sample preparation, and it will be a promising methodology for cost-effective and facile HTP N-glycosylation analysis while optimizing the manufacturing process and development for therapeutic antibodies.
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Affiliation(s)
- Mitsuhiro Kinoshita
- Department of Pharmaceutical Sciences, Kindai University, Kowakae 3-4-1, Higashi-osaka, 577-8502, Japan.
| | - Kazuki Nakajima
- Center for Joint Research Facilities Support, Research Promotion and Support Headquarters, Fujita Health University, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Sachio Yamamoto
- Department of Pharmaceutical Sciences, Kindai University, Kowakae 3-4-1, Higashi-osaka, 577-8502, Japan
| | - Shigeo Suzuki
- Department of Pharmaceutical Sciences, Kindai University, Kowakae 3-4-1, Higashi-osaka, 577-8502, Japan
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5
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Rubén LC, Laura MR, Almudena FB, Emilio GM. Glycan array analysis of Pholiota squarrosa lectin and other fucose-oriented lectins. Glycobiology 2020; 31:459-476. [PMID: 33021632 DOI: 10.1093/glycob/cwaa093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
The α(1,6)fucose residue attached to the N-glycoprotein core is suspected to play an essential role in the progression of several types of cancer. Lectins remain the first choice for probing glycan modifications, although they may lack specificity. Thus, efforts have been made to identify new lectins with a narrower core fucose (CF) detection profile. Here, we present a comparison of the classical Aleuria aurantia lectin (AAL), Lens culinaris agglutinin (LCA) and Aspergillus oryzae lectin (AOL) with the newer Pholiota squarrosa lectin (PhoSL), which has been described as being specific for core fucosylated N-glycans. To this end, we studied the binding profiles of the four lectins using mammalian glycan arrays from the Consortium of Functional Glycomics. To validate their glycan specificity, we probed AOL, LCA and PhoSL in western-blot assays using protein extracts from eight common colorectal cancer (CRC) lines and colorectal biopsies from a small cohort of patients with CRC. The results showed that (i) LCA and PhoSL were the most specific lectins for detecting the presence of CF in a concentration-dependent manner; (ii) PhoSL exhibited the highest N-glycan sequence restriction, with preferential binding to core fucosylated paucimannosidic-type N-glycans, (iii) the recognition ability of PhoSL was highly influenced by the presence of terminal N-acetyl-lactosamine; (iv) LCA bound to paucimannosidic, bi-antennary and tri-antennary core fucosylated N-glycans and (v) AOL and AAL exhibited broader specificity towards fucosylation. Together, our results support the choice of LCA as the most appropriate lectin for CF detection, as validated in protein extracts from CRC cell lines and tissue specimens from patients with CRC.
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Affiliation(s)
- López-Cortés Rubén
- Doctoral Program in Methods and Applications in Life Sciences, Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, Vigo, Pontevedra, Galicia ES36310, Spain
| | - Muinelo-Romay Laura
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), CIBERONC, Travesía da Choupana, Santiago de Compostela, A Coruña, Galicia ES15706, Spain
| | - Fernández-Briera Almudena
- Molecular Biomarkers, Biomedical Research Centre (CINBIO), Universidade de Vigo, Campus Lagoas-Marcosende, Vigo, Pontevedra, Galicia ES36310, Spain
| | - Gil Martín Emilio
- Nutrition and Food Science Group, Department of Biochemistry, Genetics and Immunology, Faculty of Biology, Universidade de Vigo. Campus Lagoas-Marcosende, Vigo, Pontevedra, Galicia ES36310, Spain
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6
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Support Vector and Locally Weighted regressions to monitor monoclonal antibody glycosylation during CHO cell culture processes, an enhanced alternative to Partial Least Squares regression. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Kotsias M, Blanas A, van Vliet SJ, Pirro M, Spencer DIR, Kozak RP. Method comparison for N-glycan profiling: Towards the standardization of glycoanalytical technologies for cell line analysis. PLoS One 2019; 14:e0223270. [PMID: 31589631 PMCID: PMC6779296 DOI: 10.1371/journal.pone.0223270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/17/2019] [Indexed: 01/18/2023] Open
Abstract
The study of protein N-glycosylation is essential in biological and biopharmaceutical research as N-glycans have been reported to regulate a wide range of physiological and pathological processes. Monitoring glycosylation in diagnosis, prognosis, as well as biopharmaceutical development and quality control are important research areas. A number of techniques for the analysis of protein N-glycosylation are currently available. Here we examine three methodologies routinely used for the release of N-glycans, in the effort to establish and standardize glycoproteomics technologies for quantitative glycan analysis from cultured cell lines. N-glycans from human gamma immunoglobulins (IgG), plasma and a pool of four cancer cell lines were released following three approaches and the performance of each method was evaluated.
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Affiliation(s)
- Maximilianos Kotsias
- Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire, England, United Kingdom
| | - Athanasios Blanas
- Amsterdam UMC, Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Sandra J. van Vliet
- Amsterdam UMC, Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Martina Pirro
- Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Daniel I. R. Spencer
- Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire, England, United Kingdom
| | - Radoslaw P. Kozak
- Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire, England, United Kingdom
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8
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Hafkenscheid L, de Moel E, Smolik I, Tanner S, Meng X, Jansen BC, Bondt A, Wuhrer M, Huizinga TWJ, Toes REM, El-Gabalawy H, Scherer HU. N-Linked Glycans in the Variable Domain of IgG Anti-Citrullinated Protein Antibodies Predict the Development of Rheumatoid Arthritis. Arthritis Rheumatol 2019; 71:1626-1633. [PMID: 31067000 PMCID: PMC6790576 DOI: 10.1002/art.40920] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/30/2019] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Anti-citrullinated protein antibodies (ACPAs) are disease-specific biomarkers in rheumatoid arthritis (RA). More than 90% of IgG ACPAs harbor N-linked glycans in the antibody variable (V) domain. The corresponding N-glycosylation sites in ACPA V-region sequences result from somatic hypermutation, a T cell-dependent process. As ample evidence indicates that T cells drive the maturation of the ACPA response prior to arthritis onset, we undertook this study to investigate whether the presence of glycans in IgG ACPA V domains predicts the transition from predisease autoimmunity to overt RA. METHODS We analyzed 2 independent sets of serum samples obtained from 126 ACPA-positive first-degree relatives (FDRs) of RA patients. Both sets originated from an Indigenous North American population and comprised cross-sectional and longitudinal samples of individuals who did or did not develop inflammatory arthritis. Serum IgG ACPAs were affinity-purified and subjected to ultra high-performance liquid chromatography-based glycan analysis. RESULTS In both data sets, FDR-derived IgG ACPA displayed markedly lower levels of V domain glycans (<50%) compared to IgG ACPA from RA patients. Notably, FDRs who later developed RA showed extensive V-domain glycosylation before the onset of arthritis. Moreover, IgG ACPA V-domain glycosylation was strongly associated with future development of RA (hazard ratio 6.07 [95% confidence interval 1.46-25.2]; P = 0.013). CONCLUSION Extensive glycosylation of the IgG ACPA V domain is present in a subset of predisposed FDRs of Indigenous North American RA patients. The presence of this feature substantially increases the risk of RA development. Based on these findings, we propose that glycosylation of the IgG ACPA V domain represents a predictive marker for RA development in ACPA-positive individuals and may serve to better target prevention measures.
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Affiliation(s)
| | - Emma de Moel
- Leiden University Medical Center, Leiden, The Netherlands
| | - Irene Smolik
- University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Xiaobo Meng
- University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Albert Bondt
- Leiden University Medical Center, Leiden, The Netherlands
| | - Manfred Wuhrer
- Leiden University Medical Center, Leiden, The Netherlands
| | | | - Rene E M Toes
- Leiden University Medical Center, Leiden, The Netherlands
| | | | - Hans U Scherer
- Leiden University Medical Center, Leiden, The Netherlands
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9
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Valk-Weeber RL, Dijkhuizen L, van Leeuwen SS. Large-scale quantitative isolation of pure protein N-linked glycans. Carbohydr Res 2019; 479:13-22. [PMID: 31100702 DOI: 10.1016/j.carres.2019.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023]
Abstract
Glycoproteins are biologically active proteins of which the attached glycans contribute to their biological functionality. Limited data is available on the functional properties of these N-glycans in isolation, without the protein core. Glycan release, typically performed with the PNGase F enzyme, is achieved on denatured proteins in the presence of detergents which are notoriously difficult to be completely removed. In this work we compared two methods aiming at recovering N-glycans in a high yield and at high purity from a PNGase F glycoprotein digest of bovine lactoferrin. Detergents were removed from the digest by two separate approaches. In the first approach, protein and glycans were precipitated with acetone and the detergent containing supernatant was discarded. In the second approach, detergent was removed by adsorption onto a polystyrene resin. Following detergent removal, the glycans were further purified by a sequence of solid phase extraction (SPE) steps. Both approaches for detergent removal yielded a final glycan purity above 85%. Recovery of the glycans from lactoferrin was, however, much lower when utilizing acetone precipitation versus the polystyrene resin; 52% versus 85% respectively. A more detailed analysis of the acetone precipitation step revealed a loss of shorter oligomannose structures specifically. A loss of glycans of lesser complexity (oligomannose and biantennary structures) was also observed for other glycoproteins (RNase B, porcine thyroglobulin, human lactoferrin). These results indicate that acetone precipitation, a commonly used step for small-scale glycan purification, is not suitable for all target glycoproteins. The polystyrene resin detergent removal step conserved the full N-glycan profile and could be applied to all mammalian glycoproteins tested. Using this optimized protocol, large-scale quantitative isolation of N-glycan structures was achieved with sufficient purity for functional studies.
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Affiliation(s)
- Rivca L Valk-Weeber
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
| | - Sander S van Leeuwen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
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10
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. 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. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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11
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Measurement of impurities to support process development and manufacture of biopharmaceuticals. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.10.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Wang T, Hoi KM, Stöckmann H, Wan C, Sim LC, Shi Jie Tay NHBK, Poo CH, Woen S, Yang Y, Zhang P, Rudd PM. LC/MS-based Intact IgG and Released Glycan Analysis for Bioprocessing Applications. Biotechnol J 2018; 13:e1700185. [PMID: 29341427 DOI: 10.1002/biot.201700185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 01/06/2018] [Indexed: 01/27/2023]
Abstract
Robust plate based antibody glycan analysis platforms are urgently needed for biopharmaceutical development and manufacturing as well as for clinical biomarker research. A 96-well plate based workflow has been developed to analyze both intact IgG antibodies and released N-glycans using an Orbitrap Fusion Mass Spectrometer and an LC/MS method on the Waters UNIFI platform. Here, such a workflow including protein A purification, PNGaseF digestion, 2-AB labeling, and SPE clean-up is described. The measured IgG glycan profile is consistent with that obtained from non-plate based method and commercial kit and has the advantage of less hands-on time. Also the application of the workflow in cell culture monitoring and clonal selection work is demonstrated. Apart from checking the major glycan structure changes among clones, post translational modifications (PTMs) such as C-terminal lysine residue clipping and N-terminal pyroglutamic acid formation can also be deduced from the workflow.
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Affiliation(s)
- Tianhua Wang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Kong Meng Hoi
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Henning Stöckmann
- NIBRT GlycoScience Group, NIBRT - The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin 4, Ireland
| | - Corrine Wan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Lyn Chiin Sim
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | | | - Ce Huang Poo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Susanto Woen
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Yuangsheng Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Peiqing Zhang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore
| | - Pauline M Rudd
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore.,NIBRT GlycoScience Group, NIBRT - The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin 4, Ireland
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13
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Effluent and serum protein N-glycosylation is associated with inflammation and peritoneal membrane transport characteristics in peritoneal dialysis patients. Sci Rep 2018; 8:979. [PMID: 29343697 PMCID: PMC5772620 DOI: 10.1038/s41598-018-19147-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 12/22/2017] [Indexed: 12/18/2022] Open
Abstract
Mass spectrometric glycomics was used as an innovative approach to identify biomarkers in serum and dialysate samples from peritoneal dialysis (PD) patients. PD is a life-saving treatment worldwide applied in more than 100,000 patients suffering from chronic kidney disease. PD treatment uses the peritoneum as a natural membrane to exchange waste products from blood to a glucose-based solution. Daily exposure of the peritoneal membrane to these solutions may cause complications such as peritonitis, fibrosis and inflammation which, in the long term, lead to the failure of the treatment. It has been shown in the last years that protein N-glycosylation is related to inflammatory and fibrotic processes. Here, by using a recently developed MALDI-TOF-MS method with linkage-specific sialic acid derivatisation, we showed that alpha2,6-sialylation, especially in triantennary N-glycans from peritoneal effluents, is associated with critical clinical outcomes in a prospective cohort of 94 PD patients. Moreover, we found an association between the levels of presumably immunoglobulin-G-related glycans as well as galactosylation of diantennary glycans with PD-related complications such as peritonitis and loss of peritoneal mesothelial cell mass. The observed glycomic changes point to changes in protein abundance and protein-specific glycosylation, representing candidate functional biomarkers of PD and associated complications.
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14
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O'Flaherty R, Trbojević-Akmačić I, Greville G, Rudd PM, Lauc G. The sweet spot for biologics: recent advances in characterization of biotherapeutic glycoproteins. Expert Rev Proteomics 2017; 15:13-29. [PMID: 29130774 DOI: 10.1080/14789450.2018.1404907] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Glycosylation is recognized as a Critical Quality Attribute for therapeutic glycoproteins such as monoclonal antibodies, fusion proteins and therapeutic replacement enzymes. Hence, efficient and quantitative glycan analysis techniques have been increasingly important for their discovery, development and quality control. The aim of this review is to highlight relevant and recent advances in analytical technologies for characterization of biotherapeutic glycoproteins. Areas covered: The review gives an overview of the glycosylation trends of biotherapeutics approved in 2016 and 2017 by FDA. It describes current and novel analytical technologies for characterization of therapeutic glycoproteins and is explored in the context of released glycan, glycopeptide or intact glycoprotein analysis. Ultra performance liquid chromatography, mass spectrometry and capillary electrophoresis technologies are explored in this context. Expert commentary: There is a need for the biopharmaceutical industry to incorporate novel state of the art analytical technologies into existing and new therapeutic glycoprotein workflows for safer and more efficient biotherapeutics and for the improvement of future biotherapeutic design. Additionally, at present, there is no 'gold-standard' approach to address all the regulatory requirements and as such this will involve the use of orthogonal glycoanalytical technologies with a view to gain diagnostic information about the therapeutic glycoprotein.
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Affiliation(s)
- Róisín O'Flaherty
- a NIBRT GlycoScience Group , National Institute for Bioprocessing, Research and Training , Blackrock, Co. Dublin , Ireland
| | | | - Gordon Greville
- a NIBRT GlycoScience Group , National Institute for Bioprocessing, Research and Training , Blackrock, Co. Dublin , Ireland
| | - Pauline M Rudd
- a NIBRT GlycoScience Group , National Institute for Bioprocessing, Research and Training , Blackrock, Co. Dublin , Ireland
| | - Gordan Lauc
- b Genos Glycoscience Research Laboratory , 10000 , Zagreb , Croatia.,c Faculty of Pharmacy and Biochemistry , University of Zagreb , Zagreb , Croatia
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15
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Yang S, Clark D, Liu Y, Li S, Zhang H. High-throughput analysis of N-glycans using AutoTip via glycoprotein immobilization. Sci Rep 2017; 7:10216. [PMID: 28860471 PMCID: PMC5578957 DOI: 10.1038/s41598-017-10487-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/11/2017] [Indexed: 12/15/2022] Open
Abstract
Analysis of a large number of samples requires an efficient, rapid and reproducible method. Automation is an ideal approach for high-throughput sample preparation. Multi-plexing sample preparation via a 96-well plate format becomes popular in recent years; however, those methods lack specificity and require several cleanup steps via chromatography purification. To overcome these drawbacks, a chemoenzymatic method has been developed utilizing protein conjugation on solid-phase. Previously, sample preparation was successfully performed in a snap-cap spin-column (SCSC) format. However, sample preparation using SCSC is time-consuming and lacks reproducibility. In this work, we integrated the chemoenzymatic technique in a pipette tip (AutoTip) that was operated by an automated liquid handler. We established a multi-step protocol involving protein immobilization, sialic acid modification, and N-glycan release. We first optimized our automated protocol using bovine fetuin as a standard glycoprotein, and then assessed the reproducibility of the AutoTip using isobaric tags for relative N-linked glycan quantification. We then applied this methodology to profile N-glycans from 58 prostate cancer patient urine samples, revealing increased sialyation on urinary N-glycans derived from prostate cancer patients. Our results indicated AutoTip has applications for high-throughput sample preparation for studying the N-linked glycans.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA.
| | - David Clark
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Yang Liu
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Shuwei Li
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, USA
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16
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Holst S, van Pelt GW, Mesker WE, Tollenaar RA, Belo AI, van Die I, Rombouts Y, Wuhrer M. High-Throughput and High-Sensitivity Mass Spectrometry-Based N-Glycomics of Mammalian Cells. Methods Mol Biol 2017; 1503:185-196. [PMID: 27743367 DOI: 10.1007/978-1-4939-6493-2_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The current protocols for glycomic analysis of cells often require a large quantity of material (5-20 million cells). In order to analyze the N-glycosylation from small amounts of cells (≤1 million) as obtained from, for example, primary cell lines or cell sorting, and in a higher throughput approach, we set up a robust 96-well format PVDF-membrane based N-glycan release protocol followed by linkage-specific sialic acid stabilization, cleanup, and MALDI-TOF-MS analysis. We further evaluated the influence of PNGase F incubation time on the N-glycan profile.
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Affiliation(s)
- Stephanie Holst
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Postzone S3, Postbus 9600, 2300, RC, Leiden, The Netherlands.
| | - Gabi W van Pelt
- Department of Surgery, Leiden University Medical Center, Postbus 9600, RC, 2300, Leiden, The Netherlands
| | - Wilma E Mesker
- Department of Surgery, Leiden University Medical Center, Postbus 9600, RC, 2300, Leiden, The Netherlands
| | - Rob A Tollenaar
- Department of Surgery, Leiden University Medical Center, Postbus 9600, RC, 2300, Leiden, The Netherlands
| | - Ana I Belo
- Department of Molecular Cell Biology and Immunology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Irma van Die
- Department of Molecular Cell Biology and Immunology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Yoann Rombouts
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Postzone S3, Postbus 9600, 2300, RC, Leiden, The Netherlands
- University Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59 000, Lille, France
| | - Manfred Wuhrer
- Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, Amsterdam, 1081, HV, The Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333, ZA, The Netherlands
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17
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Trbojević-Akmačić I, Ugrina I, Lauc G. Comparative Analysis and Validation of Different Steps in Glycomics Studies. Methods Enzymol 2017; 586:37-55. [DOI: 10.1016/bs.mie.2016.09.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Hajba L, Csanky E, Guttman A. Liquid phase separation methods for N-glycosylation analysis of glycoproteins of biomedical and biopharmaceutical interest. A critical review. Anal Chim Acta 2016; 943:8-16. [PMID: 27769380 DOI: 10.1016/j.aca.2016.08.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 12/25/2022]
Abstract
Comprehensive carbohydrate analysis of glycoproteins from human biological samples and biotherapeutics are important from diagnostic and therapeutic points of view. This review summarizes the current state-of-the-art liquid phase separation techniques used in N-glycosylation analysis. The different liquid chromatographic techniques and capillary electrophoresis methods are critically discussed in detail. Miniaturization of these methods is also important to increase throughput and decrease analysis time. The sample preparation and labeling methods for asparagine linked oligosaccharides are also addressed.
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Affiliation(s)
- Laszlo Hajba
- MTA-PE Translational Glycomics Research Group, University of Pannonia, Veszprem, Hungary
| | | | - Andras Guttman
- MTA-PE Translational Glycomics Research Group, University of Pannonia, Veszprem, Hungary; Horvath Csaba Laboratory of Bioseparation Sciences, University of Debrecen, Debrecen, Hungary.
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19
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Trbojević-Akmačić I, Vilaj M, Lauc G. High-throughput analysis of immunoglobulin G glycosylation. Expert Rev Proteomics 2016; 13:523-34. [DOI: 10.1080/14789450.2016.1174584] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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20
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Aich U, Lakbub J, Liu A. State-of-the-art technologies for rapid and high-throughput sample preparation and analysis ofN-glycans from antibodies. Electrophoresis 2016; 37:1468-88. [DOI: 10.1002/elps.201500551] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/15/2016] [Accepted: 01/17/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Udayanath Aich
- Biopharmaceutical Analytical Sciences; Biopharmaceutical Development, GlaxoSmithKline; King of Prussia PA USA
| | - Jude Lakbub
- Biopharmaceutical Analytical Sciences; Biopharmaceutical Development, GlaxoSmithKline; King of Prussia PA USA
| | - Aston Liu
- Biopharmaceutical Analytical Sciences; Biopharmaceutical Development, GlaxoSmithKline; King of Prussia PA USA
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21
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Holst S, Deuss AJM, van Pelt GW, van Vliet SJ, Garcia-Vallejo JJ, Koeleman CAM, Deelder AM, Mesker WE, Tollenaar RA, Rombouts Y, Wuhrer M. N-glycosylation Profiling of Colorectal Cancer Cell Lines Reveals Association of Fucosylation with Differentiation and Caudal Type Homebox 1 (CDX1)/Villin mRNA Expression. Mol Cell Proteomics 2015; 15:124-40. [PMID: 26537799 PMCID: PMC4762531 DOI: 10.1074/mcp.m115.051235] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 01/05/2023] Open
Abstract
Various cancers such as colorectal cancer (CRC) are associated with alterations in protein glycosylation. CRC cell lines are frequently used to study these (glyco)biological changes and their mechanisms. However, differences between CRC cell lines with regard to their glycosylation have hitherto been largely neglected. Here, we comprehensively characterized the N-glycan profiles of 25 different CRC cell lines, derived from primary tumors and metastatic sites, in order to investigate their potential as glycobiological tumor model systems and to reveal glycans associated with cell line phenotypes. We applied an optimized, high-throughput membrane-based enzymatic glycan release for small sample amounts. Released glycans were derivatized to stabilize and differentiate between α2,3- and α2,6-linked N-acetylneuraminic acids, followed by N-glycosylation analysis by MALDI-TOF(/TOF)-MS. Our results showed pronounced differences between the N-glycosylation patterns of CRC cell lines. CRC cell line profiles differed from tissue-derived N-glycan profiles with regard to their high-mannose N-glycan content but showed a large overlap for complex type N-glycans, supporting their use as a glycobiological cancer model system. Importantly, we could show that the high-mannose N-glycans did not only occur as intracellular precursors but were also present at the cell surface. The obtained CRC cell line N-glycan features were not clearly correlated with mRNA expression levels of glycosyltransferases, demonstrating the usefulness of performing the structural analysis of glycans. Finally, correlation of CRC cell line glycosylation features with cancer cell markers and phenotypes revealed an association between highly fucosylated glycans and CDX1 and/or villin mRNA expression that both correlate with cell differentiation. Together, our findings provide new insights into CRC-associated glycan changes and setting the basis for more in-depth experiments on glycan function and regulation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yoann Rombouts
- From the ‡Center for Proteomics and Metabolomics, ¶Department of RheumatologyLeiden University Medical Center, Leiden, The Netherlands; ‡‡Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F 59 000 Lille, France
| | - Manfred Wuhrer
- From the ‡Center for Proteomics and Metabolomics, ‖Department of Molecular Cell Biology and Immunology and **Division of BioAnalytical Chemistry, VU University Medical Center, Amsterdam, The Netherlands;
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22
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Vasiljevic S, Beale EV, Bonomelli C, Easthope IS, Pritchard LK, Seabright GE, Caputo AT, Scanlan CN, Dalziel M, Crispin M. Redirecting adenoviruses to tumour cells using therapeutic antibodies: Generation of a versatile human bispecific adaptor. Mol Immunol 2015; 68:234-43. [PMID: 26391350 DOI: 10.1016/j.molimm.2015.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
Abstract
Effective use of adenovirus-5 (Ad5) in cancer therapy is heavily dependent on the degree to which the virus's natural tropism can be subverted to one that favours tumour cells. This is normally achieved through either engineering of the viral fiber knob or the use of bispecific adaptors that display both adenovirus and tumour antigen receptors. One of the main limitations of these strategies is the need to tailor each engineering event to any given tumour antigen. Here, we explore bispecific adaptors that can utilise established anti-cancer therapeutic antibodies. Conjugates containing bacterially derived antibody binding motifs are efficient at retargeting virus to antibody targets. Here, we develop a humanized strategy whereby we synthesise a re-targeting adaptor based on a chimeric Ad5 ligand/antibody receptor construct. This adaptor acts as a molecular bridge analogous to therapeutic antibody mediated cross-linking of cytotoxic effector and tumour cells during immunotherapy. As a proof or principle, we demonstrate how this adaptor allows efficient viral recognition and entry into carcinoma cells through the therapeutic monoclonal antibodies Herceptin/trastuzumab and bavituximab. We show that targeting can be augmented by use of contemporary antibody enhancement strategies such as the selective elimination of competing serum IgG using "receptor refocusing" enzymes and we envisage that further improvements are achievable by enhancing the affinities between the adaptor and its ligands. Humanized bispecific adaptors offer the promise of a versatile retargeting technology that can exploit both clinically approved adenovirus and therapeutic antibodies.
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Affiliation(s)
- Snezana Vasiljevic
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Emma V Beale
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Camille Bonomelli
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Iona S Easthope
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Laura K Pritchard
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Gemma E Seabright
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Alessandro T Caputo
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Christopher N Scanlan
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Martin Dalziel
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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23
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Bladergroen MR, Reiding KR, Hipgrave Ederveen AL, Vreeker GCM, Clerc F, Holst S, Bondt A, Wuhrer M, van der Burgt YEM. Automation of High-Throughput Mass Spectrometry-Based Plasma N-Glycome Analysis with Linkage-Specific Sialic Acid Esterification. J Proteome Res 2015; 14:4080-6. [PMID: 26179816 DOI: 10.1021/acs.jproteome.5b00538] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycosylation is a post-translational modification of key importance with heterogeneous structural characteristics. Previously, we have developed a robust, high-throughput MALDI-TOF-MS method for the comprehensive profiling of human plasma N-glycans. In this approach, sialic acid residues are derivatized with linkage-specificity, namely the ethylation of α2,6-linked sialic acid residues with parallel lactone formation of α2,3-linked sialic acids. In the current study, this procedure was used as a starting point for the automation of all steps on a liquid-handling robot system. This resulted in a time-efficient and fully standardized procedure with throughput times of 2.5 h for a first set of 96 samples and approximately 1 h extra for each additional sample plate. The mass analysis of the thus-obtained glycans was highly reproducible in terms of relative quantification, with improved interday repeatability as compared to that of manual processing.
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Affiliation(s)
- Marco R Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Agnes L Hipgrave Ederveen
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Gerda C M Vreeker
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Florent Clerc
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Stephanie Holst
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Albert Bondt
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC Leiden, The Netherlands.,Department of Rheumatology, Erasmus University Medical Center , 3000 CA Rotterdam, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC Leiden, The Netherlands.,Division of BioAnalytical Chemistry, VU University Amsterdam , 1081 HV Amsterdam, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC Leiden, The Netherlands
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24
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Trbojević Akmačić I, Ugrina I, Štambuk J, Gudelj I, Vučković F, Lauc G, Pučić-Baković M. High-throughput glycomics: Optimization of sample preparation. BIOCHEMISTRY (MOSCOW) 2015; 80:934-42. [DOI: 10.1134/s0006297915070123] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Abstract
Effective characterization of protein-based therapeutic candidates such as monoclonal antibodies (mAbs) is important to facilitate their successful progression from early discovery and development stages to marketing approval. One challenge relevant to biopharmaceutical development is, understanding how the stability of a protein is affected by the presence of an attached oligosaccharide, termed a glycan. To explore the utility of molecular dynamics simulations as a complementary technique to currently available experimental methods, the Fc fragment was employed as a model system to improve our understanding of protein stabilization by glycan attachment. Long molecular dynamics simulations were performed on three Fc glycoform variants modeled using the crystal structure of a human IgG1 mAb. Two of these three glycoform variants have their glycan carbohydrates partially or completely removed. Structural differences among the glycoform variants during simulations suggest that glycan truncation and/or removal can cause quaternary structural deformation of the Fc as a result of the loss or disruption of a significant number of inter-glycan contacts that are not formed in the human IgG1 crystal structure, but do form during simulations described here. Glycan truncation/removal can also increase the tertiary structural deformation of CH2 domains, demonstrating the importance of specific carbohydrates toward stabilizing individual CH2 domains. At elevated temperatures, glycan truncation can also differentially affect structural deformation in locations (Helix-1 and Helix-2) that are far from the oligosaccharide attachment point. Deformation of these helices, which form part of the FcRn, could affect binding if these regions are unable to refold after temperature normalization. During elevated temperature simulations of the deglycosylated variant, CH2 domains collapsed onto CH3 domains. Observations from these glycan truncation/removal simulations have improved our understanding on how glycan composition can affect mAb stability.
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Affiliation(s)
- Patrick M Buck
- Pharmaceutical Research and Development; Biotherapeutics Pharmaceutical Sciences; Pfizer Inc.; Chesterfield, MO USA
| | - Sandeep Kumar
- Pharmaceutical Research and Development; Biotherapeutics Pharmaceutical Sciences; Pfizer Inc.; Chesterfield, MO USA
| | - Satish K Singh
- Pharmaceutical Research and Development; Biotherapeutics Pharmaceutical Sciences; Pfizer Inc.; Chesterfield, MO USA
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26
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High-Throughput Analysis and Automation for Glycomics Studies. Chromatographia 2014; 78:321-333. [PMID: 25814696 PMCID: PMC4363487 DOI: 10.1007/s10337-014-2803-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/17/2014] [Accepted: 10/17/2014] [Indexed: 11/12/2022]
Abstract
This review covers advances in analytical technologies for high-throughput (HTP) glycomics. Our focus is on structural studies of glycoprotein glycosylation to support biopharmaceutical realization and the discovery of glycan biomarkers for human disease. For biopharmaceuticals, there is increasing use of glycomics in Quality by Design studies to help optimize glycan profiles of drugs with a view to improving their clinical performance. Glycomics is also used in comparability studies to ensure consistency of glycosylation both throughout product development and between biosimilars and innovator drugs. In clinical studies there is as well an expanding interest in the use of glycomics—for example in Genome Wide Association Studies—to follow changes in glycosylation patterns of biological tissues and fluids with the progress of certain diseases. These include cancers, neurodegenerative disorders and inflammatory conditions. Despite rising activity in this field, there are significant challenges in performing large scale glycomics studies. The requirement is accurate identification and quantitation of individual glycan structures. However, glycoconjugate samples are often very complex and heterogeneous and contain many diverse branched glycan structures. In this article we cover HTP sample preparation and derivatization methods, sample purification, robotization, optimized glycan profiling by UHPLC, MS and multiplexed CE, as well as hyphenated techniques and automated data analysis tools. Throughout, we summarize the advantages and challenges with each of these technologies. The issues considered include reliability of the methods for glycan identification and quantitation, sample throughput, labor intensity, and affordability for large sample numbers.
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27
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Reusch D, Haberger M, Kailich T, Heidenreich AK, Kampe M, Bulau P, Wuhrer M. High-throughput glycosylation analysis of therapeutic immunoglobulin G by capillary gel electrophoresis using a DNA analyzer. MAbs 2014; 6:185-96. [PMID: 24135630 DOI: 10.4161/mabs.26712] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Fc glycosylation of therapeutic antibodies is crucial for their effector functions and their behavior in pharmacokinetics and pharmacodynamics. To monitor the Fc glycosylation in bioprocess development and characterization,high-throughput techniques for glycosylation analysis are needed. Here, we describe the development of a largely automated high-throughput glycosylation profiling method with multiplexing capillary-gel-electrophoresis (CGE) with laser induced fluorescence (LIF) detection using a DNA analyzer. After PNGaseF digestion, the released glycans were labeled with 9-aminopyrene-1,3,6-trisulfonic acid (APTS) in 96-well plates, which was followed by the simultaneous analysis of up to 48 samples. The peak assignment was conducted by HILIC-UPLC-MS/MS of the APTS-labeled glycans combined with peak fractionation and subsequent CGE-LIF analysis of the MS-characterized fractions. Quantitative data evaluation of the various IgG glycans was performed automatically using an in-house developed software solution. The excellent method accuracy and repeatability of the test system was verified by comparison with two UPLC-based methods for glycan analysis. Finally, the practical value of the developed method was demonstrated by analyzing the antibody glycosylation profiles from fermentation broths after small scale protein A purification.
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28
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Pais DAM, Carrondo MJT, Alves PM, Teixeira AP. Towards real-time monitoring of therapeutic protein quality in mammalian cell processes. Curr Opin Biotechnol 2014; 30:161-7. [PMID: 25035940 DOI: 10.1016/j.copbio.2014.06.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/22/2014] [Accepted: 06/26/2014] [Indexed: 12/25/2022]
Abstract
Protein biopharmaceuticals are mainly produced in mammalian cells which can perform human-like post-translational modifications crucial to protein function. Subject to high variability, these critical quality attributes should be monitored and controlled during the manufacturing process. However, the large time requirements for analysis have been a bottleneck. Recent advances towards automated and high-throughput techniques, combined with multivariate data analysis, are increasingly providing relevant process knowledge in near real-time. New or re-designed analytical tools suited for monitoring product quality are starting to fit in this landscape. Moreover, omics technologies are expanding our understanding of how intracellular mechanisms and the extracellular milieu influence protein quality and quantity, reshaping the adoption of Process Analytical Technology (PAT) and Quality by Design (QbD) in the biopharmaceutical industry.
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Affiliation(s)
- Daniel A M Pais
- IBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Manuel J T Carrondo
- IBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Paula M Alves
- IBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana P Teixeira
- IBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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29
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Higel F, Seidl A, Demelbauer U, Sörgel F, Frieß W. Small scale affinity purification and high sensitivity reversed phase nanoLC-MS N-glycan characterization of mAbs and fusion proteins. MAbs 2014; 6:894-903. [PMID: 24848368 PMCID: PMC4171024 DOI: 10.4161/mabs.29263] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
N-glycosylation is a complex post-translational modification with potential effects on the efficacy and safety of therapeutic proteins and known influence on the effector function of biopharmaceutical monoclonal antibodies (mAbs). Comprehensive characterization of N-glycosylation is therefore important in biopharmaceutical development. In early development, e.g. during pool or clone selection, however, only minute protein amounts of multiple samples are available for analytics. High sensitivity and high throughput methods are thus needed. An approach based on 96-well plate sample preparation and nanoLC-MS of 2- anthranilic acid or 2-aminobenzoic acid (AA) labeled N-glycans for the characterization of biopharmaceuticals in early development is reported here. With this approach, 192 samples can be processed simultaneously from complex matrices (e.g., cell culture supernatant) to purified 2-AA glycans, which are then analyzed by reversed phase nanoLC-MS. Attomolar sensitivity has been achieved by use of nanoelectrospray ionization, resulting in detailed glycan maps of mAbs and fusion proteins that are exemplarily shown in this work. Reproducibility, robustness and linearity of the approach are demonstrated, making use in a routine manner during pool or clone selection possible. Other potential fields of application, such as glycan biomarker discovery from serum samples, are also presented.
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Affiliation(s)
- Fabian Higel
- Sandoz Biopharmaceuticals; HEXAL AG; Oberhaching, Germany
| | - Andreas Seidl
- Sandoz Biopharmaceuticals; HEXAL AG; Oberhaching, Germany
| | - Uwe Demelbauer
- Sandoz Biopharmaceuticals; HEXAL AG; Oberhaching, Germany
| | - Fritz Sörgel
- IBMP; Institute for Biomedical and Pharmaceutical Research; Nuernberg-Heroldsberg, Germany; Institute of Pharmacology; Faculty of Medicine; University Duisburg-Essen; Essen, Germany
| | - Wolfgang Frieß
- Department of Pharmacy; Pharmaceutical Technology and Biopharmaceutics; Ludwig Maximilians-Universitaet Muenchen; Munich, Germany
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Gong B, Burnina I, Stadheim TA, Li H. Glycosylation characterization of recombinant human erythropoietin produced in glycoengineered Pichia pastoris by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1308-1317. [PMID: 24338886 DOI: 10.1002/jms.3291] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/30/2013] [Accepted: 10/01/2013] [Indexed: 06/03/2023]
Abstract
Glycosylation plays a critical role in the in vivo efficacy of both endogenous and recombinant erythropoietin (EPO). Using mass spectrometry, we characterized the N-/O-linked glycosylation of recombinant human EPO (rhEPO) produced in glycoengineered Pichia pastoris and compared with the glycosylation of Chinese hamster ovary (CHO) cell-derived rhEPO. While the three predicted N-linked glycosylation sites (Asn24, Asn38 and Asn83) showed complete site occupancy, Pichia- and CHO-derived rhEPO showed distinct differences in the glycan structures with the former containing sialylated bi-antennary glycoforms and the latter containing a mixture of sialylated bi-, tri- and tetra-antennary structures. Additionally, the N-linked glycans from Pichia-produced rhEPO were similar across all three sites. A low level of O-linked mannosylation was detected on Pichia-produced rhEPO at position Ser126, which is also the O-linked glycosylation site for endogenous human EPO and CHO-derived rhEPO. In summary, the mass spectrometric analyses revealed that rhEPO derived from glycoengineered Pichia has a highly uniform bi-antennary N-linked glycan composition and preserves the orthogonal O-linked glycosylation site present on endogenous human EPO and CHO-derived rhEPO.
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Affiliation(s)
- Bing Gong
- GlycoFi, Biologics Discovery, Merck & Co., Inc., 16 Cavendish Court, Lebanon, NH, 03766, USA
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