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Li M, Zuo J, Yang K, Wang P, Zhou S. Proteomics mining of cancer hallmarks on a single-cell resolution. Mass Spectrom Rev 2023. [PMID: 37051664 DOI: 10.1002/mas.21842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 11/25/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated proteome is an essential contributor in carcinogenesis. Protein fluctuations fuel the progression of malignant transformation, such as uncontrolled proliferation, metastasis, and chemo/radiotherapy resistance, which severely impair therapeutic effectiveness and cause disease recurrence and eventually mortality among cancer patients. Cellular heterogeneity is widely observed in cancer and numerous cell subtypes have been characterized that greatly influence cancer progression. Population-averaged research may not fully reveal the heterogeneity, leading to inaccurate conclusions. Thus, deep mining of the multiplex proteome at the single-cell resolution will provide new insights into cancer biology, to develop prognostic biomarkers and treatments. Considering the recent advances in single-cell proteomics, herein we review several novel technologies with particular focus on single-cell mass spectrometry analysis, and summarize their advantages and practical applications in the diagnosis and treatment for cancer. Technological development in single-cell proteomics will bring a paradigm shift in cancer detection, intervention, and therapy.
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Affiliation(s)
- Maomao Li
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Jing Zuo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ping Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
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2
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. Mass Spectrom Rev 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth 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 2020. 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. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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3
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Torok R, Auer F, Farsang R, Jona E, Jarvas G, Guttman A. The Effect of Sample Glucose Content on PNGase F-Mediated N-Glycan Release Analyzed by Capillary Electrophoresis. Molecules 2022; 27. [PMID: 36500281 DOI: 10.3390/molecules27238192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
Protein therapeutics have recently gained high importance in general health care along with applied clinical research. Therefore, it is important to understand the structure-function relationship of these new generation drugs. Asparagine-bound carbohydrates represent an important critical quality attribute of therapeutic glycoproteins, reportedly impacting the efficacy, immunogenicity, clearance rate, stability, solubility, pharmacokinetics and mode of action of the product. In most instances, these linked N-glycans are analyzed in their unconjugated form after endoglycosidase-mediated release, e.g., PNGase F-mediated liberation. In this paper, first, N-glycan release kinetics were evaluated using our previously reported in-house produced 6His-PNGase F enzyme. The resulting deglycosylation products were quantified by sodium dodecyl sulfate capillary gel electrophoresis to determine the optimal digestion time. Next, the effect of sample glucose content was investigated as a potential endoglycosidase activity modifier. A comparative Michaelis-Menten kinetics study was performed between the 6His-PNGase F and a frequently employed commercial PNGase F product with and without the presence of glucose in the digestion reaction mixture. It was found that 1 mg/mL glucose in the sample activated the 6His-PNGase F enzyme, while did not affect the release efficiency of the commercial PNGase F. Capillary isoelectric focusing revealed subtle charge heterogeneity differences between the two endoglycosidases, manifested by the lack of extra acidic charge variants in the cIEF trace of the 6His-PNGase F enzyme, which might have possibly influenced the glucose-mediated enzyme activity differences.
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Casto-Boggess LD, Holland LA, Lawer-Yolar PA, Lucas JA, Guerrette JR. Microscale Quantification of the Inhibition of Neuraminidase Using Capillary Nanogel Electrophoresis. Anal Chem 2022; 94:16151-16159. [PMID: 36343965 PMCID: PMC9686991 DOI: 10.1021/acs.analchem.2c03584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neuraminidase inhibitors modulate infections that involve sialic acids, making quantitative analyses of this inhibitory effect important for selecting and designing potential therapeutics. An automated nanogel capillary electrophoresis system is developed that integrates a 5 nL enzyme inhibition reaction in line with a 5 min separation-based assay of the enzymatic product to quantify inhibition as the half maximal inhibitory concentration (IC50) and inhibitor constant (Ki). A neuraminidase enzyme from Clostridium perfringens is non-covalently immobilized in a thermally tunable nanogel positioned in the thermally controlled region of the capillary by increasing the capillary temperature to 37 °C. Aqueous inhibitor solutions are loaded into the capillary during the nanogel patterning step to surround the enzyme zone. The capillary electrophoresis separation provides a means to distinguish the de-sialylated product, enabling the use of sialyllactose which contains the trisaccharide motif observed on serine/threonine-linked (O-linked) glycans. A universal nanogel patterning scheme is developed that does not require pre-mixing of enzymes with inhibitors when an automated capillary electrophoresis instrument is used, thus reducing the consumption of enzymes and enabling adaption of the method to different inhibitors. The universal approach is successfully applied to two classical neuraminidase inhibitors with different electrophoretic mobilities. The IC50 and Ki values obtained for N-acetyl-2,3-dehydro-2-deoxyneuraminic acid (DANA) are 13 ± 3 and 5.0 ± 0.9 μM, respectively, and 28 ± 3 and 11 ± 1 μM, respectively, for Siastatin B. These values agree with literature reports and reflect the weaker inhibition anticipated for Siastatin B in comparison to DANA.
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Affiliation(s)
- Laura D Casto-Boggess
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
| | - Paul A Lawer-Yolar
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
| | - John A Lucas
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
| | - Jessica R Guerrette
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
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Bhimwal R, Rustandi RR, Payne A, Dawod M. Recent advances in capillary gel electrophoresis for the analysis of proteins. J Chromatogr A 2022; 1682:463453. [DOI: 10.1016/j.chroma.2022.463453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022]
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Elshamy YS, Strein TG, Holland LA, Li C, DeBastiani A, Valentine SJ, Li P, Lucas JA, Shaffer TA. Nanoflow Sheath Voltage-Free Interfacing of Capillary Electrophoresis and Mass Spectrometry for the Detection of Small Molecules. Anal Chem 2022; 94:11329-11336. [PMID: 35913997 PMCID: PMC9387528 DOI: 10.1021/acs.analchem.2c02074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coupling capillary electrophoresis (CE) to mass spectrometry (MS) is a powerful strategy to leverage a high separation efficiency with structural identification. Traditional CE-MS interfacing relies upon voltage to drive this process. Additionally, sheathless interfacing requires that the electrophoresis generates a sufficient volumetric flow to sustain the ionization process. Vibrating sharp-edge spray ionization (VSSI) is a new method to interface capillary electrophoresis to mass analyzers. In contrast to traditional interfacing, VSSI is voltage-free, making it straightforward for CE and MS. New nanoflow sheath CE-VSSI-MS is introduced in this work to reduce the reliance on the separation flow rate to facilitate the transfer of analyte to the MS. The nanoflow sheath VSSI spray ionization functions from 400 to 900 nL/min. Using the new nanoflow sheath reported here, volumetric flow rate through the separation capillary is less critical, allowing the use of a small (i.e., 20 to 25 μm) inner diameter separation capillary and enabling the use of higher separation voltages and faster analysis. Moreover, the use of a nanoflow sheath enables greater flexibility in the separation conditions. The nanoflow sheath is operated using aqueous solutions in the background electrolyte and in the sheath, demonstrating the separation can be performed under normal and reversed polarity in the presence or absence of electroosmotic flow. This includes the use of a wider pH range as well. The versatility of nanoflow sheath CE-VSSI-MS is demonstrated by separating cationic, anionic, and zwitterionic molecules under a variety of separation conditions. The detection sensitivity observed with nanoflow sheath CE-VSSI-MS is comparable to that obtained with sheathless CE-VSSI-MS as well as CE-MS separations with electrospray ionization interfacing. A bare fused silica capillary is used to separate cationic β-blockers with a near-neutral background electrolyte at concentrations ranging from 1.0 nM to 1.0 μM. Under acidic conditions, 13 amino acids are separated with normal polarity at a concentration ranging from 0.25 to 5 μM. Finally, separations of anionic compounds are demonstrated using reversed polarity under conditions of suppressed electroosmotic flow through the use of a semipermanent surface coating. With a near-neutral separation electrolyte, anionic nonsteroidal anti-inflammatory drugs are detected over a concentration range of 0.1 to 5.0 μM.
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Affiliation(s)
- Yousef S Elshamy
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Timothy G Strein
- Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - John A Lucas
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Tyler A Shaffer
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
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7
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Lageveen-Kammeijer GSM, Rapp E, Chang D, Rudd PM, Kettner C, Zaia J. The minimum information required for a glycomics experiment (MIRAGE): reporting guidelines for capillary electrophoresis. Glycobiology 2022; 32:580-587. [DOI: 10.1093/glycob/cwac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
The Minimum Information Required for a Glycomics Experiment (MIRAGE) is an initiative to standardize the reporting of glycoanalytical methods and to assess their reproducibility. To date, the MIRAGE Commission has published several reporting guidelines that describe what information should be provided for sample preparation methods, mass spectrometry methods, liquid chromatography (LC) analysis, exoglycosidase digestions, glycan microarray methods and nuclear magnetic resonance methods. Here we present the first version of reporting guidelines for glyco(proteo)mics analysis by capillary electrophoresis (CE) for standardized and high-quality reporting of experimental conditions in the scientific literature. The guidelines cover all aspects of a glyco(proteo)mics CE experiment including sample preparation, CE operation mode (CZE, CGE, CEC, MEKC, cIEF, cITP), instrument configuration, capillary separation conditions, detection, data analysis, and experimental descriptors. These guidelines are linked to other MIRAGE guidelines and are freely available through the project website https://www.beilstein-institut.de/en/projects/mirage/guidelines/#ce_analysis (doi:10.3762/mirage.7).
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Affiliation(s)
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestrasse 20 – ZENIT, 39120, Magdeburg, Germany
| | - Deborah Chang
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, 715 Albany Street, Boston, MA 02118, USA
| | - Pauline M Rudd
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros, Singapore
| | - Carsten Kettner
- Beilstein-Institut, Trakehner Str. 7-9, 60487 Frankfurt am Main, Germany
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, 715 Albany Street, Boston, MA 02118, USA
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Sarkozy D, Guttman A. Capillary Sodium Dodecyl Sulfate Agarose Gel Electrophoresis of Proteins. Gels 2022; 8:gels8020067. [PMID: 35200449 PMCID: PMC8871118 DOI: 10.3390/gels8020067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Capillary sodium dodecyl sulfate gel electrophoresis has long been used for the analysis of proteins, mostly either with entangled polymer networks or translationally cross-linked gels. In this paper capillary agarose gel electrophoresis is introduced for the separation of low molecular weight immunoglobulin subunits. The light (LC~24 kDa) and heavy (HC~50 kDa) chain fragments of a monoclonal antibody therapeutic drug were used to optimize the sieving matrix composition of the agarose/Tris-borate-EDTA (TBE) systems. The agarose and boric acid contents were systematically varied between 0.2–1.0% and 320–640 mM, respectively. The influence of several physical parameters such as viscosity and electroosmotic flow were also investigated, the latter to shed light on its effect on the electrokinetic injection bias. Three dimensional Ferguson plots were utilized to better understand the sieving performance of the various agarose/TBE ratio gels, especially relying on their slope (retardation coefficient, KR) value differences. The best resolution between the LC and non-glycosylated HC IgG subunits was obtained by utilizing the molecular sieving effect of the 1% agarose/320 mM boric acid composition (ΔKR = 0.035). On the other hand, the 0.8% agarose/640 mM boric acid gel showed the highest separation power between the similar molecular weight, but different surface charge density non-glycosylated HC and HC fragments (ΔKR = 0.005). It is important to note that the agarose-based gel-buffer systems did not require any capillary regeneration steps between runs other than simple replenishment of the sieving matrix, significantly speeding up analysis cycle time.
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Affiliation(s)
- Daniel Sarkozy
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032 Debrecen, Hungary;
| | - Andras Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032 Debrecen, Hungary;
- Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, H-8200 Veszprem, Hungary
- Correspondence:
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Kaur H, Beckman J, Zhang Y, Li ZJ, Szigeti M, Guttman A. Capillary electrophoresis and the biopharmaceutical industry: Therapeutic protein analysis and characterization. Trends Analyt Chem 2021; 144:116407. [DOI: 10.1016/j.trac.2021.116407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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10
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Filep C, Guttman A. Capillary sodium dodecyl sulfate gel electrophoresis of proteins: Introducing the three dimensional Ferguson method. Anal Chim Acta 2021; 1183:338958. [PMID: 34627506 DOI: 10.1016/j.aca.2021.338958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/10/2021] [Accepted: 08/14/2021] [Indexed: 10/20/2022]
Abstract
One of the most extensively utilized rapid characterization, release and stability testing methods of therapeutic proteins in the biopharmaceutical field today is capillary SDS gel electrophoresis using borate cross-linked high molecular weight dextran. In spite of its widespread use, however, the gel composition dependent separation characteristics of this very unique sieving matrix has not been investigated yet. Introduction of three dimensional (3D) Ferguson plots, based on simultaneous variation of the dextran (D) and borate (B) concentrations generating 16 different D/B ratio gels, allowed better understanding of the electromigration process of the SDS-protein complexes. As a result of this comprehensive study, non-linear 3D logarithmic mobility vs dextran and borate concentration surfaces were obtained. Both, the molecular weight protein standards and the new modality fusion protein etanercept resulted in concave 3D Ferguson plots. The interplay between the electroosmotic flow and the viscosity of the matrices played a key role in the resulting migration time and resolution. Selectivity values were defined and evaluated in 3D graph formats for the regular and de-N-glycosylated subunits of etanercept, as well as for the latter with the 10 kDa internal standard to understand both the dextran-borate complexation and sized based selectivities. KR plots of the retardation coefficients as the function of the logarithmic molecular weights were used to more precisely assess the Mw of the samples and to obtain information about the molecular characteristics of the electromigrating SDS-protein complexes.
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Affiliation(s)
- Csenge Filep
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032, Debrecen, Hungary.
| | - Andras Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032, Debrecen, Hungary; Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, H-8200, Veszprem, Hungary.
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Makrydaki E, Kotidis P, Polizzi KM, Kontoravdi C. Hitting the sweet spot with capillary electrophoresis: advances in N-glycomics and glycoproteomics. Curr Opin Biotechnol 2021; 71:182-190. [PMID: 34438131 DOI: 10.1016/j.copbio.2021.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/04/2021] [Accepted: 07/11/2021] [Indexed: 10/20/2022]
Abstract
N-glycosylation is of paramount importance for understanding the mechanisms of various human diseases and ensuring the safety and efficacy of biotherapeutics. Traditional glycan analysis techniques include LC-based separations and MALDI-TOF-MS identification. However, the current state-of-the-art methods lack throughput and structural information, include laborious sample preparation procedures and require large sample volumes. Capillary electrophoresis (CE) has long been used for the screening and reliable quantitation of glycans, but its applications have been limited. Because of its speed, sensitivity and complementarity with standard glycan analysis techniques, CE is currently emerging as one of the most versatile and adaptable methods for glycan analysis in both academia and industry. Herein, we review the latest advancements in CE-based applications to glycomics and glycoproteomics within both the biopharmaceutical and clinical sectors.
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Affiliation(s)
- Elli Makrydaki
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Pavlos Kotidis
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom.
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Pinto IF, Mikkonen S, Josefsson L, Mäkinen ME, Soares RR, Russom A, Emmer Å, Chotteau V. Knowing more from less: miniaturization of ligand-binding assays and electrophoresis as new paradigms for at-line monitoring and control of mammalian cell bioprocesses. Curr Opin Biotechnol 2021; 71:55-64. [PMID: 34246047 DOI: 10.1016/j.copbio.2021.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/17/2021] [Accepted: 06/20/2021] [Indexed: 02/01/2023]
Abstract
Monitoring technologies for Process Analytical Technology (PAT) in mammalian cell cultures are often focusing on the same hand full parameters although a deeper knowledge and control of a larger panel of culture components would highly benefit process optimization, control and robustness. This short review highlights key advances in microfluidic affinity assays and microchip capillary electrophoresis (MCE). Aiming at the miniaturization and integration of PAT, these can detect at-line a variety of metabolites, proteins and Critical Quality Attributes (CQA's) in a bioprocess. Furthermore, discrete analytical components, which can potentially support the translation of increasingly mature microfluidic technologies towards this novel application, are also presented as a comprehensive toolbox ranging from sample preparation to signal acquisition.
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13
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Filep C, Szigeti M, Farsang R, Haberger M, Reusch D, Guttman A. Multilevel capillary gel electrophoresis characterization of new antibody modalities. Anal Chim Acta 2021; 1166:338492. [PMID: 34023000 DOI: 10.1016/j.aca.2021.338492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/30/2021] [Accepted: 04/05/2021] [Indexed: 01/06/2023]
Abstract
Capillary gel electrophoresis-based methods were applied to comprehensively characterize two development phase new modality monoclonal antibodies including a glycoengineered and a bispecific test compound. The samples were subjected to multilevel characterization at the intact (both by SDS-SGE and cIEF) as well as the reduced protein and the released N-glycan levels. SDS capillary gel electrophoresis analysis showed excellent separation of the light and heavy chains of both samples. The bispecific antibody required a special temperature gradient denaturation process and a longer capillary to resolve its two light chain fragments. Separation of PNGase F digested antibodies revealed migration time shifts, suggesting the presence of N-linked glycosylation on the corresponding subunits. For efficient glycan removal, the highly glycosylated glycoengineered monoclonal antibody was trypsin digested prior to the endoglycosidase treatment. The released glycans were profiled by capillary gel electrophoresis after APTS labeling and their oligosaccharide structures were identified by exoglycosidase based carbohydrate sequencing. Finally, capillary isoelectric focusing shed light on the charge heterogeneity of the test compounds, providing important complementary information. A flowchart was established for workflow optimization.
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Affiliation(s)
- Csenge Filep
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032, Debrecen, Hungary.
| | - Marton Szigeti
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032, Debrecen, Hungary; Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, H-8200, Veszprem, Hungary.
| | - Robert Farsang
- Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, H-8200, Veszprem, Hungary.
| | - Markus Haberger
- Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany.
| | - Dietmar Reusch
- Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany.
| | - Andras Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032, Debrecen, Hungary; Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, H-8200, Veszprem, Hungary.
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14
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Guttman A, Filep C, Karger BL. Fundamentals of Capillary Electrophoretic Migration and Separation of SDS Proteins in Borate Cross-Linked Dextran Gels. Anal Chem 2021; 93:9267-9276. [PMID: 34165952 DOI: 10.1021/acs.analchem.1c01636] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Recent progress in the development and production of new, innovative protein therapeutics require rapid and adjustable high-resolution bioseparation techniques. Sodium dodecyl sulfate capillary gel electrophoresis (SDS-CGE) using a borate (B) cross-linked dextran (D) separation matrix is widely employed today for rapid consistency analysis of therapeutic proteins in manufacturing and release testing. Transient borate cross-linking of the semirigid dextran polymer chains leads to a high-resolution separation gel for SDS-protein complexes. To understand the migration and separation basis of the D/B gel, the present work explores various gel formulations of dextran monomer (2, 5, 7.5, and 10%) and borate cross-linker (2 and 4%) concentrations. Ferguson plots were analyzed for a mixture of protein standards with molecular weights ranging from 20 to 225 kDa, and the resulting nonlinear concave curves pointed to nonclassical sieving behavior. While the 2% D/4% B gel resulted in the fastest analysis time, the 10% D/2% B gel was found to produce the greatest separation window, even higher than with the 10% D/4% B gel, due to a significant increase in the electroosmotic flow of the former composition in the direction opposite to SDS-protein complex migration. The study then focused on SDS-CGE separation of a therapeutic monoclonal antibody and its subunits. A combination of molecular weight and shape selectivity as well as, to a lesser extent, surface charge density differences (due to glycosylation on the heavy chain) influenced migration. Greater molecular weight selectivity occurred for the higher monomer concentration gels, while improved glycoselectivity was obtained using a more dilute gel, even as low as 2% D/2% B. This latter gel took advantage of the dextran-borate-glycoprotein complexation. The study revealed that by modulating the dextran (monomer) and borate (cross-linker) concentration ratios of the sieving matrix, one can optimize the separation for specific biopharmaceutical modalities with excellent column-to-column, run-to-run, and gel-to-gel migration time reproducibilities (<0.96% relative standard deviation (RSD)). The widely used 10% dextran/4% borate gel represents a good screening option, which can then be followed by a modified composition, optimized for a specific separation as necessary.
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Affiliation(s)
- András Guttman
- Csaba Horváth Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei krt, Debrecen H-4032, Hungary.,Translational Glycomics Group, Research Institute for Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem u, Veszprem H-8200, Hungary
| | - Csenge Filep
- Csaba Horváth Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei krt, Debrecen H-4032, Hungary
| | - Barry L Karger
- Barnett Institute, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Gautam S, Banazadeh A, Cho BG, Goli M, Zhong J, Mechref Y. Mesoporous Graphitized Carbon Column for Efficient Isomeric Separation of Permethylated Glycans. Anal Chem 2021; 93:5061-5070. [DOI: 10.1021/acs.analchem.0c04395] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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Filep C, Guttman A. Effect of the Monomer Cross-Linker Ratio on the Separation Selectivity of Monoclonal Antibody Subunits in Sodium Dodecyl Sulfate Capillary Gel Electrophoresis. Anal Chem 2021; 93:3535-3541. [DOI: 10.1021/acs.analchem.0c04927] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Csenge Filep
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei krt, Debrecen H-4032, Hungary
| | - András Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei krt, Debrecen H-4032, Hungary
- Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem u, Veszprem H-8200, Hungary
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Marie AL, Ray S, Lu S, Jones J, Ghiran I, Ivanov AR. High-Sensitivity Glycan Profiling of Blood-Derived Immunoglobulin G, Plasma, and Extracellular Vesicle Isolates with Capillary Zone Electrophoresis-Mass Spectrometry. Anal Chem 2021; 93:1991-2002. [PMID: 33433994 DOI: 10.1021/acs.analchem.0c03102] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We developed a highly sensitive method for profiling of N-glycans released from proteins based on capillary zone electrophoresis coupled to electrospray ionization mass spectrometry (CZE-ESI-MS) and applied the technique to glycan analysis of plasma and blood-derived isolates. The combination of dopant-enriched nitrogen (DEN)-gas introduced into the nanoelectrospray microenvironment with optimized ionization, desolvation, and CZE-MS conditions improved the detection sensitivity up to ∼100-fold, as directly compared to the conventional mode of instrument operation through peak intensity measurements. Analyses without supplemental pressure increased the resolution ∼7-fold in the separation of closely related and isobaric glycans. The developed method was evaluated for qualitative and quantitative glycan profiling of three types of blood isolates: plasma, total serum immunoglobulin G (IgG), and total plasma extracellular vesicles (EVs). The comparative glycan analysis of IgG and EV isolates and total plasma was conducted for the first time and resulted in detection of >200, >400, and >500 N-glycans for injected sample amounts equivalent to <500 nL of blood. Structural CZE-MS2 analysis resulted in the identification of highly diverse glycans, assignment of α-2,6-linked sialic acids, and differentiation of positional isomers. Unmatched depth of N-glycan profiling was achieved compared to previously reported methods for the analysis of minute amounts of similar complexity blood isolates.
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Affiliation(s)
- Anne-Lise Marie
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Somak Ray
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Shulin Lu
- Division of Allergy and Inflammation, Beth Israel Deaconess Medical Center, Harvard Medical School, 3 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Jennifer Jones
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Ionita Ghiran
- Division of Allergy and Inflammation, Beth Israel Deaconess Medical Center, Harvard Medical School, 3 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Mátyás B, Singer J, Szarka M, Lowy DA, Döncző B, Makleit P, Failoc-Rojas VE, Ramirez A, Martínez P, Sándor Z, Kincses I, Guttman A. Determination of complex type free, non-conjugated oligosaccharide glucose unit values in tomato xylem sap for early detection of nutrient deficiency. Electrophoresis 2020; 42:200-205. [PMID: 33128395 DOI: 10.1002/elps.202000254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/04/2020] [Accepted: 10/27/2020] [Indexed: 11/07/2022]
Abstract
Although knowledge on glycan biosynthesis and processing is continuously maturing, there are still a limited number of studies that examine biological functions of N-glycan structures in plants, which remain virtually unknown. Here, the statistical correlation between nutrient (nitrogen) deficiency symptoms of crops and changes in 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-labeled complex type free oligosaccharides is reported. While deficiency symptoms are predicted by multispectral images and Kjeldahl digestion, APTS-labeled complex type free oligosaccharides are identified by their glucose unit (GU) values in tomato xylem sap, using capillary electrophoresis with laser induced fluorescence detection (CE-LIF). Given the limited number of structures obtained from plants, archived in the literature, in the future, it is intended to create an open access database of promising indicators, namely, glycan structures that are presumably responsible for the nutrient deficiency caused stress in plants (http://glycoplants.org).
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Affiliation(s)
- Bence Mátyás
- Genesis Sustainable Future Ltd., 33 Rákóczi St., Sárospatak, B-A-Z, H-3950, Hungary.,Research Group of Applied Plant Glycobiology, Dama Research Center limited, Kowloon, Hong Kong
| | | | - Máté Szarka
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, Hungary.,Institute for Nuclear Research (Atomki), Debrecen, Hungary.,Vitrolink Ltd., Debrecen, Hungary
| | - Daniel A Lowy
- Genesis Sustainable Future Ltd., 33 Rákóczi St., Sárospatak, B-A-Z, H-3950, Hungary.,Research Group of Applied Plant Glycobiology, Dama Research Center limited, Kowloon, Hong Kong.,Northern Virginia Community College, Alxandria, VA, USA
| | | | - Péter Makleit
- Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Hungary
| | - Virgilio E Failoc-Rojas
- Unidad de Investigación para la Generación y Síntesis de Evidencias en Salud, Universidad San Ignacio de Loyola, Lima, Peru
| | - Andrés Ramirez
- Centro de Investigación y Transferencia de Tecnología - CIITT, Universidad Católica de Cuenca, Azogues, Ecuador
| | - Pedro Martínez
- Centro de Investigación y Transferencia de Tecnología - CIITT, Universidad Católica de Cuenca, Azogues, Ecuador
| | - Zsolt Sándor
- Research Group of Applied Plant Glycobiology, Dama Research Center limited, Kowloon, Hong Kong.,Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Hungary
| | - Ida Kincses
- Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Hungary
| | - András Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, Hungary.,Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary
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Abstract
Introduction: Glycomics, which aims to define the glycome of a biological system to better assess the biological attributes of the glycans, has attracted increasing interest. However, the complexity and diversity of glycans present challenging barriers to glycome definition. Technological advances are major drivers in glycomics.Areas covered: This review summarizes the main methods and emphasizes the most recent advances in mass spectrometry-based methods regarding glycomics following the general workflow in glycomic analysis.Expert opinion: Recent mass spectrometry-based technological advances have significantly lowered the barriers in glycomics. The field of glycomics is moving toward both generic and precise analysis.
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Affiliation(s)
- Wei-Qian Cao
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Ming-Qi Liu
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Si-Yuan Kong
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Meng-Xi Wu
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Zheng-Ze Huang
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Peng-Yuan Yang
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
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