1
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Butaye E, Somers N, Grossar L, Pauwels N, Lefere S, Devisscher L, Raevens S, Geerts A, Meuris L, Callewaert N, Van Vlierberghe H, Verhelst X. Systematic review: Glycomics as diagnostic markers for hepatocellular carcinoma. Aliment Pharmacol Ther 2024; 59:23-38. [PMID: 37877758 DOI: 10.1111/apt.17748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most prevalent primary liver cancer with one of the highest cancer-related mortality rates worldwide. Early diagnosis is crucial for improving the therapeutic options and reducing the disease-related mortality. AIM To investigate serum N-glycomics as diagnostic markers for HCC. METHODS We performed a comprehensive search in PubMed, EMBASE, Web of Science and Scopus through August 17, 2023. Eligible studies assessed the potential use of serum N-glycomics as diagnostic biomarkers for HCC. Study selection, data extraction and quality assessment were performed by two independent reviewers. RESULTS Of the 48 articles included, 11 evaluated the utility of N-glycomics for the diagnosis of HCC in whole serum while the remaining articles focused on specific protein glycoforms or protein levels. Of these specific proteins, haptoglobin, alpha-fetoprotein (AFP), kininogen (Kin), α-1-antitrypsin and Golgi protein 73 (GP73) were the most frequently studied. Increased levels of fucosylation and branching presented as the most prevalent post-translational modifications of glycoproteins in patients with HCC compared to controls. Notably, glycomics-based biomarkers may provide a clinical benefit for the diagnosis of early HCC, as several algorithms achieved AUCs between 0.92-0.97. However, these were based on single studies with limited sample sizes and should therefore be validated. CONCLUSIONS Alterations in serum N-glycomics, characterised by increased levels of fucosylation and branching, have potential as diagnostic biomarkers for HCC. Optimisation of study design, patient selection and analysing techniques are needed before clinical implementation will be possible.
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Affiliation(s)
- Emma Butaye
- Hepatology Research Unit, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Liver Research Center Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Nicky Somers
- Hepatology Research Unit, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Liver Research Center Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Lorenz Grossar
- Hepatology Research Unit, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Liver Research Center Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Nele Pauwels
- Knowledge Center for Health Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sander Lefere
- Hepatology Research Unit, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Liver Research Center Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Lindsey Devisscher
- Liver Research Center Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
- Gut-Liver Immunopharmacology Unit, Department of Basic and Applied Medical Sciences, Ghent University, Ghent, Belgium
| | - Sarah Raevens
- Liver Research Center Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Anja Geerts
- Liver Research Center Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Leander Meuris
- Department of Biochemistry and Microbiology, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Nico Callewaert
- Department of Biochemistry and Microbiology, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Hans Van Vlierberghe
- Liver Research Center Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Xavier Verhelst
- Liver Research Center Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
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2
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Trastoy B, Du JJ, Cifuente JO, Rudolph L, García-Alija M, Klontz EH, Deredge D, Sultana N, Huynh CG, Flowers MW, Li C, Sastre DE, Wang LX, Corzana F, Mallagaray A, Sundberg EJ, Guerin ME. Mechanism of antibody-specific deglycosylation and immune evasion by Streptococcal IgG-specific endoglycosidases. Nat Commun 2023; 14:1705. [PMID: 36973249 PMCID: PMC10042849 DOI: 10.1038/s41467-023-37215-3] [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: 06/19/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Bacterial pathogens have evolved intricate mechanisms to evade the human immune system, including the production of immunomodulatory enzymes. Streptococcus pyogenes serotypes secrete two multi-modular endo-β-N-acetylglucosaminidases, EndoS and EndoS2, that specifically deglycosylate the conserved N-glycan at Asn297 on IgG Fc, disabling antibody-mediated effector functions. Amongst thousands of known carbohydrate-active enzymes, EndoS and EndoS2 represent just a handful of enzymes that are specific to the protein portion of the glycoprotein substrate, not just the glycan component. Here, we present the cryoEM structure of EndoS in complex with the IgG1 Fc fragment. In combination with small-angle X-ray scattering, alanine scanning mutagenesis, hydrolytic activity measurements, enzyme kinetics, nuclear magnetic resonance and molecular dynamics analyses, we establish the mechanisms of recognition and specific deglycosylation of IgG antibodies by EndoS and EndoS2. Our results provide a rational basis from which to engineer novel enzymes with antibody and glycan selectivity for clinical and biotechnological applications.
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Affiliation(s)
- Beatriz Trastoy
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Javier O Cifuente
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Lorena Rudolph
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Mikel García-Alija
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Erik H Klontz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Nazneen Sultana
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chau G Huynh
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Maria W Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Diego E Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Francisco Corzana
- Departamento Química and Centro de Investigación en Síntesis Quı́mica, Universidad de La Rioja, 26006, Rioja, Spain
| | - Alvaro Mallagaray
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany.
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
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3
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A multiplexed microflow LC-MS/MS-PRM assay for serologic quantification of IgG N- and HPX O- glycoforms in liver fibrosis. Sci Rep 2023; 13:606. [PMID: 36635317 PMCID: PMC9837073 DOI: 10.1038/s41598-023-27382-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/02/2023] [Indexed: 01/14/2023] Open
Abstract
Targeted quantification of glycoproteins has not reached its full potential because of limitations of the existing analytical workflows. In this study, we introduce a targeted microflow LC-MS/MS-PRM method for the quantification of multiple glycopeptides in unfractionated serum samples. The entire preparation of 16 samples in a batch is completed within 3 h, and the LC-MS quantification of all the glycoforms in a sample is completed in 15 min in triplicate, including online capture and desalting. We demonstrate applicability of the workflow on a multiplexed quantification of eight N-glycoforms of immunoglobulin G (IgG) together with two O-glycoforms of hemopexin (HPX). We applied the assay to a serologic study of fibrotic liver disease in patients of HCV etiology. The results document that specific IgG- and HPX-glycoforms detect efficiently fibrotic disease of different degree, and suggest that the LC-MS/MS-PRM assays may provide rapid and reproducible biomarker assay targeting simultaneously the N- and O-glycoforms of the peptides. We propose that such high throughput multiplexed methods may advance the clinical use of the LC-MS/MS assays.
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4
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Patabandige MW, Pfeifer LD, Nguyen HT, Desaire H. Quantitative clinical glycomics strategies: A guide for selecting the best analysis approach. MASS SPECTROMETRY REVIEWS 2022; 41:901-921. [PMID: 33565652 PMCID: PMC8601598 DOI: 10.1002/mas.21688] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/13/2020] [Accepted: 01/24/2021] [Indexed: 05/05/2023]
Abstract
Glycans introduce complexity to the proteins to which they are attached. These modifications vary during the progression of many diseases; thus, they serve as potential biomarkers for disease diagnosis and prognosis. The immense structural diversity of glycans makes glycosylation analysis and quantitation difficult. Fortunately, recent advances in analytical techniques provide the opportunity to quantify even low-abundant glycopeptides and glycans derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Understanding the strengths and weaknesses of different quantitative glycomics analysis methods is important for selecting the best strategy to analyze glycosylation changes in any given set of clinical samples. To provide guidance towards selecting the proper approach, we discuss four widely used quantitative glycomics analysis platforms, including fluorescence-based analysis of released N-linked glycans and three different varieties of MS-based analysis: liquid chromatography (LC)-mass spectrometry (MS) analysis of glycopeptides, matrix-assisted laser desorption ionization-time of flight MS, and LC-ESI-MS analysis of released N-linked glycans. These methods' strengths and weaknesses are compared, particularly associated with the figures of merit that are important for clinical biomarker studies, including: the initial sample requirements, the methods' throughput, sample preparation time, the number of species identified, the methods' utility for isomer separation and structural characterization, method-related challenges associated with quantitation, repeatability, the expertise required, and the cost for each analysis. This review, therefore, provides unique guidance to researchers who endeavor to undertake a clinical glycomics analysis by offering insights on the available analysis technologies.
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Affiliation(s)
- Milani Wijeweera Patabandige
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Leah D. Pfeifer
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Hanna T. Nguyen
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Heather Desaire
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, KS 66047, United States
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5
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Verhelst X, Geerts A, Colman R, Vanlander A, Degroote H, Abreu de Carvalho L, Meuris L, Berrevoet F, Rogiers X, Callewaert N, Van Vlierberghe H. Serum Glycomics on Postoperative Day 7 Are Associated With Graft Loss Within 3 Months After Liver Transplantation Regardless of Early Allograft Dysfunction. Transplantation 2021; 105:2404-2410. [PMID: 33273318 DOI: 10.1097/tp.0000000000003567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Prediction of outcome after liver transplantation (LT) is limited by the lack of robust predictors of graft failure. In this prospective study, we aimed to define a serum glycomic signature in the first week after LT that is associated with graft loss at 3 mo after LT. METHODS Patients were included between January 1, 2011, and February 28, 2017. Glycomic analysis was performed using DNA sequencer-associated fluorophore-associated capillary electrophoresis on a serum sample 1 wk after LT. Making use of Lasso regression, an optimal glycomic signature was identified associated with 3-mo graft survival. RESULTS In this cohort of 131 patients, graft loss at 3 mo occurred in 14 patients (11.9%). The optimal mode, called the GlycoTransplantTest, yielded an area under the curve of 0.95 for association with graft loss at 3 mo. Using an optimized cutoff for this biomarker, sensitivity was 86% and specificity 89%. Negative predictive value was 98%. Odds ratio for graft loss at 3 mo was 70.211 (P < 0.001; 95% confidence interval, 10.876-453.231). CONCLUSIONS A serum glycomic signature is highly associated with graft loss at 3 mo. It could support decision making in early retransplantation.
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Affiliation(s)
- Xavier Verhelst
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
- Hepatology Research Unit, Ghent University, Ghent, Belgium
- European Reference Network, RARE LIVER, Ghent, Belgium
| | - Anja Geerts
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
- Hepatology Research Unit, Ghent University, Ghent, Belgium
- European Reference Network, RARE LIVER, Ghent, Belgium
| | - Roos Colman
- Biostatistical Unit, Ghent University, Ghent, Belgium
| | - Aude Vanlander
- Department of General and Hepatobiliary Surgery, Liver Transplantation Service, Ghent University Hospital Medical School, Ghent, Belgium
| | - Helena Degroote
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
- Hepatology Research Unit, Ghent University, Ghent, Belgium
- European Reference Network, RARE LIVER, Ghent, Belgium
| | - Luis Abreu de Carvalho
- Department of General and Hepatobiliary Surgery, Liver Transplantation Service, Ghent University Hospital Medical School, Ghent, Belgium
| | - Leander Meuris
- Department for Molecular Biomedical Research, Unit for Medical Biotechnology, VIB, Ghent, Belgium
| | - Frederik Berrevoet
- Department of General and Hepatobiliary Surgery, Liver Transplantation Service, Ghent University Hospital Medical School, Ghent, Belgium
| | - Xavier Rogiers
- Department of General and Hepatobiliary Surgery, Liver Transplantation Service, Ghent University Hospital Medical School, Ghent, Belgium
| | - Nico Callewaert
- Department for Molecular Biomedical Research, Unit for Medical Biotechnology, VIB, Ghent, Belgium
| | - Hans Van Vlierberghe
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
- Hepatology Research Unit, Ghent University, Ghent, Belgium
- European Reference Network, RARE LIVER, Ghent, Belgium
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6
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Abstract
Changes in immunoglobulin G (IgG) glycosylation pattern have been observed in a vast array of auto- and alloimmune, infectious, cardiometabolic, malignant, and other diseases. This chapter contains an updated catalog of over 140 studies within which IgG glycosylation analysis was performed in a disease setting. Since the composition of IgG glycans is known to modulate its effector functions, it is suggested that a changed IgG glycosylation pattern in patients might be involved in disease development and progression, representing a predisposition and/or a functional effector in disease pathology. In contrast to the glycopattern of bulk serum IgG, which likely relates to the systemic inflammatory background, the glycosylation profile of antigen-specific IgG probably plays a direct role in disease pathology in several infectious and allo- and autoimmune antibody-dependent diseases. Depending on the specifics of any given disease, IgG glycosylation read-out might therefore in the future be developed into a useful clinical biomarker or a supplementary to currently used biomarkers.
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Affiliation(s)
- Marija Pezer
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia.
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7
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Sjögren J, Lood R, Nägeli A. On enzymatic remodeling of IgG glycosylation; unique tools with broad applications. Glycobiology 2020; 30:254-267. [PMID: 31616919 PMCID: PMC7109354 DOI: 10.1093/glycob/cwz085] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/05/2019] [Accepted: 09/30/2019] [Indexed: 01/14/2023] Open
Abstract
The importance of IgG glycosylation has been known for many years not only by scientists in glycobiology but also by human pathogens that have evolved specific enzymes to modify these glycans with fundamental impact on IgG function. The rise of IgG as a major therapeutic scaffold for many cancer and immunological indications combined with the availability of unique enzymes acting specifically on IgG Fc-glycans have spurred a range of applications to study this important post-translational modification on IgG. This review article introduces why the IgG glycans are of distinguished interest, gives a background on the unique enzymatic tools available to study the IgG glycans and finally presents an overview of applications utilizing these enzymes for various modifications of the IgG glycans. The applications covered include site-specific glycan transglycosylation and conjugation, analytical workflows for monoclonal antibodies and serum diagnostics. Additionally, the review looks ahead and discusses the importance of O-glycosylation for IgG3, Fc-fusion proteins and other new formats of biopharmaceuticals.
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Affiliation(s)
| | - Rolf Lood
- Genovis AB, Scheelevägen 2, 223 63 Lund, Sweden
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8
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de Haan N, Falck D, Wuhrer M. Monitoring of immunoglobulin N- and O-glycosylation in health and disease. Glycobiology 2020; 30:226-240. [PMID: 31281930 PMCID: PMC7225405 DOI: 10.1093/glycob/cwz048] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/11/2022] Open
Abstract
Protein N- and O-glycosylation are well known co- and post-translational modifications of immunoglobulins. Antibody glycosylation on the Fab and Fc portion is known to influence antigen binding and effector functions, respectively. To study associations between antibody glycosylation profiles and (patho) physiological states as well as antibody functionality, advanced technologies and methods are required. In-depth structural characterization of antibody glycosylation usually relies on the separation and tandem mass spectrometric (MS) analysis of released glycans. Protein- and site-specific information, on the other hand, may be obtained by the MS analysis of glycopeptides. With the development of high-resolution mass spectrometers, antibody glycosylation analysis at the intact or middle-up level has gained more interest, providing an integrated view of different post-translational modifications (including glycosylation). Alongside the in-depth methods, there is also great interest in robust, high-throughput techniques for routine glycosylation profiling in biopharma and clinical laboratories. With an emphasis on IgG Fc glycosylation, several highly robust separation-based techniques are employed for this purpose. In this review, we describe recent advances in MS methods, separation techniques and orthogonal approaches for the characterization of immunoglobulin glycosylation in different settings. We put emphasis on the current status and expected developments of antibody glycosylation analysis in biomedical, biopharmaceutical and clinical research.
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Affiliation(s)
- Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
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9
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Rebello OD, Gardner RA, Urbanowicz PA, Bolam DN, Crouch LI, Falck D, Spencer DIR. A novel glycosidase plate-based assay for the quantification of galactosylation and sialylation on human IgG. Glycoconj J 2020; 37:691-702. [PMID: 33064245 PMCID: PMC7679266 DOI: 10.1007/s10719-020-09953-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023]
Abstract
Changes in human IgG galactosylation and sialylation have been associated with several inflammatory diseases which are a major burden on the health care system. A large body of work on well-established glycomic and glycopeptidomic assays has repeatedly demonstrated inflammation-induced changes in IgG glycosylation. However, these assays are usually based on specialized analytical instrumentation which could be considered a technical barrier for uptake by some laboratories. Hence there is a growing demand for simple biochemical assays for analyzing these glycosylation changes. We have addressed this need by introducing a novel glycosidase plate-based assay for the absolute quantification of galactosylation and sialylation on IgG. IgG glycoproteins are treated with specific exoglycosidases to release the galactose and/or sialic acid residues. The released galactose monosaccharides are subsequently used in an enzymatic redox reaction that produces a fluorescence signal that is quantitative for the amount of galactosylation and, in-turn, sialylation on IgG. The glycosidase plate-based assay has the potential to be a simple, initial screening assay or an alternative assay to the usage of high-end analytical platforms such as HILIC-FLD-MSn when considering the analysis of galactosylation and sialylation on IgG. We have demonstrated this by comparing our assay to an industrial established HILIC-FLD-MSn glycomic analysis of 15 patient samples and obtained a Pearson’s r correlation coefficient of 0.8208 between the two methods.
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Affiliation(s)
- Osmond D Rebello
- Ludger Ltd, Culham Science Centre, Abingdon, UK. .,Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands.
| | | | | | - David N Bolam
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lucy I Crouch
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
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10
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Rebello OD, Nicolardi S, Lageveen-Kammeijer GSM, Nouta J, Gardner RA, Mesker WE, Tollenaar RAEM, Spencer DIR, Wuhrer M, Falck D. A Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Assay for the Relative Quantitation of Antennary Fucosylated N-Glycans in Human Plasma. Front Chem 2020; 8:138. [PMID: 32185163 PMCID: PMC7059190 DOI: 10.3389/fchem.2020.00138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/14/2020] [Indexed: 12/29/2022] Open
Abstract
Changes in the abundance of antennary fucosylated glycans in human total plasma N-glycome (TPNG) have been associated with several diseases ranging from diabetes to various forms of cancer. However, it is challenging to address this important part of the human glycome. Most commonly, time-consuming chromatographic separations are performed to differentially quantify core and antenna fucosylation. Obtaining sufficient resolution for larger, more complex glycans can be challenging. We introduce a matrix-assisted laser desorption/ionization—mass spectrometry (MALDI-MS) assay for the relative quantitation of antennary fucosylation in TPNG. N-linked glycans are released from plasma by PNGase F and further treated with a core fucosidase before performing a linkage-informative sialic acid derivatization. The core fucosylated glycans are thus depleted while the remaining antennary fucosylated glycans are quantitated. Simultaneous quantitation of α2,3-linked sialic acids and antennary fucosylation allows an estimation of the sialyl-Lewis x motif. The approach is feasible using either ultrahigh-resolution Fourier-transform ion cyclotron resonance mass spectrometry or time-of-flight mass spectrometry. The assay was used to investigate changes of antennary fucosylation as clinically relevant marker in 14 colorectal cancer patients. In accordance with a previous report, we found elevated levels of antennary fucosylation pre-surgery which decreased after tumor resection. The assay has the potential for revealing antennary fucosylation signatures in various conditions including diabetes and different types of cancer.
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Affiliation(s)
- Osmond D Rebello
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands.,Ludger Ltd, Culham Science Centre, Abingdon, United Kingdom
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Jan Nouta
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Wilma E Mesker
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | | | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
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11
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Verhelst X, Dias AM, Colombel JF, Vermeire S, Van Vlierberghe H, Callewaert N, Pinho SS. Protein Glycosylation as a Diagnostic and Prognostic Marker of Chronic Inflammatory Gastrointestinal and Liver Diseases. Gastroenterology 2020; 158:95-110. [PMID: 31626754 DOI: 10.1053/j.gastro.2019.08.060] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/03/2019] [Accepted: 08/23/2019] [Indexed: 12/16/2022]
Abstract
Glycans are sequences of carbohydrates that are added to proteins or lipids to modulate their structure and function. Glycans modify proteins required for regulation of immune cells, and alterations have been associated with inflammatory conditions. For example, specific glycans regulate T-cell activation, structures, and functions of immunoglobulins; interactions between microbes and immune and epithelial cells; and malignant transformation in the intestine and liver. We review the effects of protein glycosylation in regulation of gastrointestinal and liver functions, and how alterations in glycosylation serve as diagnostic or prognostic factors, or as targets for therapy.
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Affiliation(s)
- Xavier Verhelst
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Ana M Dias
- Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | | | - Severine Vermeire
- Translational Research in Gastrointestinal Disorders, Department of Clinical and Experimental Medicine, Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Hans Van Vlierberghe
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Nico Callewaert
- Vlaams Instituut voor Biotechnologie-UGent Center for Medical Biotechnology, Gent, Belgium
| | - Salomé S Pinho
- Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; Institute for Research and Innovation in Health, University of Porto, Porto, Portugal; Medical Faculty, University of Porto, Porto, Portugal.
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Hua D, Patabandige MW, Go EP, Desaire H. The Aristotle Classifier: Using the Whole Glycomic Profile To Indicate a Disease State. Anal Chem 2019; 91:11070-11077. [PMID: 31407893 DOI: 10.1021/acs.analchem.9b01606] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
"The totality is not, as it were, a mere heap, but the whole is something besides the parts."-Aristotle. We built a classifier that uses the totality of the glycomic profile, not restricted to a few glycoforms, to differentiate samples from two different sources. This approach, which relies on using thousands of features, is a radical departure from current strategies, where most of the glycomic profile is ignored in favor of selecting a few features, or even a single feature, meant to capture the differences in sample types. The classifier can be used to differentiate the source of the material; applicable sources may be different species of animals, different protein production methods, or, most importantly, different biological states (disease vs healthy). The classifier can be used on glycomic data in any form, including derivatized monosaccharides, intact glycans, or glycopeptides. It takes advantage of the fact that changing the source material can cause a change in the glycomic profile in many subtle ways: some glycoforms can be upregulated, some downregulated, some may appear unchanged, yet their proportion-with respect to other forms present-can be altered to a detectable degree. By classifying samples using the entirety of their glycan abundances, along with the glycans' relative proportions to each other, the "Aristotle Classifier" is more effective at capturing the underlying trends than standard classification procedures used in glycomics, including PCA (principal components analysis). It also outperforms workflows where a single, representative glycomic-based biomarker is used to classify samples. We describe the Aristotle Classifier and provide several examples of its utility for biomarker studies and other classification problems using glycomic data from several sources.
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Affiliation(s)
- David Hua
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
| | | | - Eden P Go
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
| | - Heather Desaire
- Department of Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
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13
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Klontz EH, Trastoy B, Deredge D, Fields JK, Li C, Orwenyo J, Marina A, Beadenkopf R, Günther S, Flores J, Wintrode PL, Wang LX, Guerin ME, Sundberg EJ. Molecular Basis of Broad Spectrum N-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2. ACS CENTRAL SCIENCE 2019; 5:524-538. [PMID: 30937380 PMCID: PMC6439443 DOI: 10.1021/acscentsci.8b00917] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 06/02/2023]
Abstract
Immunoglobulin G (IgG) glycosylation critically modulates antibody effector functions. Streptococcus pyogenes secretes a unique endo-β-N-acetylglucosaminidase, EndoS2, which deglycosylates the conserved N-linked glycan at Asn297 on IgG Fc to eliminate its effector functions and evade the immune system. EndoS2 and specific point mutants have been used to chemoenzymatically synthesize antibodies with customizable glycosylation for gain of functions. EndoS2 is useful in these schemes because it accommodates a broad range of N-glycans, including high-mannose, complex, and hybrid types; however, its mechanism of substrate recognition is poorly understood. We present crystal structures of EndoS2 alone and bound to complex and high-mannose glycans; the broad N-glycan specificity is governed by critical loops that shape the binding site of EndoS2. Furthermore, hydrolytic experiments, domain-swap chimeras, and hydrogen-deuterium exchange mass spectrometry reveal the importance of the carbohydrate-binding module in the mechanism of IgG recognition by EndoS2, providing insights into engineering enzymes to catalyze customizable glycosylation reactions.
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Affiliation(s)
- Erik H. Klontz
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Beatriz Trastoy
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Daniel Deredge
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - James K. Fields
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Chao Li
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Jared Orwenyo
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Alberto Marina
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Robert Beadenkopf
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Sebastian Günther
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Photon
Science, Deutsches Elektronen-Synchrotron, Hamburg 22607, Germany
| | - Jair Flores
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Patrick L. Wintrode
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Lai-Xi Wang
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Marcelo E. Guerin
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48013 Bilbao, Spain
| | - Eric J. Sundberg
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Department
of Medicine, University of Maryland School
of Medicine, Baltimore, Maryland 21201, United States
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