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Xu Z, Liu Y, He S, Sun R, Zhu C, Li S, Hai S, Luo Y, Zhao Y, Dai L. Integrative Proteomics and N-Glycoproteomics Analyses of Rheumatoid Arthritis Synovium Reveal Immune-Associated Glycopeptides. Mol Cell Proteomics 2023; 22:100540. [PMID: 37019382 PMCID: PMC10176071 DOI: 10.1016/j.mcpro.2023.100540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/10/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Rheumatoid arthritis (RA) is a typical autoimmune disease characterized by synovial inflammation, synovial tissue hyperplasia, and destruction of bone and cartilage. Protein glycosylation plays key roles in the pathogenesis of RA but in-depth glycoproteomics analysis of synovial tissues is still lacking. Here, by using a strategy to quantify intact N-glycopeptides, we identified 1260 intact N-glycopeptides from 481 N-glycosites on 334 glycoproteins in RA synovium. Bioinformatics analysis revealed that the hyper-glycosylated proteins in RA were closely linked to immune responses. By using DNASTAR software, we identified 20 N-glycopeptides whose prototype peptides were highly immunogenic. We next calculated the enrichment scores of nine types of immune cells using specific gene sets from public single-cell transcriptomics data of RA and revealed that the N-glycosylation levels at some sites, such as IGSF10_N2147, MOXD2P_N404, and PTCH2_N812, were significantly correlated with the enrichment scores of certain immune cell types. Furthermore, we showed that aberrant N-glycosylation in the RA synovium was related to increased expression of glycosylation enzymes. Collectively, this work presents, for the first time, the N-glycoproteome of RA synovium and describes immune-associated glycosylation, providing novel insights into RA pathogenesis.
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Affiliation(s)
- Zhiqiang Xu
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yi Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Siyu He
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Rui Sun
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Chenxi Zhu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Shuangqing Li
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shan Hai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yubin Luo
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhao
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China.
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China.
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Chen MX, Su HH, Shiao CY, Chang YT, Chang MC, Kao CC, Wang SY, Shih HC, Tsai IL. Affinity Purification Coupled to Stable Isotope Dilution LC-MS/MS Analysis to Discover IgG4 Glycosylation Profiles for Autoimmune Pancreatitis. Int J Mol Sci 2021; 22:ijms222111527. [PMID: 34768956 PMCID: PMC8584136 DOI: 10.3390/ijms222111527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 01/13/2023] Open
Abstract
Type 1 autoimmune pancreatitis (AIP) is categorized as an IgG4-related disease (IgG4-RD), where a high concentration of plasma IgG4 is one of the common biomarkers among patients. IgG Fc-glycosylation has been reported to be potential biosignatures for diseases. However, human IgG3 and IgG4 Fc-glycopeptides from populations in Asia were found to be isobaric ions when using LC-MS/MS as an analytical tool. In this study, an analytical workflow that coupled affinity purification and stable isotope dilution LC-MS/MS was developed to dissect IgG4 glycosylation profiles for autoimmune pancreatitis. Comparing the IgG4 and glycosylation profiles among healthy controls, patients with pancreatic ductal adenocarcinoma (PDAC), and AIP, the IgG4 glycosylations from the AIP group were found to have more digalactosylation (compared to PDAC) and less monogalactosylation (compared to HC). In addition, higher fucosylation and sialylation profiles were also discovered for the AIP group. The workflow is efficient and selective for IgG4 glycopeptides, and can be used for clinical biosignature discovery.
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Affiliation(s)
- Michael X. Chen
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Victoria, BC V8Z6R5, Canada;
- Division of Medical Sciences, University of Victoria, Victoria, BC V8W2Y2, Canada
| | - Ho-Hsuan Su
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (H.-H.S.); (C.-Y.S.)
| | - Ching-Ya Shiao
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (H.-H.S.); (C.-Y.S.)
| | - Yu-Ting Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan; (Y.-T.C.); (M.-C.C.)
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Ming-Chu Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan; (Y.-T.C.); (M.-C.C.)
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Chih-Chin Kao
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan;
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Taipei Medical University-Research Center of Urology and Kidney (TMU-RCUK), Taipei Medical University, Taipei 11031, Taiwan
| | - San-Yuan Wang
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan;
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
| | - Hsi-Chang Shih
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan;
| | - I-Lin Tsai
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (H.-H.S.); (C.-Y.S.)
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan;
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
- Correspondence:
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Helali Y, Sharma S, Vandeput M, Welba D, Van Antwerpen P, Marchant A, Delporte C. Fc Glycosylation Characterization of Human Immunoglobulins G Using Immunocapture and LC-MS. Methods Mol Biol 2021; 2271:57-71. [PMID: 33907999 DOI: 10.1007/978-1-0716-1241-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Immunoglobulins G (IgG) are proteins produced by the immune system of higher life forms that play a central role in the defense against microbial pathogens. IgG bind pathogens with the hypervariable Fab component and mediate a diversity of effector functions by binding to immune effector cells via their crystallizable (Fc) component. All IgG Fc carry a polymorphic N-glycan that regulates its binding properties and thereby its effector functions. The glycosylation profile of IgG Fc is modulated by physiological and pathological conditions, including infectious diseases and inflammatory disorders. Characterization of IgG Fc glycosylation profiles is a promising approach to understand the pathogenesis of diseases involving the immune system and to develop novel biomarkers of disease activity. Measuring the proportion of the different IgG Fc glycoforms remains an analytical challenge, that requires a sensitive and reproducible analytical approach.This chapter describes an optimized approach for the preparation and the analysis of Fc N-glycans from total serum or plasma IgG using magnetic beads, RapiFluor MS label©, and LC-MS.
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Affiliation(s)
- Yosra Helali
- Pharmacognosy, Bioanalysis and Drug Discovery and Analytical Platform, RD3 Department, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium.
| | - Shilpee Sharma
- Institute for Medical Immunology, Faculty of Medicine, Université libre de Bruxelles, Brussels, Belgium
| | - Marie Vandeput
- Pharmacognosy, Bioanalysis and Drug Discovery and Analytical Platform, RD3 Department, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Dansala Welba
- Institute for Medical Immunology, Faculty of Medicine, Université libre de Bruxelles, Brussels, Belgium
| | - Pierre Van Antwerpen
- Pharmacognosy, Bioanalysis and Drug Discovery and Analytical Platform, RD3 Department, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Arnaud Marchant
- Institute for Medical Immunology, Faculty of Medicine, Université libre de Bruxelles, Brussels, Belgium
| | - Cédric Delporte
- Pharmacognosy, Bioanalysis and Drug Discovery and Analytical Platform, RD3 Department, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
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Delafield DG, Li L. Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation. Mol Cell Proteomics 2021; 20:100054. [PMID: 32576592 PMCID: PMC8724918 DOI: 10.1074/mcp.r120.002095] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/13/2022] Open
Abstract
Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. Mass-spectrometry-based strategies for glycomic quantitation have grown to include metabolic incorporation of stable isotopes, deposition of mass difference and mass defect isotopic labels, and isobaric chemical labeling, providing researchers with ample tools for accurate and robust quantitation. Beyond this, workflows have been designed to harness instrument capability for label-free quantification, and numerous software packages have been developed to facilitate reliable spectrum scoring. In this review, we present and highlight the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification.
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Affiliation(s)
- Daniel G Delafield
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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Markina YV, Gerasimova EV, Markin AM, Glanz VY, Wu WK, Sobenin IA, Orekhov AN. Sialylated Immunoglobulins for the Treatment of Immuno-Inflammatory Diseases. Int J Mol Sci 2020; 21:ijms21155472. [PMID: 32751832 PMCID: PMC7432344 DOI: 10.3390/ijms21155472] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/20/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023] Open
Abstract
Immunoglobulins are the potent effector proteins of the humoral immune response. In the course of evolution, immunoglobulins have formed extremely diverse types of molecular structures with antigen-recognizing, antigen-binding, and effector functions embedded in a single molecule. Polysaccharide moiety of immunoglobulins plays the essential role in immunoglobulin functioning. There is growing evidence that the carbohydrate composition of immunoglobulin-linked glycans, and especially their terminal sialic acid residues, provide a key effect on the effector functions of immunoglobulins. Possibly, sialylation of Fc glycan is a common mechanism of IgG anti-inflammatory action in vivo. Thus, the post-translational modification (glycosylation) of immunoglobulins opens up significant possibilities in the diagnosis of both immunological and inflammatory disorders and in their therapies. This review is focused on the analysis of glycosylation of immunoglobulins, which can be a promising addition to improve existing strategies for the diagnosis and treatment of various immuno-inflammatory diseases.
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Affiliation(s)
- Yuliya V. Markina
- Laboratory of Cellular and Molecular Pathology of the Cardiovascular System, Institute of Human Morphology, 3 Tsyurupy Street, 117418 Moscow, Russia; (A.M.M.); (V.Y.G.); (I.A.S.); (A.N.O.)
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiyskaya Street, 125315 Moscow, Russia
- Correspondence: ; Tel.: +7-905-336-67-76
| | - Elena V. Gerasimova
- Department of Systemic Rheumatic Diseases, V.A. Nasonova Research Institute of Rheumatology, 34A Kashirskoe Shosse, 115522 Moscow, Russia;
| | - Alexander M. Markin
- Laboratory of Cellular and Molecular Pathology of the Cardiovascular System, Institute of Human Morphology, 3 Tsyurupy Street, 117418 Moscow, Russia; (A.M.M.); (V.Y.G.); (I.A.S.); (A.N.O.)
| | - Victor Y. Glanz
- Laboratory of Cellular and Molecular Pathology of the Cardiovascular System, Institute of Human Morphology, 3 Tsyurupy Street, 117418 Moscow, Russia; (A.M.M.); (V.Y.G.); (I.A.S.); (A.N.O.)
| | - Wei-Kai Wu
- Department of Internal Medicine, National Taiwan University Hospital, Bei-Hu Branch, Taipei 108, Taiwan;
| | - Igor A. Sobenin
- Laboratory of Cellular and Molecular Pathology of the Cardiovascular System, Institute of Human Morphology, 3 Tsyurupy Street, 117418 Moscow, Russia; (A.M.M.); (V.Y.G.); (I.A.S.); (A.N.O.)
- Laboratory of Medical Genetics, Institute of Experimental Cardiology, National Medical Research Center of Cardiology, 15A 3-rd Cherepkovskaya Street, 121552 Moscow, Russia
| | - Alexander N. Orekhov
- Laboratory of Cellular and Molecular Pathology of the Cardiovascular System, Institute of Human Morphology, 3 Tsyurupy Street, 117418 Moscow, Russia; (A.M.M.); (V.Y.G.); (I.A.S.); (A.N.O.)
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiyskaya Street, 125315 Moscow, Russia
- Institute for Atherosclerosis Research, Skolkovo Innovative Center, 121609 Moscow, Russia
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Development of efficient on-bead protein elution process coupled to ultra-high performance liquid chromatography-tandem mass spectrometry to determine immunoglobulin G subclass and glycosylation for discovery of bio-signatures in pancreatic disease. J Chromatogr A 2020; 1621:461039. [PMID: 32295703 DOI: 10.1016/j.chroma.2020.461039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/30/2022]
Abstract
Type 1 autoimmune pancreatitis (AIP) is a kind of IgG4-related disease in which higher IgG4 and total IgG levels have been found in patient serum. Due to the similar imaging features and laboratory parameters between AIP and pancreatic ductal adenocarcinoma (PDAC), a differential diagnosis is still challenging. Since IgG profiles can be potential bio-signatures for disease, we developed and validated a method which coupled on-bead enzymatic protein elution process to an efficient UHPLC-MS/MS method to determine IgG subclass and glycosylation. A stable-isotope labeled IgG was incorporated as internal standard to achieve accurate quantification. For calibration curves, the correlation coefficients for total IgG and the four IgG subclasses were higher than 0.995. Intraday (n = 5) and interday (n = 3) precisions of the peak area ratios of LLOQ, low, medium, and high QC samples were all less than 6.6% relative standard deviation (% RSD), and the accuracies were between 93.5 and 114.9%. Calibration curves, precision, and accuracy were also evaluated for 26 IgG glycopeptides. The method was applied to samples from healthy controls and patients with AIP and PDAC. Distinct IgG patterns were discovered among the groups, and 7 glycopeptides showed high potential in differentiating AIP and PDAC. The results demonstrated that the developed method is suitable for multi-feature analysis of human IgG, and the discovered IgG profiles can be used as bio-signatures for AIP and PDAC.
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