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Ulke J, Schwedler C, Krüger J, Stein V, Geserick P, Kleinridders A, Kappert K. High-fat diet alters N-glycosylation of PTPRJ in murine liver. J Nutr Biochem 2024; 123:109500. [PMID: 37875230 DOI: 10.1016/j.jnutbio.2023.109500] [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: 04/21/2023] [Revised: 10/10/2023] [Accepted: 10/21/2023] [Indexed: 10/26/2023]
Abstract
Protein tyrosine phosphatases (PTPs) regulate multiple signaling pathways. Disruption of tyrosine phosphorylation through imbalanced action between protein tyrosine kinases (RTKs) and PTPs is a hallmark of metabolic disorders, including insulin resistance. A representative member of the receptor-type PTP family, PTPRJ (DEP-1), was previously identified as a negative regulator of insulin signaling and possesses post-translational glycosylation sites. In this regard, it seems of great importance to decipher the structure of PTPRJ's glycosylation, particularly in the context of metabolic disturbances, but this has not been done in detail. Thus, here we aimed at characterizing the glycosylation pattern of PTPRJ in liver. We show that N-glycosylation accounts for up to half of PTPRJ's molecular weight. Applying mass spectrometry, we detected increased levels of high-mannose structures in PTPRJ in liver tissue of obese mice compared to lean littermates. In addition, complex neutral structures without fucose were also elevated in PTPRJ of high-fat diet (HFD) mice. Conversely, complex fucosylated N-glycans as well as sialylated bi- and triantennary N-glycans, were significantly reduced in PTPRJ of HFD-derived liver tissue compared to LFD by ∼two fold (P≤.01, P≤.0001 and P≤.001, respectively). In congruence with these findings, the mannosidase MAN2A1, responsible for the conversion of high-mannose to complex N-glycans, was significantly downregulated under HFD conditions. Here we present for the first time that HFD-induced obesity impacts on the glycosylation pattern of the insulin signaling component PTPRJ in liver. These findings may inspire new research on the glycosylation of PTPs in metabolic diseases and may open up new therapeutic approaches.
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Affiliation(s)
- Jannis Ulke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Augustenburger Platz 1, 13353 Berlin, Germany; Charité - Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Berlin, Germany
| | - Christian Schwedler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Janine Krüger
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Augustenburger Platz 1, 13353 Berlin, Germany; Charité - Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Berlin, Germany
| | - Vanessa Stein
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Augustenburger Platz 1, 13353 Berlin, Germany; Charité - Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Berlin, Germany
| | - Peter Geserick
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Augustenburger Platz 1, 13353 Berlin, Germany; Charité - Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Berlin, Germany
| | - André Kleinridders
- Department of Molecular and Experimental Nutritional Medicine, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Kai Kappert
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Augustenburger Platz 1, 13353 Berlin, Germany; Charité - Universitätsmedizin Berlin, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Berlin, Germany.
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Lado-Baleato Ó, Torre J, O’Flaherty R, Alonso-Sampedro M, Carballo I, Fernández-Merino C, Vidal C, Gude F, Saldova R, González-Quintela A. Age-Related Changes in Serum N-Glycome in Men and Women-Clusters Associated with Comorbidity. Biomolecules 2023; 14:17. [PMID: 38254617 PMCID: PMC10813383 DOI: 10.3390/biom14010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
(1) Aim: To describe, in a general adult population, the serum N-glycome in relation to age in men and women, and investigate the association of N-glycome patterns with age-related comorbidity; (2) Methods: The serum N-glycome was studied by hydrophilic interaction chromatography with ultra-performance liquid chromatography in 1516 randomly selected adults (55.3% women; age range 18-91 years). Covariates included lifestyle factors, metabolic disorders, inflammatory markers, and an index of comorbidity. Principal component analysis was used to define clusters of individuals based on the 46 glycan peaks obtained in chromatograms; (3) Results: The serum N-glycome changed with ageing, with significant differences between men and women, both in individual N-glycan peaks and in groups defined by common features (branching, galactosylation, sialylation, fucosylation, and oligomannose). Through K-means clustering algorithm, the individuals were grouped into a cluster characterized by abundance of simpler N-glycans and a cluster characterized by abundance of higher-order N-glycans. The individuals of the first cluster were older, showed higher concentrations of glucose and glycation markers, higher levels of some inflammatory markers, lower glomerular filtration rate, and greater comorbidity index; (4) Conclusions: The serum N-glycome changes with ageing with sex dimorphism. The N-glycome could be, in line with the inflammaging hypothesis, a marker of unhealthy aging.
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Affiliation(s)
- Óscar Lado-Baleato
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
- ISCIII Support Platforms for Clinical Research, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostel, 15706 Santiago de Compostela, Spain
| | - Jorge Torre
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
| | - Róisín O’Flaherty
- GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, A94 X099 Dublin, Ireland (R.S.)
- Department of Chemistry, Maynooth University, W23 F2K8 Maynooth, Ireland
| | - Manuela Alonso-Sampedro
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
| | - Iago Carballo
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
| | - Carmen Fernández-Merino
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
- Primary Care, Santiago de Compostela Area, 15706 Santiago de Compostela, Spain
| | - Carmen Vidal
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
| | - Francisco Gude
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
- Primary Care, Santiago de Compostela Area, 15706 Santiago de Compostela, Spain
| | - Radka Saldova
- GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, A94 X099 Dublin, Ireland (R.S.)
- UCD School of Medicine, College of Health and Agricultural Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Arturo González-Quintela
- Research Methodology Group, Health Research Institute of Santiago de Compostela (IDIS), Galician Health Service, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; (Ó.L.-B.); (J.T.); (M.A.-S.); (I.C.); (C.F.-M.); (C.V.); (F.G.)
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3
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Kalla R, Adams AT, Nowak JK, Bergemalm D, Vatn S, Ventham NT, Kennedy NA, Ricanek P, Lindstrom J, Söderholm J, Pierik M, D’Amato M, Gomollón F, Olbjørn C, Richmond R, Relton C, Jahnsen J, Vatn MH, Halfvarson J, Satsangi J. Analysis of Systemic Epigenetic Alterations in Inflammatory Bowel Disease: Defining Geographical, Genetic and Immune-Inflammatory influences on the Circulating Methylome. J Crohns Colitis 2023; 17:170-184. [PMID: 36029471 PMCID: PMC10024547 DOI: 10.1093/ecco-jcc/jjac127] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Epigenetic alterations may provide valuable insights into gene-environment interactions in the pathogenesis of inflammatory bowel disease [IBD]. METHODS Genome-wide methylation was measured from peripheral blood using the Illumina 450k platform in a case-control study in an inception cohort (295 controls, 154 Crohn's disease [CD], 161 ulcerative colitis [UC], 28 IBD unclassified [IBD-U)] with covariates of age, sex and cell counts, deconvoluted by the Houseman method. Genotyping was performed using Illumina HumanOmniExpressExome-8 BeadChips and gene expression using the Ion AmpliSeq Human Gene Expression Core Panel. Treatment escalation was characterized by the need for biological agents or surgery after initial disease remission. RESULTS A total of 137 differentially methylated positions [DMPs] were identified in IBD, including VMP1/MIR21 [p = 9.11 × 10-15] and RPS6KA2 [6.43 × 10-13], with consistency seen across Scandinavia and the UK. Dysregulated loci demonstrate strong genetic influence, notably VMP1 [p = 1.53 × 10-15]. Age acceleration is seen in IBD [coefficient 0.94, p < 2.2 × 10-16]. Several immuno-active genes demonstrated highly significant correlations between methylation and gene expression in IBD, in particular OSM: IBD r = -0.32, p = 3.64 × 10-7 vs non-IBD r = -0.14, p = 0.77]. Multi-omic integration of the methylome, genome and transcriptome also implicated specific pathways that associate with immune activation, response and regulation at disease inception. At follow-up, a signature of three DMPs [TAP1, TESPA1, RPTOR] were associated with treatment escalation to biological agents or surgery (hazard ratio of 5.19 [CI: 2.14-12.56], logrank p = 9.70 × 10-4). CONCLUSION These data demonstrate consistent epigenetic alterations at diagnosis in European patients with IBD, providing insights into the pathogenetic importance and translational potential of epigenetic mapping in complex disease.
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Affiliation(s)
- Rahul Kalla
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Alex T Adams
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jan K Nowak
- Department of Paediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simen Vatn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Nicholas T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas A Kennedy
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Exeter IBD and Pharmacogenetics group, University of Exeter, Exeter, UK
| | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Lindstrom
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Johan Söderholm
- Department of Surgery and Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Marie Pierik
- Maastricht University Medical Centre (MUMC), Department of Gastroenterology and Hepatology, Maastricht, Netherlands
| | - Mauro D’Amato
- CIC bioGUNE – BRTA, Derio, SpainIKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Christine Olbjørn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Rebecca Richmond
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Caroline Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jack Satsangi
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Mouse tissue glycome atlas 2022 highlights inter-organ variation in major N-glycan profiles. Sci Rep 2022; 12:17804. [PMID: 36280747 PMCID: PMC9592591 DOI: 10.1038/s41598-022-21758-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/30/2022] [Indexed: 01/19/2023] Open
Abstract
This study presents "mouse tissue glycome atlas" representing the profiles of major N-glycans of mouse glycoproteins that may define their essential functions in the surface glycocalyx of mouse organs/tissues and serum-derived extracellular vesicles (exosomes). Cell surface glycocalyx composed of a variety of N-glycans attached covalently to the membrane proteins, notably characteristic "N-glycosylation patterns" of the glycocalyx, plays a critical role for the regulation of cell differentiation, cell adhesion, homeostatic immune response, and biodistribution of secreted exosomes. Given that the integrity of cell surface glycocalyx correlates significantly with maintenance of the cellular morphology and homeostatic immune functions, dynamic alterations of N-glycosylation patterns in the normal glycocalyx caused by cellular abnormalities may serve as highly sensitive and promising biomarkers. Although it is believed that inter-organs variations in N-glycosylation patterns exist, information of the glycan diversity in mouse organs/tissues remains to be elusive. Here we communicate for the first-time N-glycosylation patterns of 16 mouse organs/tissues, serum, and serum-derived exosomes of Slc:ddY mice using an established solid-phase glycoblotting platform for the rapid, easy, and high throughput MALDI-TOFMS-based quantitative glycomics. The present results elicited occurrence of the organ/tissue-characteristic N-glycosylation patterns that can be discriminated to each other. Basic machine learning analysis using this N-glycome dataset enabled classification between 16 mouse organs/tissues with the highest F1 score (69.7-100%) when neural network algorithm was used. A preliminary examination demonstrated that machine learning analysis of mouse lung N-glycome dataset by random forest algorithm allows for the discrimination of lungs among the different mouse strains such as the outbred mouse Slc:ddY, inbred mouse DBA/2Crslc, and systemic lupus erythematosus model mouse MRL-lpr/lpr with the highest F1 score (74.5-83.8%). Our results strongly implicate importance of "human organ/tissue glycome atlas" for understanding the crucial and diversified roles of glycocalyx determined by the organ/tissue-characteristic N-glycosylation patterns and the discovery research for N-glycome-based disease-specific biomarkers and therapeutic targets.
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Bućan I, Škunca Herman J, Jerončić Tomić I, Gornik O, Vatavuk Z, Bućan K, Lauc G, Polašek O. N-Glycosylation Patterns across the Age-Related Macular Degeneration Spectrum. Molecules 2022; 27:molecules27061774. [PMID: 35335137 PMCID: PMC8949900 DOI: 10.3390/molecules27061774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023] Open
Abstract
The pathogenesis of age-related macular degeneration (AMD) remains elusive, despite numerous research studies. Therefore, we aimed to investigate the changes of plasma and IgG-specific N-glycosylation across the disease severity spectrum. We examined 2835 subjects from the 10.001 Dalmatians project, originating from the isolated Croatian islands of Vis and Korčula. All subjects were classified into four groups, namely (i) bilateral AMD, (ii) unilateral AMD, (iii) early-onset drusen, and (iv) controls. We analysed plasma and IgG N-glycans measured by HPLC and their association with retinal fundus photographs. There were 106 (3.7%) detected cases of AMD; 66 of them were bilateral. In addition, 45 (0.9%) subjects were recorded as having early-onset retinal drusen. We detected several interesting differences across the analysed groups, suggesting that N-glycans can be used as a biomarker for AMD. Multivariate analysis suggested a significant decrease in the immunomodulatory bi-antennary glycan structures in unilateral AMD (adjusted odds ratio 0.43 (95% confidence interval 0.22–0.79)). We also detected a substantial increase in the pro-inflammatory tetra-antennary plasma glycans in bilateral AMD (7.90 (2.94–20.95)). Notably, some of these associations were not identified in the aggregated analysis, where all three disease stages were collapsed into a single category, suggesting the need for better-refined phenotypes and the use of disease severity stages in the analysis of more complex diseases. Age-related macular degeneration progression is characterised by the complex interplay of various mechanisms, some of which can be detected by measuring plasma and IgG N-glycans. As opposed to a simple case-control study, more advanced and refined study designs are needed to understand the pathogenesis of complex diseases.
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Affiliation(s)
- Ivona Bućan
- Clinical Hospital Centre Split, 21000 Split, Croatia; (I.B.); (K.B.)
| | - Jelena Škunca Herman
- Clinical Hospital Centre Sisters of Mercy, 10000 Zagreb, Croatia; (J.Š.H.); (Z.V.)
| | - Iris Jerončić Tomić
- Department of Public Health, University of Split School of Medicine, 21000 Split, Croatia;
| | - Olga Gornik
- Department of Ophthalmology, University of Split School of Medicine, 21000 Split, Croatia;
- Genos Ltd., 10000 Zagreb, Croatia;
| | - Zoran Vatavuk
- Clinical Hospital Centre Sisters of Mercy, 10000 Zagreb, Croatia; (J.Š.H.); (Z.V.)
| | - Kajo Bućan
- Clinical Hospital Centre Split, 21000 Split, Croatia; (I.B.); (K.B.)
- Department of Ophthalmology, University of Split School of Medicine, 21000 Split, Croatia;
| | - Gordan Lauc
- Genos Ltd., 10000 Zagreb, Croatia;
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Ozren Polašek
- Department of Public Health, University of Split School of Medicine, 21000 Split, Croatia;
- Algebra LAB, Algebra University College, Ilica 242, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-91-5163443
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6
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Ip PP, Li Q, Lin WH, Chang CC, Fann CSJ, Chen HY, Liu FT, Lebrilla CB, Yang CC, Liao F. Analysis of site-specific glycan profiles of serum proteins in patients with multiple sclerosis or neuromyelitis optica spectrum disorder - a pilot study. Glycobiology 2021; 31:1230-1238. [PMID: 34132764 DOI: 10.1093/glycob/cwab053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/14/2022] Open
Abstract
Glycosylation is important for biological functions of proteins and greatly affected by diseases. Exploring the glycosylation profile of the protein-specific glycosylation and/or the site-specific glycosylation may help understand disease etiology, differentiate diseases, and ultimately develop therapeutics. Patients with multiple sclerosis (MS) and patients with neuromyelitis optica spectrum disorder (NMOSD) are sometimes difficult to differentiate due to the similarity in their clinical symptoms. The disease-related glycosylation profiles of MS and NMOSD have not yet been well studied. Here, we analyzed site-specific glycan profiles of serum proteins of these patients by using a recently developed mass spectrometry technique. A total of 286 glycopeptides from 49 serum glycoproteins were quantified and compared between healthy controls (n = 6), remitting MS (n = 45) and remitting NMOSD (n = 23) patients. Significant differences in the levels of site-specific N-glycans on inflammation-associated components [IgM, IgG1, IgG2, complement components 8b (CO8B), attractin], central nerve system-damage-related serum proteins [apolipoprotein D (APOD), alpha-1-antitrypsin, plasma kallikrein and ADAMTS-like protein 3] were observed among three study groups. We furthered demonstrated that site-specific N-glycans on APOD on site 98, CO8B on sites 243 and 553 are potential markers to differentiate MS from NMOSD with an area under receiver operating curve value greater than 0.75. All these observations indicate that remitting MS or NMOSD patients possess a unique disease-associated glyco-signature in their serum proteins. We conclude that monitoring one's serum protein glycan profile using this high-throughput analysis may provide an additional diagnostic criterion for differentiating diseases, monitoring disease status and estimating response-to-treatment effect.
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Affiliation(s)
- Peng Peng Ip
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | - Qiongyu Li
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Wei-Han Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | - Chien-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | | | - Huan-Yuan Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | - Fu-Tong Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Chih-Chao Yang
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Fang Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taipei 115, Taiwan
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7
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Blaschke CRK, McDowell CT, Black AP, Mehta AS, Angel PM, Drake RR. Glycan Imaging Mass Spectrometry: Progress in Developing Clinical Diagnostic Assays for Tissues, Biofluids, and Cells. Clin Lab Med 2021; 41:247-266. [PMID: 34020762 PMCID: PMC8862151 DOI: 10.1016/j.cll.2021.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
N-glycan imaging mass spectrometry (IMS) can rapidly and reproducibly identify changes in disease-associated N-linked glycosylation that are linked with histopathology features in standard formalin-fixed paraffin-embedded tissue samples. It can detect multiple N-glycans simultaneously and has been used to identify specific N-glycans and carbohydrate structural motifs as possible cancer biomarkers. Recent advancements in instrumentation and sample preparation are also discussed. The tissue N-glycan IMS workflow has been adapted to new glass slide-based assays for effective and rapid analysis of clinical biofluids, cultured cells, and immunoarray-captured glycoproteins for detection of changes in glycosylation associated with disease.
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Affiliation(s)
- Calvin R K Blaschke
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Colin T McDowell
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Alyson P Black
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA.
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8
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Keser T, Tijardović M, Gornik I, Lukić E, Lauc G, Gornik O, Novokmet M. High-Throughput and Site-Specific N-Glycosylation Analysis of Human Alpha-1-Acid Glycoprotein Offers a Great Potential for New Biomarker Discovery. Mol Cell Proteomics 2021; 20:100044. [PMID: 33493676 PMCID: PMC7950198 DOI: 10.1074/mcp.ra120.002433] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/29/2020] [Indexed: 12/11/2022] Open
Abstract
Alpha-1-acid glycoprotein (AGP) is an acute phase glycoprotein in blood, which is primarily synthetized in the liver and whose biological role is not completely understood. It consists of 45% carbohydrates that are present in the form of five N-linked complex glycans. AGP N-glycosylation was shown to be changed in many different diseases, and some changes appear to be disease-specific; thus, it has a great diagnostic and prognostic potential. However, AGP glycosylation was mainly analyzed in small cohorts and without detailed site-specific glycan information. Here, we developed a cost-effective method for a high-throughput and site-specific N-glycosylation LC-MS analysis of AGP which can be applied on large cohorts, aid in search for novel disease biomarkers, and enable better understanding of AGP's role and function in health and disease. The method does not require isolation of AGP with antibodies and affinity chromatography, but AGP is enriched by acid precipitation from 5 μl of bloodplasma in a 96-well format. After trypsinization, AGP glycopeptides are purified using a hydrophilic interaction chromatography-based solid-phase extraction and analyzed by reversed-phase-liquid chromatography-electrospray ionization-MS. We used our method to show for the first time that AGP N-glycan profile is stable in healthy individuals (14 individuals in three time points), which is a requirement for evaluation of its diagnostic potential. Furthermore, we tested our method on a population including individuals with registered hyperglycemia in critical illness (59 cases and 49 controls), which represents a significantly increased risk of developing type 2 diabetes. Individuals at higher risk of diabetes presented increased N-glycan branching on AGP's second glycosylation site and lower sialylation of N-glycans on AGP's third and AGP1's fourth glycosylation site. Although this should be confirmed on a larger prospective cohort, it indicates that site-specific AGP N-glycan profile could help distinguish individuals who are at risk of type 2 diabetes.
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Affiliation(s)
- Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia.
| | - Marko Tijardović
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Ivan Gornik
- Department of Emergency Medicine, Clinical Hospital Zagreb, Zagreb, Croatia
| | - Edita Lukić
- Division of Anesthesiology for Cardiovascular Surgery and Intensive Care Medicine, Medical University of Graz, Graz, Austria
| | - Gordan Lauc
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia; Genos Ltd., Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Olga Gornik
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mislav Novokmet
- Genos Ltd., Genos Glycoscience Research Laboratory, Zagreb, Croatia.
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9
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Abstract
Human lifespan has increased significantly in the last 200 years, emphasizing our need to age healthily. Insights into molecular mechanisms of aging might allow us to slow down its rate or even revert it. Similar to aging, glycosylation is regulated by an intricate interplay of genetic and environmental factors. The dynamics of glycopattern variation during aging has been mostly explored for plasma/serum and immunoglobulin G (IgG) N-glycome, as we describe thoroughly in this chapter. In addition, we discuss the potential functional role of agalactosylated IgG glycans in aging, through modulation of inflammation level, as proposed by the concept of inflammaging. We also comment on the potential to use the plasma/serum and IgG N-glycome as a biomarker of healthy aging and on the interventions that modulate the IgG glycopattern. Finally, we discuss the current knowledge about animal models for human plasma/serum and IgG glycosylation and mention other, less explored, instances of glycopattern changes during organismal aging and cellular senescence.
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10
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Tataru CA, David MM. Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease. PLoS Comput Biol 2020; 16:e1007859. [PMID: 32365061 PMCID: PMC7244183 DOI: 10.1371/journal.pcbi.1007859] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 05/22/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022] Open
Abstract
Microbiomes are complex ecological systems that play crucial roles in understanding natural phenomena from human disease to climate change. Especially in human gut microbiome studies, where collecting clinical samples can be arduous, the number of taxa considered in any one study often exceeds the number of samples ten to one hundred-fold. This discrepancy decreases the power of studies to identify meaningful differences between samples, increases the likelihood of false positive results, and subsequently limits reproducibility. Despite the vast collections of microbiome data already available, biome-specific patterns of microbial structure are not currently leveraged to inform studies. Here, we derive microbiome-level properties by applying an embedding algorithm to quantify taxon co-occurrence patterns in over 18,000 samples from the American Gut Project (AGP) microbiome crowdsourcing effort. We then compare the predictive power of models trained using properties, normalized taxonomic count data, and another commonly used dimensionality reduction method, Principal Component Analysis in categorizing samples from individuals with inflammatory bowel disease (IBD) and healthy controls. We show that predictive models trained using property data are the most accurate, robust, and generalizable, and that property-based models can be trained on one dataset and deployed on another with positive results. Furthermore, we find that properties correlate significantly with known metabolic pathways. Using these properties, we are able to extract known and new bacterial metabolic pathways associated with inflammatory bowel disease across two completely independent studies. By providing a set of pre-trained embeddings, we allow any V4 16S amplicon study to apply the publicly informed properties to increase the statistical power, reproducibility, and generalizability of analysis.
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Affiliation(s)
- Christine A. Tataru
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Maude M. David
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon, United States of America
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11
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Wu Z, Li H, Liu D, Tao L, Zhang J, Liang B, Liu X, Wang X, Li X, Wang Y, Wang W, Guo X. IgG Glycosylation Profile and the Glycan Score Are Associated with Type 2 Diabetes in Independent Chinese Populations: A Case-Control Study. J Diabetes Res 2020; 2020:5041346. [PMID: 32587867 PMCID: PMC7301241 DOI: 10.1155/2020/5041346] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/18/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The relationship between the IgG glycan panel and type 2 diabetes remains unclear in Chinese population. We aimed to investigate the association of the IgG glycan profile and glycan score with type 2 diabetes. METHODS In the discovery population, 162 individuals diagnosed with type 2 diabetes and 162 matched controls from Beijing health management cohort were included. We analyzed the IgG glycan profile and composed a glycan score for type 2 diabetes. Findings were validated in the replication population from Beijing Xuanwu community cohort (280 cases and 508 controls). Area under curve (AUC) using 10-fold and bootstrap validation, net reclassification index (NRI), and integrated discrimination index (IDI) were calculated for the glycan score. RESULTS In the discovery population, 5 initial IgG glycans and 7 derived traits were significantly associated with type 2 diabetes after Bonferroni correction and Lasso selection, which were validated in the replication population subsequently. The glycan score composed of these IgG glycans and traits showed a strong association with type 2 diabetes (combined odds ratio (OR): 3.78) and its risk factors. In the replication population, AUC of the model involving clinical traits improved from 0.74 to above 0.90, and the values of NRI and IDI were 0.35 and 0.42, respectively, with the glycan score added. CONCLUSIONS IgG glycosylation profiles were associated with type 2 diabetes and the glycan score may be a novel indicator for diabetes which reflected a proinflammatory status.
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Affiliation(s)
- Zhiyuan Wu
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Haibin Li
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Di Liu
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Lixin Tao
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Jie Zhang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Baolu Liang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Xiangtong Liu
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Xiaonan Wang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Xia Li
- Department of Mathematics and Statistics, La Trobe University, Australia
| | - Youxin Wang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Wei Wang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
- Department of Public Health, School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Xiuhua Guo
- Beijing Municipal Key Laboratory of Clinical Epidemiology, Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
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12
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Dotz V, Wuhrer M. N-glycome signatures in human plasma: associations with physiology and major diseases. FEBS Lett 2019; 593:2966-2976. [PMID: 31509238 DOI: 10.1002/1873-3468.13598] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/02/2019] [Indexed: 12/18/2022]
Abstract
N-glycome analysis in total plasma or serum yields information about the levels and glycosylation patterns of major plasma glycoproteins, including immunoglobulins, acute-phase proteins, and apolipoproteins. Until recently, glycomic studies in disease settings largely suffered from small cohort sizes, poor analytical resolution, and poor comparability of results owing to the diversity of analytical techniques. Here, we report on recent advances in high-throughput mass spectrometry glycomics technology that enabled elucidation of N-glycome signatures in the plasma of patients with type 2 diabetes, inflammatory bowel disease, or colorectal cancer. Use of this technology revealed both commonalities and differences among disease fingerprints. Moreover, we summarize findings on glycomic signatures associated with age, sex, and body mass index. High-throughput, high-resolution glycomics technologies, together with robust data analysis workflows, will advance clinical translation.
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Affiliation(s)
- Viktoria Dotz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, the Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, the Netherlands
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13
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Rudman N, Gornik O, Lauc G. Altered N-glycosylation profiles as potential biomarkers and drug targets in diabetes. FEBS Lett 2019; 593:1598-1615. [PMID: 31215021 DOI: 10.1002/1873-3468.13495] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/16/2022]
Abstract
N-glycosylation is a ubiquitous protein modification, and N-glycosylation profiles are emerging as both biomarkers and functional effectors in various types of diabetes. Genome-wide association studies identified glycosyltransferase genes as candidate causal genes for type 1 and type 2 diabetes. Studies focused on N-glycosylation changes in type 2 diabetes demonstrated that patients can be distinguished from healthy controls based on N-glycome composition. In addition, individuals at an increased risk of future disease development could be identified based on N-glycome profiles. Moreover, accumulating evidence indicates that N-glycans have a major role in preventing the impairment of glucose-stimulated insulin secretion by maintaining the glucose transporter in proper orientation, indicating that interindividual variation in protein N-glycosylation might be a novel risk factor contributing to diabetes development. Defective N-glycosylation of T cells has been implicated in type 1 diabetes pathogenesis. Furthermore, studies of N-glycan alterations have successfully been used to identify individuals with rare types of diabetes (such as the HNF1A-MODY), and also to evaluate functional significance of novel diabetes-associated mutations. In conclusion, both N-glycans and glycosyltransferases emerge as potential therapeutic targets in diabetes.
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Affiliation(s)
- Najda Rudman
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Croatia
| | - Olga Gornik
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Croatia.,Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Gordan Lauc
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Croatia.,Genos Glycoscience Research Laboratory, Zagreb, Croatia
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14
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Macaluso FS, Cavallaro F, Felice C, Mazza M, Armuzzi A, Gionchetti P, Vecchi M, Orlando A. Risk factors and timing for colectomy in chronically active refractory ulcerative colitis: A systematic review. Dig Liver Dis 2019; 51:613-620. [PMID: 30826279 DOI: 10.1016/j.dld.2019.01.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/20/2019] [Accepted: 01/21/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND In patients with chronic refractory ulcerative colitis (UC) the precise timing for indication to colectomy is unclear. AIMS We performed a systematic review of the literature on the risk factors for colectomy in patients with chronic refractory UC in the biologic era. METHODS PubMed Central/Medline and Embase were systemically searched for records published between January 2000 and December 2017. Current evidence was summarized and filtered by expert opinion. RESULTS 70 studies were included in the qualitative synthesis. Several factors were found to be associated with a higher or reduced risk for colectomy, including variables at baseline - such as progression from proctitis/left-sided to extensive colitis, extensive colitis at diagnosis, high baseline C Reactive Protein or erythrocyte sedimentation rate, male gender, and younger age at diagnosis - previous medical history, and factors arising during therapy with biologics, including the absence of clinical response after induction with infliximab or adalimumab, and the lack of mucosal healing during therapy with anti-TNFs. CONCLUSIONS Two main points may help physicians to decide when the surgical option may be considered in patients with chronic refractory UC: (1) a first risk stratification can be obtained by analyzing factors at baseline and medical history, including the previous exposure to anti-TNFs; (2) during therapy with biologics, the early assessment (after 12-16 weeks of treatment) of clinical and endoscopic response is a strong predictor of the subsequent risk of colectomy.
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Affiliation(s)
| | - Flaminia Cavallaro
- Gastroenterology & Digestive Endoscopy Unit, IRCCS Policlinico San Donato, Milano, Italy
| | - Carla Felice
- IBD Unit, "Presidio Columbus" Foundation Hospital "A. Gemelli IRCCS" - Sacro Cuore Catholic University, Rome
| | - Marta Mazza
- Department of Medical and Surgical Sciences (DIMEC), Policlinico S.Orsola-Malpighi, University of Bologna, Italy
| | - Alessandro Armuzzi
- IBD Unit, "Presidio Columbus" Foundation Hospital "A. Gemelli IRCCS" - Sacro Cuore Catholic University, Rome
| | - Paolo Gionchetti
- Department of Medical and Surgical Sciences (DIMEC), Policlinico S.Orsola-Malpighi, University of Bologna, Italy
| | - Maurizio Vecchi
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Pathophysiology and Organ Transplantation, University of Milan, Italy
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15
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Zhang Z, Westhrin M, Bondt A, Wuhrer M, Standal T, Holst S. Serum protein N-glycosylation changes in multiple myeloma. Biochim Biophys Acta Gen Subj 2019; 1863:960-970. [DOI: 10.1016/j.bbagen.2019.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 02/22/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
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16
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Mahmoud ME, Rehan IF, El-Dawy Ahmed K, Abdelrahman A, Mohammadi S, Abou-Elnaga AF, Youssef M, Diab HM, Salman D, Elnagar A, Mohammed HH, Shanab O, Ibrahim RM, Ahmed EKH, Hesham AEL, Gupta A. Identification of serum N-glycoproteins as a biological correlate underlying chronic stress response in mice. Mol Biol Rep 2019; 46:2733-2748. [PMID: 30915686 DOI: 10.1007/s11033-019-04717-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/23/2019] [Indexed: 12/11/2022]
Abstract
Glycosylation is a post-translational protein modification in eukaryotes and plays an important role in controlling several diseases. N-glycan structure is emerging as a new paradigm for biomarker discovery of neuropsychiatric disorders. However, the relationship between N-glycosylation pattern and depression is not well elucidated to date. This study aimed to explore whether serum N-glycan structures are altered in depressive-like behavior using a stress based mouse model. We used two groups of BALB/c mice; (i) treated group exposed to chronic unpredictable mild stress (CUMS) as a model of depression, and (ii) control group. Behavioral tests in mice (e.g., sucrose preference test, forced swimming test, and fear conditioning test) were used to evaluate the threshold level to which mice displayed a depressive-like phenotype. Serum N-glycans were analyzed carefully using glycoblotting followed by Matrix-assisted laser desorption ionization-time of flight/mass spectrometry (MALDI-TOF/MS) to exhibit N-glycan expression levels and to illustrate the changes in the N-glycome profile. N-glycan expression levels were commonly altered in the depressive-like model and correlated well with the behavioral data. Our results indicated that sialylated N-glycan was identified as a biomarker associated with depressive symptoms, which may have utility as a candidate biomarker for the clinical diagnosis and monitoring of depression.
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Affiliation(s)
- Motamed Elsayed Mahmoud
- Department of Animal Behavior and Husbandry, Faculty of Veterinary Medicine, Sohag University, Sohag, 82524, Egypt.
| | - Ibrahim F Rehan
- Department of Animal Behavior and Husbandry, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt.
| | - Kh El-Dawy Ahmed
- Department of Biochemistry, Faculty of Veterinary Medicine, Zagazig University, El-Zeraa Street, 114, Zagazig, 44511, Egypt
| | - Amany Abdelrahman
- Department of Physiology, Faculty of Medicine, Sohag University, Sohag, 82524, Egypt
| | - Saeed Mohammadi
- Department of Tissue Engineering and Applied Cell Sciences, University of Medical Sciences, Tehran, 1985711151, Iran.,Biointerfaces Institute, McMaster University, 1280 Main St W, Hamilton, ON, L8S 0A3, Canada
| | - Ahmed F Abou-Elnaga
- Department of Husbandry and Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Mohammed Youssef
- Department of Animal Physiology, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Hassan Mahmoud Diab
- Department of Animal Hygiene, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Doaa Salman
- Department of Animal Medicine, Faculty of Veterinary Medicine, Sohag University, Sohag, 82524, Egypt
| | - Asmaa Elnagar
- Department of Biochemistry, Faculty of Veterinary Medicine, Zagazig University, El-Zeraa Street, 114, Zagazig, 44511, Egypt
| | - Hesham H Mohammed
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Zagazig University, El-Zeraa Street, 114, Zagazig, 44511, Egypt
| | - Obeid Shanab
- Department of Biochemistry, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Rawia M Ibrahim
- Clinical Laboratory Diagnosis, Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Eslam K H Ahmed
- Department of Animal Behavior and Husbandry, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Abd El-Latif Hesham
- Genetics Department, Faculty of Agriculture, Assiut University, Assiut, 71516, Egypt.
| | - Arti Gupta
- Department of Zoology, Sri Avadh Raj Singh Smarak Degree College, Gonda, India
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17
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Dias AM, Pereira MS, Padrão NA, Alves I, Marcos-Pinto R, Lago P, Pinho SS. Glycans as critical regulators of gut immunity in homeostasis and disease. Cell Immunol 2018; 333:9-18. [DOI: 10.1016/j.cellimm.2018.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 07/04/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
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18
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Yoshida Y, Furukawa JI, Naito S, Higashino K, Numata Y, Shinohara Y. Identification of unique glycoisoforms of vitamin D-binding protein and haptoglobin as biomarker candidates in hepatocarcinogenesis of STAM mice. Glycoconj J 2018; 35:467-476. [DOI: 10.1007/s10719-018-9838-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 08/02/2018] [Accepted: 08/09/2018] [Indexed: 01/13/2023]
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19
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Clerc F, Novokmet M, Dotz V, Reiding KR, de Haan N, Kammeijer GSM, Dalebout H, Bladergroen MR, Vukovic F, Rapp E, Targan SR, Barron G, Manetti N, Latiano A, McGovern DPB, Annese V, Lauc G, Wuhrer M. Plasma N-Glycan Signatures Are Associated With Features of Inflammatory Bowel Diseases. Gastroenterology 2018; 155:829-843. [PMID: 29792883 DOI: 10.1053/j.gastro.2018.05.030] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 04/07/2018] [Accepted: 05/15/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Biomarkers are needed for early detection of Crohn's disease (CD) and ulcerative colitis (UC) or to predict patient outcomes. Glycosylation is a common and complex posttranslational modification of proteins that affects their structure and activity. We compared plasma N-glycosylation profiles between patients with CD or UC and healthy individuals (controls). METHODS We analyzed the total plasma N-glycomes of 2635 patients with inflammatory bowel diseases and 996 controls by mass spectrometry with a linkage-specific sialic acid derivatization technique. Plasma samples were acquired from 2 hospitals in Italy (discovery cohort, 1989 patients with inflammatory bowel disease [IBD] and 570 controls) and 1 medical center in the United States (validation cohort, 646 cases of IBD and 426 controls). Sixty-three glycoforms met our criteria for relative quantification and were extracted from the raw data with the software MassyTools. Common features shared by the glycan compositions were combined in 78 derived traits, including the number of antennae of complex-type glycans and levels of fucosylation, bisection, galactosylation, and sialylation. Associations of plasma N-glycomes with age, sex, CD, UC, and IBD-related parameters such as disease location, surgery and medication, level of C-reactive protein, and sedimentation rate were tested by linear and logistic regression. RESULTS Plasma samples from patients with IBD had a higher abundance of large-size glycans compared with controls, a decreased relative abundance of hybrid and high-mannose structures, lower fucosylation, lower galactosylation, and higher sialylation (α2,3- and α2,6-linked). We could discriminate plasma from patients with CD from that of patients with UC based on higher bisection, lower galactosylation, and higher sialylation (α2,3-linked). Glycosylation patterns were associated with disease location and progression, the need for a more potent medication, and surgery. These results were replicated in a large independent cohort. CONCLUSIONS We performed high-throughput analysis to compare total plasma N-glycomes of individuals with vs without IBD and to identify patterns associated with disease features and the need for treatment. These profiles might be used in diagnosis and for predicting patients' responses to treatment.
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Affiliation(s)
- Florent Clerc
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Viktoria Dotz
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Guinevere S M Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Marco R Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Frano Vukovic
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; glyXera GmbH, Magdeburg, Germany
| | | | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gildardo Barron
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Natalia Manetti
- Unit of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence, Italy
| | - Anna Latiano
- Unit of Gastroenterology, IRCCS-CSS (Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza) Hospital, San Giovanni Rotondo, Italy
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Vito Annese
- Unit of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence, Italy; Unit of Gastroenterology, IRCCS-CSS (Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza) Hospital, San Giovanni Rotondo, Italy
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
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20
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Ferdosi S, Ho TH, Castle EP, Stanton ML, Borges CR. Behavior of blood plasma glycan features in bladder cancer. PLoS One 2018; 13:e0201208. [PMID: 30040854 PMCID: PMC6057681 DOI: 10.1371/journal.pone.0201208] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/10/2018] [Indexed: 01/01/2023] Open
Abstract
Despite systemic therapy and cystectomy, bladder cancer is characterized by a high recurrence rate. Serum glycomics represents a promising source of prognostic markers for monitoring patients. Our approach, which we refer to as "glycan node analysis", constitutes the first example of molecularly "bottom-up" glycomics. It is based on a global glycan methylation analysis procedure that is applied to whole blood plasma/serum. The approach detects and quantifies partially methylated alditol acetates arising from unique glycan features such as α2-6 sialylation, β1-4 branching, and core fucosylation that have been pooled together from across all intact glycans within a sample into a single GC-MS chromatographic peak. We applied this method to 122 plasma samples from former and current bladder cancer patients (n = 72 former cancer patients with currently no evidence of disease (NED); n = 38 non-muscle invasive bladder cancer (NMIBC) patients; and n = 12 muscle invasive bladder cancer (MIBC) patients) along with plasma from 30 certifiably healthy living kidney donors. Markers for α2-6 sialylation, β1-4 branching, β1-6 branching, and outer-arm fucosylation were able to separate current and former (NED) cases from certifiably healthy controls (ROC curve c-statistics ~ 0.80); but NED, NMIBC, and MIBC were not distinguished from one another. Based on the unexpectedly high levels of these glycan nodes in the NED patients, we hypothesized that recurrence of this disease could be predicted by some of the elevated glycan features. Indeed, α2-6 sialylation and β1-6 branching were able to predict recurrence from the NED state using a Cox proportional hazards regression model adjusted for age, gender, and time from cancer. The levels of these two glycan features were correlated to C-reactive protein concentration, an inflammation marker and known prognostic indicator for bladder cancer, further strengthening the link between inflammation and abnormal plasma protein glycosylation.
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Affiliation(s)
- Shadi Ferdosi
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, AZ, United States of America
| | - Thai H. Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, AZ, United States of America
| | - Erik P. Castle
- Department of Urology, Mayo Clinic, Phoenix, AZ, United States of America
| | - Melissa L. Stanton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ, United States of America
| | - Chad R. Borges
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, AZ, United States of America
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21
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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Promoter methylation of the MGAT3 and BACH2 genes correlates with the composition of the immunoglobulin G glycome in inflammatory bowel disease. Clin Epigenetics 2018; 10:75. [PMID: 29991969 PMCID: PMC5987481 DOI: 10.1186/s13148-018-0507-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/22/2018] [Indexed: 12/16/2022] Open
Abstract
Background Many genome- and epigenome-wide association studies (GWAS and EWAS) and studies of promoter methylation of candidate genes for inflammatory bowel disease (IBD) have demonstrated significant associations between genetic and epigenetic changes and IBD. Independent GWA studies have identified genetic variants in the BACH2, IL6ST, LAMB1, IKZF1, and MGAT3 loci to be associated with both IBD and immunoglobulin G (IgG) glycosylation. Methods Using bisulfite pyrosequencing, we analyzed CpG methylation in promoter regions of these five genes from peripheral blood of several hundred IBD patients and healthy controls (HCs) from two independent cohorts, respectively. Results We found significant differences in the methylation levels in the MGAT3 and BACH2 genes between both Crohn’s disease and ulcerative colitis when compared to HC. The same pattern of methylation changes was identified for both genes in CD19+ B cells isolated from the whole blood of a subset of the IBD patients. A correlation analysis was performed between the MGAT3 and BACH2 promoter methylation and individual IgG glycans, measured in the same individuals of the two large cohorts. MGAT3 promoter methylation correlated significantly with galactosylation, sialylation, and bisecting GlcNAc on IgG of the same patients, suggesting that activity of the GnT-III enzyme, encoded by this gene, might be altered in IBD. The correlations between the BACH2 promoter methylation and IgG glycans were less obvious, since BACH2 is not a glycosyltransferase and therefore may affect IgG glycosylation only indirectly. Conclusions Our results suggest that epigenetic deregulation of key glycosylation genes might lead to an increase in pro-inflammatory properties of IgG in IBD through a decrease in galactosylation and sialylation and an increase of bisecting GlcNAc on digalactosylated glycan structures. Finally, we showed that CpG methylation in the promoter of the MGAT3 gene is altered in CD3+ T cells isolated from inflamed mucosa of patients with ulcerative colitis from a third smaller cohort, for which biopsies were available, suggesting a functional role of this glyco-gene in IBD pathogenesis. Electronic supplementary material The online version of this article (10.1186/s13148-018-0507-y) contains supplementary material, which is available to authorized users.
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23
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Ferdosi S, Rehder DS, Maranian P, Castle EP, Ho TH, Pass HI, Cramer DW, Anderson KS, Fu L, Cole DEC, Le T, Wu X, Borges CR. Stage Dependence, Cell-Origin Independence, and Prognostic Capacity of Serum Glycan Fucosylation, β1-4 Branching, β1-6 Branching, and α2-6 Sialylation in Cancer. J Proteome Res 2018; 17:543-558. [PMID: 29129073 PMCID: PMC5978412 DOI: 10.1021/acs.jproteome.7b00672] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycans represent a promising but only marginally accessed source of cancer markers. We previously reported the development of a molecularly bottom-up approach to plasma and serum (P/S) glycomics based on glycan linkage analysis that captures features such as α2-6 sialylation, β1-6 branching, and core fucosylation as single analytical signals. Based on the behavior of P/S glycans established to date, we hypothesized that the alteration of P/S glycans observed in cancer would be independent of the tissue in which the tumor originated yet exhibit stage dependence that varied little between cancers classified on the basis of tumor origin. Herein, the diagnostic utility of this bottom-up approach as applied to lung cancer patients (n = 127 stage I; n = 20 stage II; n = 81 stage III; and n = 90 stage IV) as well as prostate (n = 40 stage II), serous ovarian (n = 59 stage III), and pancreatic cancer patients (n = 15 rapid autopsy) compared to certifiably healthy individuals (n = 30), nominally healthy individuals (n = 166), and risk-matched controls (n = 300) is reported. Diagnostic performance in lung cancer was stage-dependent, with markers for terminal (total) fucosylation, α2-6 sialylation, β1-4 branching, β1-6 branching, and outer-arm fucosylation most able to differentiate cases from controls. These markers behaved in a similar stage-dependent manner in other types of cancer as well. Notable differences between certifiably healthy individuals and case-matched controls were observed. These markers were not significantly elevated in liver fibrosis. Using a Cox proportional hazards regression model, the marker for α2-6 sialylation was found to predict both progression and survival in lung cancer patients after adjusting for age, gender, smoking status, and stage. The potential mechanistic role of aberrant P/S glycans in cancer progression is discussed.
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Affiliation(s)
- Shadi Ferdosi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, United States
| | - Douglas S. Rehder
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, United States
| | - Paul Maranian
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, United States
| | - Erik P. Castle
- Department of Urology, Mayo Clinic, Phoenix, Arizona 85054, United States
| | - Thai H. Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, Arizona 85054, United States
| | - Harvey I. Pass
- Cardiothoracic Surgery, NYU Langone Medical Center, New York, New York 10016, United States
| | - Daniel W. Cramer
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115, United States
| | - Karen S. Anderson
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, United States
| | - Lei Fu
- Department of Clinical Pathology, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David E. C. Cole
- Department of Clinical Pathology, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tao Le
- University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Xifeng Wu
- University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Chad R. Borges
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, United States
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24
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Keser T, Gornik I, Vučković F, Selak N, Pavić T, Lukić E, Gudelj I, Gašparović H, Biočina B, Tilin T, Wennerström A, Männistö S, Salomaa V, Havulinna A, Wang W, Wilson JF, Chaturvedi N, Perola M, Campbell H, Lauc G, Gornik O. Increased plasma N-glycome complexity is associated with higher risk of type 2 diabetes. Diabetologia 2017; 60:2352-2360. [PMID: 28905229 DOI: 10.1007/s00125-017-4426-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/26/2017] [Indexed: 02/01/2023]
Abstract
AIMS/HYPOTHESIS Better understanding of type 2 diabetes and its prevention is a pressing need. Changes in human plasma N-glycome are associated with many diseases and represent promising diagnostic and prognostic biomarkers. Variations in glucose metabolism directly affect glycosylation through the hexosamine pathway but studies of plasma glycome in type 2 diabetes are scarce. The aim of this study was to determine whether plasma protein N-glycome is changed in individuals who are at greater risk of developing type 2 diabetes. METHODS Using a chromatographic approach, we analysed N-linked glycans from plasma proteins in two populations comprising individuals with registered hyperglycaemia during critical illness (increased risk for development of type 2 diabetes) and individuals who stayed normoglycaemic during the same condition: AcuteInflammation (59 cases vs 49 controls) and AcuteInflammation Replication (52 cases vs 14 controls) populations. N-glycome was also studied in individuals from FinRisk (37 incident cases of type 2 diabetes collected at baseline vs 37 controls), Orkney Complex Disease Study (ORCADES; 94 individuals with HbA1c > 6.5% [47.5 mmol/mol] vs 658 controls) and Southall and Brent Revisited (SABRE) cohort studies (307 individuals with HbA1c > 6.5% [47.5 mmol/mol] vs 307 controls). RESULTS Individuals with increased risk for diabetes type 2 development (AcuteInflammation and AcuteInflammation Replication populations), incident cases of type 2 diabetes collected at baseline (FinRisk population) and individuals with elevated HbA1c (ORCADES and SABRE populations) all presented with increased branching, galactosylation and sialylation of plasma protein N-glycans and these changes were of similar magnitude. CONCLUSIONS/INTERPRETATION Increased complexity of plasma N-glycan structures is associated with higher risk of developing type 2 diabetes and poorer regulation of blood glucose levels. Although further research is needed, this finding could offer a potential new approach for improvement in prevention of diabetes and its complications.
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Affiliation(s)
- Toma Keser
- University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, 10 000, Zagreb, Croatia
| | - Ivan Gornik
- Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | | | - Najda Selak
- University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, 10 000, Zagreb, Croatia
| | - Tamara Pavić
- University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, 10 000, Zagreb, Croatia
| | - Edita Lukić
- Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | - Ivan Gudelj
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Hrvoje Gašparović
- Department of Cardiac Surgery, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Bojan Biočina
- Department of Cardiac Surgery, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Therese Tilin
- Institute of Cardiovascular Science, University College London, London, UK
| | | | - Satu Männistö
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Aki Havulinna
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Nish Chaturvedi
- Institute of Cardiovascular Science, University College London, London, UK
| | - Markus Perola
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Gordan Lauc
- University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, 10 000, Zagreb, Croatia
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Olga Gornik
- University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kovačića 1, 10 000, Zagreb, Croatia.
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Cao L, Qu Y, Zhang Z, Wang Z, Prytkova I, Wu S. Intact glycopeptide characterization using mass spectrometry. Expert Rev Proteomics 2017; 13:513-22. [PMID: 27140194 DOI: 10.1586/14789450.2016.1172965] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Glycosylation is one of the most prominent and extensively studied protein post-translational modifications. However, traditional proteomic studies at the peptide level (bottom-up) rarely characterize intact glycopeptides (glycosylated peptides without removing glycans), so no glycoprotein heterogeneity information is retained. Intact glycopeptide characterization, on the other hand, provides opportunities to simultaneously elucidate the glycan structure and the glycosylation site needed to reveal the actual biological function of protein glycosylation. Recently, significant improvements have been made in the characterization of intact glycopeptides, ranging from enrichment and separation, mass spectroscopy (MS) detection, to bioinformatics analysis. In this review, we recapitulated currently available intact glycopeptide characterization methods with respect to their advantages and limitations as well as their potential applications.
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Affiliation(s)
- Li Cao
- a Pharma Research and Development , R&D Platform Technology & Science, GSK , King of Prussia , PA , USA
| | - Yi Qu
- b ChemEco Division , Evans Analytical Group , Hercules , CA , USA
| | - Zhaorui Zhang
- c Process Research & Development , AbbVie , North Chicago , IL , USA
| | - Zhe Wang
- d Department of Chemistry and Biochemistry , University of Oklahoma , Norman , OK , USA
| | - Iya Prytkova
- d Department of Chemistry and Biochemistry , University of Oklahoma , Norman , OK , USA
| | - Si Wu
- d Department of Chemistry and Biochemistry , University of Oklahoma , Norman , OK , USA
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26
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Noro D, Yoneyama T, Hatakeyama S, Tobisawa Y, Mori K, Hashimoto Y, Koie T, Tanaka M, Nishimura SI, Sasaki H, Saito M, Harada H, Chikaraishi T, Ishida H, Tanabe K, Satoh S, Ohyama C. Serum Aberrant N-Glycan Profile as a Marker Associated with Early Antibody-Mediated Rejection in Patients Receiving a Living Donor Kidney Transplant. Int J Mol Sci 2017; 18:ijms18081731. [PMID: 28786963 PMCID: PMC5578121 DOI: 10.3390/ijms18081731] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/01/2017] [Accepted: 08/07/2017] [Indexed: 02/03/2023] Open
Abstract
We determined if the serum N-glycan profile can be used as a diagnostic marker of antibody-mediated rejection (ABMR) in living donor kidney transplant (LKTx) recipients. Glycoblotting, combined with mass spectrometry, was used to retrospectively examine N-glycan levels in the postoperative sera of 197 LKTx recipients of whom 16 recipients had ABMR with or without T-cell-mediated rejection (TCMR), 40 recipients had TCMR, and 141 recipients had no adverse events. Multivariate discriminant analysis for prediction of ABMR was performed by inputting an ABMR event as an explanatory variable and sex, age, and serum N-glycan level as objective variables. The N-glycan score was calculated by multiplying the level of candidate objective variables by objective function values. The ABMR predictive performance of the N-glycan score was assessed by receiver operator characteristic curve and Kaplan-Meier curve analyses. The N-glycan score discriminated ABMR with 81.25% sensitivity, 87.85% specificity, and an area under the curve (AUC) of 0.892 that was far superior to that of preformed donor-specific antibody status (AUC, 0.761). Recipients with N-glycan-positive scores >0.8770 had significantly shorter ABMR survival than that of recipients with N-glycan-negative scores. Although the limitations of our study includ its small sample size and retrospective nature, the serum N-glycan score may contribute to prediction of ABMR.
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Affiliation(s)
- Daisuke Noro
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Tohru Yoneyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
- Department of Advanced Transplant and Regenerative Medicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Shingo Hatakeyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Yuki Tobisawa
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Kazuyuki Mori
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Yasuhiro Hashimoto
- Department of Advanced Transplant and Regenerative Medicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Takuya Koie
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | - Masakazu Tanaka
- Graduate School of Life Science, Frontier Research Center for Advanced Material and Life Science, Hokkaido University, Sapporo 060-0810, Japan.
| | - Shin-Ichiro Nishimura
- Graduate School of Life Science, Frontier Research Center for Advanced Material and Life Science, Hokkaido University, Sapporo 060-0810, Japan.
| | - Hideo Sasaki
- Department of Urology, St. Marianna University of Medicine, Kawasaki 216-8511, Japan.
| | - Mitsuru Saito
- Department of Urology, Akita University Graduate School of Medicine, Akita 010-8543, Japan.
| | - Hiroshi Harada
- Department of Kidney Transplant Surgery, Sapporo City General Hospital, Sapporo 060-8611, Japan.
| | - Tatsuya Chikaraishi
- Department of Urology, St. Marianna University of Medicine, Kawasaki 216-8511, Japan.
| | - Hideki Ishida
- Department of Urology, Tokyo-Woman's Medical University, Tokyo 162-8666, Japan.
| | - Kazunari Tanabe
- Department of Urology, Tokyo-Woman's Medical University, Tokyo 162-8666, Japan.
| | - Shigeru Satoh
- Department of Urology, Akita University Graduate School of Medicine, Akita 010-8543, Japan.
| | - Chikara Ohyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
- Department of Advanced Transplant and Regenerative Medicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
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Sato R, Tsuchiya KJ, Matsuzaki H, Takei N, Itoh H, Kanayama N, Suda T, Watanabe H, Ohashi T, Tanaka M, Nishimura SI, Maekawa M. Fetal Environment and Glycosylation Status in Neonatal Cord Blood: A Comprehensive Mass Spectrometry-based Glycosylation Analysis. Medicine (Baltimore) 2016; 95:e3219. [PMID: 27057853 PMCID: PMC4998769 DOI: 10.1097/md.0000000000003219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 11/25/2022] Open
Abstract
Fetal environment is known to be a major predictive factor of type 2 diabetes and cardiovascular disease. However, associations of fetal environment and cord blood glycoforms are uncertain. In this study, we aimed to determine whether glycosylation status in neonatal cord blood is associated with perinatal outcomes reflecting a poor fetal environment.Thirty-six low birth weight (LBW) infants and 120 normal birth weight infants were recruited from a longitudinal birth cohort. We conducted a comprehensive cord blood N-glycan analysis using matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. Associations of N-glycans with perinatal outcomes, including LBW, small for gestational age, and levels of cord blood leptin and adiponectin, were evaluated using logistic or multiple regression. We also prospectively explored correlations between N-glycans and 6 or 18-month rapid weight gain (>0.67 SD score).A total of 35 N-glycans were detected (m/z value 1362.481-3865.407). Of these, abundance levels of G3414 (m/z value 3414.238) were inversely correlated with LBW and small for gestational age. Abundance levels of G1915 (m/z value 1914.698), G2744 (m/z value 2743.994), G3049 (m/z value 3049.105), and G3719 (m/z value 3719.349) were inversely related to LBW. The total N-glycan abundance levels were strongly positively correlated with levels of leptin and adiponectin in cord blood. In a prospective exploratory analysis, the 5 LBW-related N-glycans (G1915, G2744, G3049, G3414, and G3719) were all inversely associated with 6 or 18-month rapid weight gain. These N-glycans are structurally categorized into 2 different categories: fucosylated bi or tri-antennary N-glycans; and tri or tetra-antennary N-glycans without fucosylation.In conclusion, mass spectrometry-based cord blood glycosylation analysis shows that 5 types of N-glycans are potential predictors of a poor fetal environment.
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Affiliation(s)
- Ryosuke Sato
- From the Pharmaceuticals and Medical Devices Agency (RS), Tokyo; Department of Internal Medicine II (RS, TS), Hamamatsu University School of Medicine, Hamamatsu; Research Center for Child Mental Development (KJT, HM, NT), Hamamatsu University School of Medicine, Hamamatsu; Research Center for Child Mental Development (HM), University of Fukui, Fukui; Department of Obstetrics and Gynecology (HI, NK); Department of Clinical Pharmacology and Therapeutics (HW), Hamamatsu University School of Medicine, Hamamatsu; Graduate School of Life Science and Frontier Research Center for Post-Genome Science and Technology (TO, MT, S-IN), Hokkaido University, Sapporo; and Department of Laboratory Medicine (MM), Hamamatsu University School of Medicine, Hamamatsu, Japan
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Gizaw ST, Ohashi T, Tanaka M, Hinou H, Nishimura SI. Glycoblotting method allows for rapid and efficient glycome profiling of human Alzheimer's disease brain, serum and cerebrospinal fluid towards potential biomarker discovery. Biochim Biophys Acta Gen Subj 2016; 1860:1716-27. [PMID: 26968461 DOI: 10.1016/j.bbagen.2016.03.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Understanding of the significance of posttranslational glycosylation in Alzheimer's disease (AD) is of growing importance for the investigation of the pathogenesis of AD as well as discovery research of the disease-specific serum biomarkers. METHODS We designed a standard protocol for the glycoblotting combined with MALDI-TOFMS to perform rapid and quantitative profiling of the glycan parts of glycoproteins (N-glycans) and glycosphingolipids (GSLs) using human AD's post-mortem samples such as brain tissues (dissected cerebral cortices such as frontal, parietal, occipital, and temporal domains), serum and cerebrospinal fluid (CSF). RESULTS The structural profiles of the major N-glycans released from glycoproteins and the total expression levels of the glycans were found to be mostly similar between the brain tissues of the AD patients and those of the normal control group. In contrast, the expression levels of the serum and CSF protein N-glycans such as bisect-type and multiply branched glycoforms were increased significantly in AD patient group. In addition, the levels of some gangliosides such as GM1, GM2 and GM3 appeared to alter in the AD patient brain and serum samples when compared with the normal control groups. CONCLUSION Alteration of the expression levels of major N- and GSL-glycans in human brain tissues, serum and CSF of AD patients can be monitored quantitatively by means of the glycoblotting-based standard protocols. GENERAL SIGNIFICANCE The changes in the expression levels of the glycans derived from the human post-mortem samples uncovered by the standardized glycoblotting method provides potential serum biomarkers in central nervous system disorders and can contribute to the insight into the molecular mechanisms in the pathogenesis of neurodegenerative diseases and future drug discovery. Most importantly, the present preliminary trials using human post-mortem samples of AD patients suggest that large-scale serum glycomics cohort by means of various-types of human AD patients as well as the normal control sera can facilitate the discovery research of highly sensitive and reliable serum biomarkers for an early diagnosis of AD. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
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Affiliation(s)
- Solomon T Gizaw
- Field of Drug Discovery Research, Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21 W11, Sapporo 001-0021, Japan
| | - Tetsu Ohashi
- Medicinal Chemistry Pharmaceuticals, Co., Ltd, N21 W12, Sapporo 001-0021, Japan
| | - Masakazu Tanaka
- Medicinal Chemistry Pharmaceuticals, Co., Ltd, N21 W12, Sapporo 001-0021, Japan
| | - Hiroshi Hinou
- Field of Drug Discovery Research, Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21 W11, Sapporo 001-0021, Japan; Medicinal Chemistry Pharmaceuticals, Co., Ltd, N21 W12, Sapporo 001-0021, Japan
| | - Shin-Ichiro Nishimura
- Field of Drug Discovery Research, Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21 W11, Sapporo 001-0021, Japan; Medicinal Chemistry Pharmaceuticals, Co., Ltd, N21 W12, Sapporo 001-0021, Japan.
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29
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Rehan IF, Ueda K, Mitani T, Amano M, Hinou H, Ohashi T, Kondo S, Nishimura SI. Large-Scale Glycomics of Livestock: Discovery of Highly Sensitive Serum Biomarkers Indicating an Environmental Stress Affecting Immune Responses and Productivity of Holstein Dairy Cows. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:10578-10590. [PMID: 26595672 DOI: 10.1021/acs.jafc.5b04304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Because various stresses strongly influence the food productivity of livestock, biomarkers to indicate unmeasurable environmental stress in domestic animals are of increasing importance. Thermal comfort is one of the basic principles of dairy cow welfare that enhances productivity. To discover sensitive biomarkers that monitor such environmental stresses in dairy cows, we herein performed, for the first time, large-scale glycomics on 336 lactating Holstein cow serum samples over 9 months between February and October. Glycoblotting combined with MALDI-TOF/MS and DMB/HPLC allowed for comprehensive glycomics of whole serum glycoproteins. The results obtained revealed seasonal alterations in serum N-glycan levels and their structural characteristics, such as an increase in high-mannose type N-glycans in spring, the occurrence of di/triantennary complex type N-glycans terminating with two or three Neu5Gc residues in summer and autumn, and N-glycans in winter dominantly displaying Neu5Ac. A multivariate analysis revealed a correlation between the serum expression levels of these season-specific glycoforms and productivity.
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Affiliation(s)
- Ibrahim F Rehan
- Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University , N21, W11, Kita-ku, Sapporo 001-0021, Japan
- Animal Behaviour and Management Department, Faculty of Veterinary Medicine, South Valley University , Qena 83523, Egypt
| | - Koichiro Ueda
- Animal Production System, Graduate School of Agriculture, Hokkaido University , N9, W9, Sapporo 060-8589, Japan
| | - Tomohiro Mitani
- Animal Production System, Graduate School of Agriculture, Hokkaido University , N9, W9, Sapporo 060-8589, Japan
| | - Maho Amano
- Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University , N21, W11, Kita-ku, Sapporo 001-0021, Japan
| | - Hiroshi Hinou
- Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University , N21, W11, Kita-ku, Sapporo 001-0021, Japan
| | - Tetsu Ohashi
- Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University , N21, W11, Kita-ku, Sapporo 001-0021, Japan
- Medicinal Chemistry Pharmaceuticals Co., Ltd., N21, W12, Kita-ku, Sapporo 001-0021, Japan
| | - Seiji Kondo
- Animal Production System, Graduate School of Agriculture, Hokkaido University , N9, W9, Sapporo 060-8589, Japan
| | - Shin-Ichiro Nishimura
- Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University , N21, W11, Kita-ku, Sapporo 001-0021, Japan
- Medicinal Chemistry Pharmaceuticals Co., Ltd., N21, W12, Kita-ku, Sapporo 001-0021, Japan
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Tomoda T, Nouso K, Kato H, Miyahara K, Dohi C, Morimoto Y, Kinugasa H, Akimoto Y, Matsumoto K, Yamamoto N, Noma Y, Horiguchi S, Tsutsumi K, Amano M, Nishimura SI, Yamamoto K. Alteration of serum N-glycan profile in patients with autoimmune pancreatitis. Pancreatology 2015; 16:44-51. [PMID: 26723536 DOI: 10.1016/j.pan.2015.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 10/06/2015] [Accepted: 11/10/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The aims of this study were to determine the change in whole-serum N-glycan profile in autoimmune pancreatitis (AIP) patients and to investigate its clinical utility. METHODS We collected serum from 21 AIP patients before any treatment, and from 60 healthy volunteers (HLTs). Serum glycan profile was measured by comprehensive and quantitative high-throughput glycome analysis. RESULTS Of the 53 glycans detected, 14 were differentially expressed in AIP patients. Pathway analysis demonstrated that agalactosyl and monogalactosyl bi-antennary glycans were elevated in AIP patients. Among the 14 glycans, #3410, #3510, and #4510 showed high area under receiver operating characteristic (AUROC) values (0.955, 0.964, and 0.968 respectively) for the diagnosis of AIP. These three glycans were mainly bound to immunoglobulin G; however, their serum levels were significantly higher, even in AIP patients who showed lower serum IgG4 levels, than in HLTs. CONCLUSIONS We demonstrated, for the first time, whole-serum glycan profiles of AIP patients and showed that the levels of glycans #3410, #3510, and #4510 were increased in AIP patients. These glycans might be valuable biomarkers of AIP.
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Affiliation(s)
- Takeshi Tomoda
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan.
| | - Kazuhiro Nouso
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Hironari Kato
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Koji Miyahara
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Chihiro Dohi
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Yuki Morimoto
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Hideaki Kinugasa
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Yutaka Akimoto
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Kazuyuki Matsumoto
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Naoki Yamamoto
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Yasuhiro Noma
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Shigeru Horiguchi
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Koichiro Tsutsumi
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Maho Amano
- Field of Drug Discovery Research, Faculty of Advanced Life Science & Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan; Medicinal Chemistry Pharmaceuticals, Co., Ltd., Sapporo, Hokkaido, Japan
| | - Shin-Ichiro Nishimura
- Field of Drug Discovery Research, Faculty of Advanced Life Science & Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan; Medicinal Chemistry Pharmaceuticals, Co., Ltd., Sapporo, Hokkaido, Japan
| | - Kazuhide Yamamoto
- Departments of Gastroenterology & Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
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Miura Y, Hashii N, Tsumoto H, Takakura D, Ohta Y, Abe Y, Arai Y, Kawasaki N, Hirose N, Endo T. Change in N-Glycosylation of Plasma Proteins in Japanese Semisupercentenarians. PLoS One 2015; 10:e0142645. [PMID: 26559536 PMCID: PMC4641608 DOI: 10.1371/journal.pone.0142645] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/23/2015] [Indexed: 12/26/2022] Open
Abstract
An N-glycomic analysis of plasma proteins was performed in Japanese semisupercentenarians (SSCs) (mean 106.7 years), aged controls (mean 71.6 years), and young controls (mean 30.2 years) by liquid chromatography/mass spectrometry (LC/MS) using a graphitized carbon column. Characteristic N-glycans in SSCs were discriminated using a multivariate analysis; orthogonal projections to latent structures (O-PLS). The results obtained showed that multi-branched and highly sialylated N-glycans as well as agalacto- and/or bisecting N-glycans were increased in SSCs, while biantennary N-glycans were decreased. Since multi-branched and highly sialylated N-glycans have been implicated in anti-inflammatory activities, these changes may play a role in the enhanced chronic inflammation observed in SSCs. The levels of inflammatory proteins, such as CRP, adiponectin, IL-6, and TNF-α, were elevated in SSCs. These results suggested that responses to inflammation may play an important role in extreme longevity and healthy aging in humans. This is the first study to show that the N-glycans of plasma proteins were associated with extreme longevity and healthy aging in humans.
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Affiliation(s)
- Yuri Miura
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Daisuke Takakura
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
| | - Yuki Ohta
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
| | - Yukiko Abe
- Center for Supercentenarian Research, Keio University School of Medicine, Tokyo, Japan
| | - Yasumichi Arai
- Center for Supercentenarian Research, Keio University School of Medicine, Tokyo, Japan
| | - Nana Kawasaki
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
| | - Nobuyoshi Hirose
- Center for Supercentenarian Research, Keio University School of Medicine, Tokyo, Japan
| | - Tamao Endo
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
- * E-mail:
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Gizaw ST, Koda T, Amano M, Kamimura K, Ohashi T, Hinou H, Nishimura SI. A comprehensive glycome profiling of Huntington's disease transgenic mice. Biochim Biophys Acta Gen Subj 2015; 1850:1704-18. [DOI: 10.1016/j.bbagen.2015.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/28/2015] [Accepted: 04/15/2015] [Indexed: 12/13/2022]
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Inafuku S, Noda K, Amano M, Nishimura SI, Ishida S. Increase of SialylatedN-Glycansin Eyes with Neovascular Glaucoma Secondary to Proliferative Diabetic Retinopathy. Curr Eye Res 2015; 41:721-4. [DOI: 10.3109/02713683.2015.1068816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
BACKGROUND Glycobiology is an underexplored research area in inflammatory bowel disease (IBD), and glycans are relevant to many etiological mechanisms described in IBD. Alterations in N-glycans attached to the immunoglobulin G (IgG) Fc fragment can affect molecular structure and immunological function. Recent genome-wide association studies reveal pleiotropy between IBD and IgG glycosylation. This study aims to explore IgG glycan changes in ulcerative colitis (UC) and Crohn's disease (CD). METHODS IgG glycome composition in patients with UC (n = 507), CD (n = 287), and controls (n = 320) was analyzed by ultra performance liquid chromatography. RESULTS Statistically significant differences in IgG glycome composition between patients with UC or CD, compared with controls, were observed. Both UC and CD were associated with significantly decreased IgG galactosylation (digalactosylation, UC: odds ratio [OR] = 0.71; 95% confidence interval [CI], 0.5-0.9; P = 0.01; CD: OR = 0.41; CI, 0.3-0.6; P = 1.4 × 10) and significant decrease in the proportion of sialylated structures in CD (OR = 0.46, CI, 0.3-0.6, P = 8.4 × 10). Logistic regression models incorporating measured IgG glycan traits were able to distinguish UC and CD from controls (UC: P = 2.13 × 10 and CD: P = 2.20 × 10), with receiver-operator characteristic curves demonstrating better performance of the CD model (area under curve [AUC] = 0.77) over the UC model (AUC = 0.72) (P = 0.026). The ratio of the presence to absence of bisecting GlcNAc in monogalactosylated structures was increased in patients with UC undergoing colectomy compared with no colectomy (FDR-adjusted, P = 0.05). CONCLUSIONS The observed differences indicate significantly increased inflammatory potential of IgG in IBD. Changes in IgG glycosylation may contribute to IBD pathogenesis and could alter monoclonal antibody therapeutic efficacy. IgG glycan profiles have translational potential as IBD biomarkers.
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35
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Changes to serum sample tube and processing methodology does not cause Intra-Individual [corrected] variation in automated whole serum N-glycan profiling in health and disease. PLoS One 2015; 10:e0123028. [PMID: 25831126 PMCID: PMC4382121 DOI: 10.1371/journal.pone.0123028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/16/2015] [Indexed: 01/08/2023] Open
Abstract
Introduction Serum N-glycans have been identified as putative biomarkers for numerous diseases. The impact of different serum sample tubes and processing methods on N-glycan analysis has received relatively little attention. This study aimed to determine the effect of different sample tubes and processing methods on the whole serum N-glycan profile in both health and disease. A secondary objective was to describe a robot automated N-glycan release, labeling and cleanup process for use in a biomarker discovery system. Methods 25 patients with active and quiescent inflammatory bowel disease and controls had three different serum sample tubes taken at the same draw. Two different processing methods were used for three types of tube (with and without gel-separation medium). Samples were randomised and processed in a blinded fashion. Whole serum N-glycan release, 2-aminobenzamide labeling and cleanup was automated using a Hamilton Microlab STARlet Liquid Handling robot. Samples were analysed using a hydrophilic interaction liquid chromatography/ethylene bridged hybrid(BEH) column on an ultra-high performance liquid chromatography instrument. Data were analysed quantitatively by pairwise correlation and hierarchical clustering using the area under each chromatogram peak. Qualitatively, a blinded assessor attempted to match chromatograms to each individual. Results There was small intra-individual variation in serum N-glycan profiles from samples collected using different sample processing methods. Intra-individual correlation coefficients were between 0.99 and 1. Unsupervised hierarchical clustering and principal coordinate analyses accurately matched samples from the same individual. Qualitative analysis demonstrated good chromatogram overlay and a blinded assessor was able to accurately match individuals based on chromatogram profile, regardless of disease status. Conclusions The three different serum sample tubes processed using the described methods cause minimal inter-individual variation in serum whole N-glycan profile when processed using an automated workstream. This has important implications for N-glycan biomarker discovery studies using different serum processing standard operating procedures.
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Ventham NT, Kalla R, Kennedy NA, Satsangi J, Arnott ID. Predicting outcomes in acute severe ulcerative colitis. Expert Rev Gastroenterol Hepatol 2015; 9:405-15. [PMID: 25494666 DOI: 10.1586/17474124.2015.992880] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Response to corticosteroid treatment in acute severe ulcerative colitis (ASUC) has changed very little in the past 50 years. Predicting those at risk at an early stage helps stratify patients into those who may require second line therapy or early surgical treatment. Traditionally, risk scores have used a combination of clinical, radiological and biochemical parameters; established indices include the 'Travis' and 'Ho' scores. Recently, inflammatory bowel disease genetic risk alleles have been built into models to predict outcome in ASUC. Given the multifactorial nature of inflammatory bowel disease pathogenesis, in the future, composite scores integrating clinical, biochemical, serological, genetic and other '-omic' data will be increasingly investigated. Although these new genetic prediction models are promising, they have yet to supplant traditional scores, which remain the best practice. In this modern era of rescue therapies in ASUC, robust scoring systems to predict failure of ciclosporine and infliximab must be devised.
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Affiliation(s)
- Nicholas T Ventham
- Centre for Genomics and Molecular medicine, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
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Yamasaki Y, Nouso K, Miyahara K, Wada N, Dohi C, Morimoto Y, Kinugasa H, Takeuchi Y, Yasunaka T, Kuwaki K, Onishi H, Ikeda F, Miyake Y, Nakamura S, Shiraha H, Takaki A, Iwasaki Y, Amano M, Nishimura SI, Yamamoto K. Use of non-invasive serum glycan markers to distinguish non-alcoholic steatohepatitis from simple steatosis. J Gastroenterol Hepatol 2015; 30:528-34. [PMID: 25168691 DOI: 10.1111/jgh.12726] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/06/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Serum glycans have been reported to be promising diagnostic markers for many inflammatory diseases and cancers. The aims of this study were to investigate whole glycan expression in patients with non-alcoholic fatty liver diseases and to evaluate the potential use of glycan profiles as new clinical biomarkers to distinguish non-alcoholic steatohepatitis (NASH) from simple steatosis (SS). METHODS We collected sera from 42 histologically proven NASH and 15 SS patients prior to treatment. Serum glycan profiles were measured by comprehensive, quantitative, high-throughput glycome analysis, and diagnostic values of serum glycans for NASH prediction were examined. RESULTS Among the 41 serum glycans examined, the expression levels of 8 glycans in NASH were significantly higher than those of SS. Out of these eight glycans, three glycans (m/z 1955, 2032, and 2584) showed high areas under the receiver operating characteristic curve (0.833, 0.863, and 0.866, respectively) for distinguishing NASH from SS. In multivariate analyses with clinical parameters and serum glycans, these three glycans were significant predictive factors for distinguishing NASH from SS. The odds ratio of m/z 1955, 2032, and 2584 were 48.5, 6.46, and 11.8, respectively. These glycans also correlated significantly with lobular inflammation, ballooning, and fibrosis, but not with steatosis. CONCLUSION We clearly demonstrated whole-serum glycan profiles in NASH patients, and the feasibility of serum glycans (m/z 1955, 2032, and 2584) as new noninvasive biomarkers for distinguishing NASH from SS.
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Affiliation(s)
- Yasushi Yamasaki
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Okayama
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Theodoratou E, Campbell H, Ventham NT, Kolarich D, Pučić-Baković M, Zoldoš V, Fernandes D, Pemberton IK, Rudan I, Kennedy NA, Wuhrer M, Nimmo E, Annese V, McGovern DPB, Satsangi J, Lauc G. The role of glycosylation in IBD. Nat Rev Gastroenterol Hepatol 2014; 11:588-600. [PMID: 24912389 DOI: 10.1038/nrgastro.2014.78] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A number of genetic and immunological studies give impetus for investigating the role of glycosylation in IBD. Experimental mouse models have helped to delineate the role of glycosylation in intestinal mucins and to explore the putative pathogenic role of glycosylation in colitis. These experiments have been extended to human studies investigating the glycosylation patterns of intestinal mucins as well as levels of glycans of serum glycoproteins and expression of glycan receptors. These early human studies have generated interesting hypotheses regarding the pathogenic role of glycans in IBD, but have generally been restricted to fairly small underpowered studies. Decreased glycosylation has been observed in the intestinal mucus of patients with IBD, suggesting that a defective inner mucus layer might lead to increased bacterial contact with the epithelium, potentially triggering inflammation. In sera, decreased galactosylation of IgG has been suggested as a diagnostic marker for IBD. Advances in glycoprofiling technology make it technically feasible and affordable to perform high-throughput glycan pattern analyses and to build on previous work investigating a much wider range of glycan parameters in large numbers of patients.
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Affiliation(s)
- Evropi Theodoratou
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, EH8 9AG, Edinburgh, UK
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, EH8 9AG, Edinburgh, UK
| | - Nicholas T Ventham
- Centre for Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Edinburgh, UK
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1 OT Golm, 14476, Potsdam, Germany
| | | | - Vlatka Zoldoš
- University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
| | | | - Iain K Pemberton
- IP Research Consulting SAS, 34 Rue Carnot, 93160 Noisy-le-Grand, Paris, France
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, EH8 9AG, Edinburgh, UK
| | - Nicholas A Kennedy
- Centre for Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Edinburgh, UK
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Elaine Nimmo
- Centre for Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Edinburgh, UK
| | - Vito Annese
- Department of Medical and Surgical Specialities, Division of Gastroenterology, AOU Careggi University Hospital, Largo Brambilla 13, 50139 Florence, Italy
| | - Dermot P B McGovern
- F.Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Suite D4063, Los Angeles, CA 90048, USA
| | - Jack Satsangi
- Centre for Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Edinburgh, UK
| | - Gordan Lauc
- Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry, Trg maršala Tita 14, 10000 Zagreb, Croatia
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A comparison of N-glycan profiles in human plasma and vitreous fluid. Graefes Arch Clin Exp Ophthalmol 2014; 252:1235-43. [DOI: 10.1007/s00417-014-2671-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/30/2014] [Accepted: 05/08/2014] [Indexed: 01/31/2023] Open
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40
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Ishihara T, Kakiya K, Takahashi K, Miwa H, Rokushima M, Yoshinaga T, Tanaka Y, Ito T, Togame H, Takemoto H, Amano M, Iwasaki N, Minami A, Nishimura SI. Discovery of novel differentiation markers in the early stage of chondrogenesis by glycoform-focused reverse proteomics and genomics. Biochim Biophys Acta Gen Subj 2013; 1840:645-55. [PMID: 24161698 DOI: 10.1016/j.bbagen.2013.10.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/20/2013] [Accepted: 10/16/2013] [Indexed: 12/18/2022]
Abstract
BACKGROUND Osteoarthritis (OA) is one of the most common chronic diseases among adults, especially the elderly, which is characterized by destruction of the articular cartilage. Despite affecting more than 100 million individuals all over the world, therapy is currently limited to treating pain, which is a principal symptom of OA. New approaches to the treatment of OA that induce regeneration and repair of cartilage are strongly needed. METHODS To discover potent markers for chondrogenic differentiation, glycoform-focused reverse proteomics and genomics were performed on the basis of glycoblotting-based comprehensive approach. RESULTS Expression levels of high-mannose type N-glycans were up-regulated significantly at the late stage of differentiation of the mouse chondroprogenitor cells. Among 246 glycoproteins carrying this glycotype identified by ConA affinity chromatography and LC/MS, it was demonstrated that 52% are classified as cell surface glycoproteins. Gene expression levels indicated that mRNAs for 15 glycoproteins increased distinctly in the earlier stages during differentiation compared with Type II collagen. The feasibility of mouse chondrocyte markers in human chondrogenesis model was demonstrated by testing gene expression levels of these 15 glycoproteins during differentiation in human mesenchymal stem cells. CONCLUSION The results showed clearly an evidence of up-regulation of 5 genes, ectonucleotide pyrophosphatase/phosphodiesterase family member 1, collagen alpha-1(III) chain, collagen alpha-1(XI) chain, aquaporin-1, and netrin receptor UNC5B, in the early stages of differentiation. GENERAL SIGNIFICANCE These cell surface 5 glycoproteins become highly sensitive differentiation markers of human chondrocytes that contribute to regenerative therapies, and development of novel therapeutic reagents.
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Affiliation(s)
- Takeshi Ishihara
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co. Ltd., Kita-ku, Sapporo 001-0021, Japan
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