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Kontodimas V, Yaman M, Greis K, Lettow M, Pagel K, Marianski M. Reinvestigation of the internal glycan rearrangement of Lewis a and blood group type H1 epitopes. Phys Chem Chem Phys 2024; 26:14160-14170. [PMID: 38712976 PMCID: PMC11147448 DOI: 10.1039/d3cp04491b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Protonated ions of fucose-containing oligosaccharides are prone to undergo internal glycan rearrangement which results in chimeric fragments that obfuscate mass-spectrometric analysis. Lack of accessible tools that would facilitate systematic analysis of glycans in the gas phase limits our understanding of this phenomenon. In this work, we use density functional theory modeling to interpret cryogenic IR spectra of Lewis a and blood group type H1 trisaccharides and to establish whether these trisaccharides undergo the rearrangement during gas-phase analysis. Structurally unconstrained search reveals that none of the parent ions constitute a thermodynamic global minimum. In contrast, predicted collision cross sections and anharmonic IR spectra provide a good match to available experimental data which allowed us to conclude that fucose migration does not occur in these antigens. By comparing the predicted structures with those obtained for Lewis x and blood group type H2 epitopes, we demonstrate that the availability of the mobile proton and a large difference in the relative stability of the parent ions and rearrangement products constitute the prerequisites for the rearrangement reaction.
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Affiliation(s)
- Vasilis Kontodimas
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
| | - Murat Yaman
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Kim Greis
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Maike Lettow
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Mateusz Marianski
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
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2
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Darula Z, Pap Á, Medzihradszky KF. Extended Sialylated O-Glycan Repertoire of Human Urinary Glycoproteins Discovered and Characterized Using Electron-Transfer/Higher-Energy Collision Dissociation. J Proteome Res 2018; 18:280-291. [PMID: 30407017 DOI: 10.1021/acs.jproteome.8b00587] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A relatively novel activation technique, electron-transfer/higher-energy collision dissociation (EThcD) was used in the LC-MS/MS analysis of tryptic glycopeptides enriched with wheat germ agglutinin from human urine samples. We focused on the characterization of mucin-type O-glycopeptides. EThcD in a single spectrum provided information on both the peptide modified and the glycan carried. Unexpectedly, glycan oxonium ions indicated the presence of O-acetyl, and even O-diacetyl-sialic acids. B and Y fragment ions revealed that (i) in core 1 structures the Gal residue featured the O-acetyl-sialic acid, when there was only one in the glycan; (ii) several glycopeptides featured core 1 glycans with disialic acids, in certain instances O-acetylated; (iii) the disialic acid was linked to the GalNAc residue whatever the degree of O-acetylation; (iv) core 2 isomers with a single O-acetyl-sialic acid were chromatographically resolved. Glycan fragmentation also helped to decipher additional core 2 oligosaccharides: a LacdiNAc-like structure, glycans carrying sialyl LewisX/A at different stages of O-acetylation, and blood antigens. A sialo core 3 structure was also identified. We believe this is the first study when such structures were characterized from a very complex mixture and were linked not only to a specific protein, but also the sites of modifications have been determined.
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Affiliation(s)
- Zsuzsanna Darula
- Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62. , H-6726 Szeged , Hungary
| | - Ádám Pap
- Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62. , H-6726 Szeged , Hungary.,Doctoral School in Biology, Faculty of Science and Informatics , University of Szeged , Kozep fasor 52. , H-6726 Szeged , Hungary
| | - Katalin F Medzihradszky
- Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62. , H-6726 Szeged , Hungary
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3
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Hirano M. An Endocytic Receptor, Megalin-Ligand Interactions: Effects of Glycosylation. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1752.1j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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Hirano M. An Endocytic Receptor, Megalin-Ligand Interactions: Effects of Glycosylation. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1752.1e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Miura Y, Hashii N, Ohta Y, Itakura Y, Tsumoto H, Suzuki J, Takakura D, Abe Y, Arai Y, Toyoda M, Kawasaki N, Hirose N, Endo T. Characteristic glycopeptides associated with extreme human longevity identified through plasma glycoproteomics. Biochim Biophys Acta Gen Subj 2018; 1862:1462-1471. [PMID: 29580922 DOI: 10.1016/j.bbagen.2018.03.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/07/2018] [Accepted: 03/21/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Glycosylation is highly susceptible to changes of the physiological conditions, and accordingly, is a potential biomarker associated with several diseases and/or longevity. Semi-supercentenarians (SSCs; older than 105 years) are thought to be a model of human longevity. Thus, we performed glycoproteomics using plasma samples of SSCs, and identified proteins and conjugated N-glycans that are characteristic of extreme human longevity. METHODS Plasma proteins from Japanese semi-supercentenarians (SSCs, 106-109 years), aged controls (70-88 years), and young controls (20-38 years) were analysed by using lectin microarrays and liquid chromatography/mass spectrometry (LC/MS). Peak area ratios of glycopeptides to corresponding normalising peptides were subjected to orthogonal projections to latent structures discriminant analysis (OPLS-DA). Furthermore, plasma levels of clinical biomarkers were measured. RESULTS We found two lectins such as Phaseolus vulgaris, and Erythrina cristagalli (ECA), of which protein binding were characteristically increased in SSCs. Peak area ratios of ECA-enriched glycopeptides were successfully discriminated between SSCs and controls using OPLS-DA, and indicated that tri-antennary and sialylated N-glycans of haptoglobin at Asn207 and Asn211 sites were characterized in SSCs. Sialylated glycans of haptoglobin are a potential biomarker of several diseases, such as hepatocellular carcinoma, liver cirrhosis, and IgA-nephritis. However, the SSCs analysed here did not suffer from these diseases. CONCLUSIONS Tri-antennary and sialylated N-glycans on haptoglobin at the Asn207 and Asn211 sites were abundant in SSCs and characteristic of extreme human longevity. GENERAL SIGNIFICANCE We found abundant glycans in SSCs, which may be associated with human longevity.
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Affiliation(s)
- Yuri Miura
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 3-25-26 Tono-machi, Kawasaki-ku, Kawasaki-shi 210-9501, Kanagawa, Japan
| | - Yuki Ohta
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 3-25-26 Tono-machi, Kawasaki-ku, Kawasaki-shi 210-9501, Kanagawa, Japan
| | - Yoko Itakura
- Research Team for Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Junya Suzuki
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 3-25-26 Tono-machi, Kawasaki-ku, Kawasaki-shi 210-9501, Kanagawa, Japan
| | - Daisuke Takakura
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 3-25-26 Tono-machi, Kawasaki-ku, Kawasaki-shi 210-9501, Kanagawa, Japan
| | - Yukiko Abe
- Center for Supercentenarian Medical Research, Keio University School of Medicine, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yasumichi Arai
- Center for Supercentenarian Medical Research, Keio University School of Medicine, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masashi Toyoda
- Research Team for Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Nana Kawasaki
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 3-25-26 Tono-machi, Kawasaki-ku, Kawasaki-shi 210-9501, Kanagawa, Japan
| | - Nobuyoshi Hirose
- Center for Supercentenarian Medical Research, Keio University School of Medicine, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Tamao Endo
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan.
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Noro E, Togayachi A, Sato T, Tomioka A, Fujita M, Sukegawa M, Suzuki N, Kaji H, Narimatsu H. Large-Scale Identification of N-Glycan Glycoproteins Carrying Lewis x and Site-Specific N-Glycan Alterations in Fut9 Knockout Mice. J Proteome Res 2015; 14:3823-34. [PMID: 26244810 DOI: 10.1021/acs.jproteome.5b00178] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The Lewis x (Le(x)) structure (Galβ1-4(Fucα1-3)GlcNAc-R) is a carbohydrate epitope comprising the stage-specific embryonic antigen-1 (SSEA-1) and CD15, and it is synthesized by α1,3-fucosyltransferase 9 (Fut9). Fut9 is expressed specifically in the stomach, kidney, brain, and in leukocytes, suggesting a specific function in these tissues. In this study, the N-linked glycan mass spectrometry profile of wild-type mouse kidney glycoproteins revealed the presence of abundant terminal fucoses, which were lost following knockout of the Fut9 gene; the terminal fucose was therefore concluded to be Le(x). These results suggested that Le(x) presence is widespread rather than being limited to specific proteins. We endeavored to comprehensively identify the Le(x) carriers in the mouse kidney. Glycopeptides carrying fucosylated glycans were collected by Aleuria aurantia lectin (AAL) affinity chromatography from kidney homogenates of wild-type and Fut9 knockout mice. The site-specific N-glycomes on the glycopeptides were subsequently analyzed by adopting a new glycoproteomic technology composed of dissociation-independent assignment of glycopeptide signals and accurate mass-based prediction of the N-glycome on the glycopeptides. Our analyses demonstrated that 24/32 glycoproteins contained the Le(x) N-glycan structure in wild-type kidney; of these, Le(x) was lost from 21 in the knockout mice. This is the first report of large-scale identification of Le(x)-carrying glycoproteins from a native sample based on the site-specific glycome analysis.
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Affiliation(s)
- Erika Noro
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan.,Department of Biomolecular Function, Doctoral Program in Life System Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
| | - Akira Togayachi
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Takashi Sato
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Azusa Tomioka
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Mika Fujita
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Masako Sukegawa
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Nami Suzuki
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Hiroyuki Kaji
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan
| | - Hisashi Narimatsu
- Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba 305-8568, Japan.,Department of Biomolecular Function, Doctoral Program in Life System Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
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Saraswat M, Joenväära S, Musante L, Peltoniemi H, Holthofer H, Renkonen R. N-linked (N-) glycoproteomics of urinary exosomes. [Corrected]. Mol Cell Proteomics 2014; 14:263-76. [PMID: 25452312 DOI: 10.1074/mcp.m114.040345] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Epithelial cells lining the urinary tract secrete urinary exosomes (40-100 nm) that can be targeted to specific cells modulating their functionality. One potential targeting mechanism is adhesion between vesicle surface glycoproteins and target cells. This makes the glycopeptide analysis of exosomes important. Exosomes reflect the physiological state of the parent cells; therefore, they are a good source of biomarkers for urological and other diseases. Moreover, the urine collection is easy and noninvasive and urinary exosomes give information about renal and systemic organ systems. Accordingly, multiple studies on proteomic characterization of urinary exosomes in health and disease have been published. However, no systematic analysis of their glycoproteomic profile has been carried out to date, whereas a conserved glycan signature has been found for exosomes from urine and other sources including T cell lines and human milk. Here, we have enriched and identified the N-glycopeptides from these vesicles. These enriched N-glycopeptides were solved for their peptide sequence, glycan composition, structure, and glycosylation site using collision-induced dissociation MS/MS (CID-tandem MS) data interpreted by a publicly available software GlycopeptideId. Released glycans from the same sample was also analyzed with MALDI-MS. We have identified the N-glycoproteome of urinary exosomes. In total 126 N-glycopeptides from 51 N-glycosylation sites belonging to 37 glycoproteins were found in our results. The peptide sequences of these N-glycopeptides were identified unambiguously and their glycan composition (for 125 N-glycopeptides) and structures (for 87 N-glycopeptides) were proposed. A corresponding glycomic analysis with released N-glycans was also performed. We identified 66 unique nonmodified N-glycan compositions and in addition 13 sulfated/phosphorylated glycans were also found. This is the first systematic analysis of N-glycoproteome of urinary exosomes.
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Affiliation(s)
- Mayank Saraswat
- From the ‡Transplantation Laboratory, Haartman Institute, PO Box 21, Haartmaninkatu 3, FI-00014 University of Helsinki, Finland
| | - Sakari Joenväära
- §HUSLAB, Helsinki University Central Hospital, Helsinki, Finland
| | - Luca Musante
- ¶Centre for Bioanalytical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Hannu Peltoniemi
- ‖Applied Numerics Ltd, Nuottapolku 10 A 8, 00330 Helsinki, Finland
| | - Harry Holthofer
- ¶Centre for Bioanalytical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Risto Renkonen
- From the ‡Transplantation Laboratory, Haartman Institute, PO Box 21, Haartmaninkatu 3, FI-00014 University of Helsinki, Finland; §HUSLAB, Helsinki University Central Hospital, Helsinki, Finland;
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Ashline DJ, Hanneman AJS, Zhang H, Reinhold VN. Structural documentation of glycan epitopes: sequential mass spectrometry and spectral matching. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:444-53. [PMID: 24385394 PMCID: PMC3950938 DOI: 10.1007/s13361-013-0776-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/09/2013] [Accepted: 10/09/2013] [Indexed: 05/27/2023]
Abstract
Documenting mass spectral data is a fundamental aspect of accepted protocols. In this report, we contrast MS(n) sequential disassembly spectra obtained from natural and synthetic glycan epitopes. The epitopes considered are clusters found on conjugate termini of lipids and N- and O-glycans of proteins. The latter are most frequently pendant through a CID-labile HexNAc glycosidic linkage. The synthetic samples were supplied by collaborating colleagues and commercial sources and usually possessed a readily released reducing-end linker, a by-product of synthesis. All samples were comparably methylated, extracted, and MS(n) disassembled to compare their linkage and branching spectral details. Both sample types provide B-ion type fragments early in a disassembly pathway and their compositions are a suggestion of structure. Further steps of disassembly are necessary to confirm the details of linkage and branching. Included in this study were various Lewis and H antigens, 3- and 6-linked sialyl-lactosamine, NeuAc-2,8-NeuAc dimer, and Galα1,3Gal. Sample infusion provided high quality spectral data whereas disassembly to small fragments generates reproducible high signal/noise spectra for spectral matching. All samples were analyzed as sodium adducted positive ions. This study includes comparability statistics and evaluations on several mass spectrometers.
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Affiliation(s)
| | | | - Hailong Zhang
- The Glycomics Center, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824
| | - Vernon N. Reinhold
- The Glycomics Center, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824
- Glycan Connections, LLC, Lee, New Hampshire, 03861
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9
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Rho JH, Lampe PD. High-Throughput Analysis of Plasma Hybrid Markers for Early Detection of Cancers. Proteomes 2014; 2:1-17. [PMID: 28250367 PMCID: PMC5302729 DOI: 10.3390/proteomes2010001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/17/2013] [Accepted: 01/08/2014] [Indexed: 12/29/2022] Open
Abstract
Biomarkers for the early detection of cancer in the general population have to perform with high sensitivity and specificity in order to prevent the costs associated with over-diagnosis. There are only a few current tissue or blood markers that are recommended for generalized cancer screening. Despite the recognition that combinations of multiple biomarkers will likely improve their utility, biomarker panels are usually limited to a single class of molecules. Tissues and body fluids including plasma and serum contain not only proteins, DNA and microRNAs that are differentially expressed in cancers but further cancer specific information might be gleaned by comparing different classes of biomolecules. For example, the level of a certain microRNA might be related to the level of a particular protein in a cancer specific manner. Proteins might have cancer-specific post-translational modifications (e.g., phosphorylation or glycosylation) or lead to the generation of autoantibodies. Most currently approved biomarkers are glycoproteins. Autoantibodies can be produced as a host's early surveillance response to cancer-specific proteins in pre-symptomatic and pre-diagnostic stages of cancer. Thus, measurement of the level of a protein, the level of its glycosylation or phosphorylation and whether autoantibodies are produced to it can yield multi-dimensional information on each protein. We consider specific proteins that show consistent cancer-specific changes in two or three of these measurements to be "hybrid markers". We hypothesize these markers will suffer less variation between different individuals since one component can act to "standardize" the other measurement. As a proof of principle, a 180 plasma sample set consisting of 120 cases (60 colon cancers and 60 adenomas) and 60 controls were analyzed using our high-density antibody array for changes in their protein, IgG-complex and sialyl-Lewis A (SLeA) modified proteins. At p < 0.05, expression changes in 1,070 proteins, 49 IgG-complexes (11 present in the protein list) and 488 Lewis X-modified proteins (57 on the protein list) were observed. The biomarkers significant on both lists are potential hybrid markers. Thus, plasma hybrid markers have the potential to create a new class of early detection markers of cancers.
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Affiliation(s)
- Jung-Hyun Rho
- Translational Research Program, Human Biology and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.
| | - Paul D Lampe
- Translational Research Program, Human Biology and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.
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Discovery of sialyl Lewis A and Lewis X modified protein cancer biomarkers using high density antibody arrays. J Proteomics 2013; 96:291-9. [PMID: 24185138 DOI: 10.1016/j.jprot.2013.10.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/05/2013] [Accepted: 10/19/2013] [Indexed: 01/14/2023]
Abstract
UNLABELLED We report on a high-dimensional method to globally profile glycoproteins that are modified with sialyl Lewis A or Lewis X glycans. Specifically, glycoproteins in serum or plasma are fractionated on a high-density antibody microarray (i.e., each are localized to their specific antibody spot) and are specifically detected via fluorescently labeled anti-sialyl Lewis A or anti-Lewis X antibodies with quantification in a microarray scanner. Non-glycosylated proteins or glycoproteins with other glycan motifs do not interfere with this assay. The whole process is very rapid and applicable for high-throughput screening without the need for purification of glycoproteins from the samples. Using these methods, sialyl Lewis A or Lewis X moieties were found to be expressed on many previously unreported secreted or membrane associated proteins. Furthermore, the combination of sialyl Lewis A or Lewis X content with protein level increased the ability of certain glycoproteins to distinguish 30 patients with stage III and IV colon cancer from 60 control samples. Thus, this highly sensitive method is capable of discovering novel specific glycan modifications on proteins, many of which will likely be useful for disease detection and monitoring. BIOLOGICAL SIGNIFICANCE In this paper, we show that we can detect cancer-specific glycan modifications on thousands of proteins using a high-density antibody array paired with a glycan specific antibody to probe the bound glycoproteins. To our knowledge, our array is by far the largest and densest that has ever been used for global profiling of specific glycan modification on proteins. Analysis of colon cancer patient plasma for sialyl Lewis A and Lewis X modifications revealed previously unknown protein carriers of these modifications and significant increases in these specific glycans on some proteins in people with cancer versus healthy controls, suggesting this method could be used to discover novel biomarkers.
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Abstract
Extracellular glycoproteins frequently carry terminal sialic acids on their N-linked and/or O-linked glycan structures. In this chapter a sialic acid specific capture-and-release protocol for the enrichment of N- and O-glycopeptides originating from glycoproteins in complex biological samples is described. The enriched glycopeptides are subjected to reversed phase liquid chromatography (LC) interfaced with electrospray ionization and multistage tandem mass spectrometry (MS(n)). The glycopeptide precursor ions are fragmented by collision-induced dissociation (CID) for analysis of the glycan parts in the MS(2) spectra. Further fragmentation (i.e., MS(3)) of deglycosylated peptide ions results in peptide backbone fragmentation, which is used in protein database searches to identify protein sequences. For O-glycopeptides the use of both CID and electron capture dissociation (ECD) fragmentation of the peptide backbone with intact glycans still attached are used to pinpoint the glycosylation sites of glycopeptides containing several Ser/Thr residues. The step-by-step protocols for fragmentation analyses of O- and N-glycopeptides enriched from human cerebrospinal fluid are described.
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Affiliation(s)
- Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.
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12
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Ongay S, Boichenko A, Govorukhina N, Bischoff R. Glycopeptide enrichment and separation for protein glycosylation analysis. J Sep Sci 2012; 35:2341-72. [DOI: 10.1002/jssc.201200434] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | | | | | - Rainer Bischoff
- Department of Analytical Biochemistry; University of Groningen; Groningen The Netherlands
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13
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Nilsson J, Halim A, Grahn A, Larson G. Targeting the glycoproteome. Glycoconj J 2012; 30:119-36. [PMID: 22886069 PMCID: PMC3552370 DOI: 10.1007/s10719-012-9438-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 07/06/2012] [Accepted: 07/26/2012] [Indexed: 12/12/2022]
Abstract
Despite numerous original publications describing the structural complexity of N- and O-linked glycans on glycoproteins, only very few answer the basic question of which particular glycans are linked to which amino acid residues along the polypeptide chain. Such structural information is of fundamental importance for understanding the biological roles of complex glycosylations as well as deciphering their non-template driven biosynthesis. This review focuses on presenting and commenting on recent strategies, specifically aimed at identifying the glycoproteome of cultured cells and biological samples, using targeted and global enrichment procedures and utilizing the high resolution power, high through-put capacity and complementary fragmentation techniques of tandem mass spectrometry. The goal is to give an update of this emerging field of protein and glyco-sciences and suggest routes to bridge the data gap between the two aspects of glycoprotein characteristics, i.e. glycan structures and their attachment sites.
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Affiliation(s)
- Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg 413 45, Sweden
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Cabras T, Boi R, Pisano E, Iavarone F, Fanali C, Nemolato S, Faa G, Castagnola M, Messana I. HPLC-ESI-MS and MS/MS structural characterization of multifucosylated N-glycoforms of the basic proline-rich protein IB-8a CON1+ in human saliva. J Sep Sci 2012; 35:1079-86. [DOI: 10.1002/jssc.201101066] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tiziana Cabras
- Dipartimento di Scienze della Vita e dell'Ambiente; Università di Cagliari; Italy
| | - Roberto Boi
- Istituto di Biochimica e Biochimica Clinica and/or Istituto per la Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Università Cattolica; Roma; Italy
| | - Elisabetta Pisano
- Dipartimento di Chirurgia e Scienze Odontostomatologiche; Università di Cagliari; Italy
| | - Federica Iavarone
- Istituto di Biochimica e Biochimica Clinica and/or Istituto per la Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Università Cattolica; Roma; Italy
| | - Chiara Fanali
- Istituto di Biochimica e Biochimica Clinica and/or Istituto per la Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Università Cattolica; Roma; Italy
| | - Sonia Nemolato
- Dipartimento di Citomorfologia; Università di Cagliari; Italy
| | - Gavino Faa
- Dipartimento di Citomorfologia; Università di Cagliari; Italy
| | - Massimo Castagnola
- Istituto di Biochimica e Biochimica Clinica and/or Istituto per la Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Università Cattolica; Roma; Italy
| | - Irene Messana
- Dipartimento di Scienze della Vita e dell'Ambiente; Università di Cagliari; Italy
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Zauner G, Koeleman CAM, Deelder AM, Wuhrer M. Mass spectrometric O-glycan analysis after combined O-glycan release by beta-elimination and 1-phenyl-3-methyl-5-pyrazolone labeling. Biochim Biophys Acta Gen Subj 2011; 1820:1420-8. [PMID: 21803123 DOI: 10.1016/j.bbagen.2011.07.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/08/2011] [Accepted: 07/09/2011] [Indexed: 01/06/2023]
Abstract
BACKGROUND Analysis of protein glycosylation is an important first step towards establishing the functions of glycans in health and disease. In contrast to N-glycans which are generally enzymatically released for analysis, there is no corresponding enzyme for O-glycan liberation. Therefore, O-glycans are generally released by chemical methods involving tedious procedures. METHODS Here, a straightforward method for the combined release and labeling of O-linked glycans from glycoproteins is described. Dimethylamine serves as the releasing agent, and 1-phenyl-3-methyl-5-pyrazolone (PMP) is employed for a prompt reaction with the reducing end of the freshly released O-glycan structures via an aldol condensation followed by a Michael-type addition resulting in a 2:1 stoichiometry of PMP per glycan. Samples are analyzed by nanoLC coupled to mass spectrometry. RESULTS Mucin from bovine submaxillary gland was used as a model protein to evaluate and optimize the approach that was further applied to bile salt stimulated lipase (BSSL) isolated from human milk. Next to previously reported O-glycan structures two additional oligosaccharides could be detected for BSSL. GENERAL SIGNIFICANCE In conclusion, the facile protocol established is suitable for the analysis of complex O-linked oligosaccharides from various biological samples. This article is part of a Special Issue entitled Glycoproteomics.
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Affiliation(s)
- Gerhild Zauner
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Postbus 9600, 2300 RC, Leiden, The Netherlands
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Wuhrer M, Deelder AM, van der Burgt YEM. Mass spectrometric glycan rearrangements. MASS SPECTROMETRY REVIEWS 2011; 30:664-80. [PMID: 21560141 DOI: 10.1002/mas.20337] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 02/28/2011] [Accepted: 03/28/2011] [Indexed: 05/04/2023]
Abstract
Mass spectrometric rearrangement reactions have been reported for a large variety of compounds such as peptides, lipids, and carbohydrates. In the case of carbohydrates this phenomenon has been described as internal residue loss. Resulting fragment ions may be misinterpreted as fragments arising from conventional glycosidic bond cleavages, which may result in incorrect structural assignment. Therefore, awareness of the occurrence of glycan rearrangements is important for avoiding misinterpretation of tandem mass spectra. In this review mass spectrometric rearrangements of both derivatized and underivatized (native) oligosaccharide structures are discussed. Similar phenomena have been reported for glycopeptides, labeled glycan structures and other biomolecules containing a carbohydrate part. Rearrangements in oligosaccharides and glycoconjugates have been observed with different types of mass spectrometers. Most of the observed carbohydrate rearrangement reactions appear to be linked to the presence of a proton. Hence, tandem mass spectrometric analysis of alkali adducts or deprotonated ions often prevents rearrangement reactions, while they may happen with high efficacy with protonated glycoconjugates.
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Affiliation(s)
- Manfred Wuhrer
- Leiden University Medical Center, Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden, The Netherlands.
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Pan S, Chen R, Aebersold R, Brentnall TA. Mass spectrometry based glycoproteomics--from a proteomics perspective. Mol Cell Proteomics 2010; 10:R110.003251. [PMID: 20736408 DOI: 10.1074/mcp.r110.003251] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Glycosylation is one of the most important and common forms of protein post-translational modification that is involved in many physiological functions and biological pathways. Altered glycosylation has been associated with a variety of diseases, including cancer, inflammatory and degenerative diseases. Glycoproteins are becoming important targets for the development of biomarkers for disease diagnosis, prognosis, and therapeutic response to drugs. The emerging technology of glycoproteomics, which focuses on glycoproteome analysis, is increasingly becoming an important tool for biomarker discovery. An in-depth, comprehensive identification of aberrant glycoproteins, and further, quantitative detection of specific glycosylation abnormalities in a complex environment require a concerted approach drawing from a variety of techniques. This report provides an overview of the recent advances in mass spectrometry based glycoproteomic methods and technology, in the context of biomarker discovery and clinical application.
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Affiliation(s)
- Sheng Pan
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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Chen Y, Liu M, Yan G, Lu H, Yang P. One-pipeline approach achieving glycoprotein identification and obtaining intact glycopeptide information by tandem mass spectrometry. MOLECULAR BIOSYSTEMS 2010; 6:2417-22. [DOI: 10.1039/c0mb00024h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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