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Li H, Wang X, Huang X, He Y, Zhang Y, Hao C, Zeng P, Zhang M, Gao Y, Yang D, Shan M, Dou H, Li X, Chang X, Tian Z, Zhang L. Circulating Glycan Monosaccharide Composite-Based Biomarker Diagnoses Colorectal Cancer at Early Stages and Predicts Prognosis. Front Oncol 2022; 12:852044. [PMID: 35574422 PMCID: PMC9099097 DOI: 10.3389/fonc.2022.852044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/06/2022] [Indexed: 12/29/2022] Open
Abstract
Introduction Early diagnosis could lead to a cure of colorectal cancer (CRC). Since CRC is related to aging and lifestyles, we tested if the environmental information-enriched monosaccharide composite (MC) of circulating glycans could serve as an early diagnostic biomarker for CRC. Meanwhile, we evaluated its role in predicting prognosis. Methods HPAEC-PAD was used to quantify glycan monosaccharide compositions from a total of 467 serum samples including CRC patients, colorectal adenoma (CRA) patients and healthy individuals. Two diagnostic model was constructed by logistic regression analysis. The diagnostic performance of the two models was verified in the retrospective validation group and the prospective validation group. The prognostic performance of the model was assessed by survival analysis. Results The concentrations of monosaccharides in serum were significantly higher in CRA and CRC patients than in healthy individuals. Two diagnostic models were constructed: MC1 was used to distinguish between healthy individuals and CRC; MC2 was used to distinguish between healthy individuals and CRA. Area under receptor operating characteristic curve (AUC) of MC2 and MC1 was 0.8025 and 0.9403 respectively. However, the AUC of CEA between healthy individuals and CRC was 0.7384. Moreover, in early stage of CRC (without lymph node metastasis), the positive rates of CEA and MC1 were 28% and 80%, respectively. The follow-up data showed that the increased MC1 value was associated with poor survival in patients with CRC (p=0.0010, HR=5.30). Discussion The MC1 model is superior to CEA in the diagnosis of CRC, especially in the early diagnosis. MC1 can be used for predicting prognosis of CRC patients, and elevated MC1 values indicate poor survival.
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Affiliation(s)
- Haoran Li
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xueling Wang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
- Center for Clinical Research, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaodan Huang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yanli He
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yiran Zhang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
- Shandong Institute of Orthopedics and Traumatology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Cui Hao
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Pengjiao Zeng
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Meng Zhang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yanyun Gao
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Dandan Yang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ming Shan
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Huaiqian Dou
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoyu Li
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaotian Chang
- Center for Clinical Research, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Lijuan Zhang, ; Xiaotian Chang, ; Zibin Tian,
| | - Zibin Tian
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Lijuan Zhang, ; Xiaotian Chang, ; Zibin Tian,
| | - Lijuan Zhang
- Systems Biology & Medicine Center for Complex Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Lijuan Zhang, ; Xiaotian Chang, ; Zibin Tian,
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2
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Zhong L, Zhu L, Cai ZW. Mass Spectrometry-based Proteomics and Glycoproteomics in COVID-19 Biomarkers Identification: A Mini-review. JOURNAL OF ANALYSIS AND TESTING 2021; 5:298-313. [PMID: 34513131 PMCID: PMC8423835 DOI: 10.1007/s41664-021-00197-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/27/2021] [Indexed: 12/11/2022]
Abstract
The first corona-pandemic, coronavirus disease 2019 (COVID-19) caused a huge health crisis and incalculable damage worldwide. Knowledge of how to cure the disease is urgently needed. Emerging immune escaping mutants of the virus suggested that it may be potentially persistent in human society as a regular health threat as the flu virus. Therefore, it is imperative to identify appropriate biomarkers to indicate pathological and physiological states, and more importantly, clinic outcomes. Proteins are the performers of life functions, and their abundance and modification status can directly reflect the immune status. Protein glycosylation serves a great impact in modulating protein function. The use of both unmodified and glycosylated proteins as biomarkers has also been proved feasible in the studies of SARS, Zika virus, influenza, etc. In recent years, mass spectrometry-based glycoproteomics, as well as proteomics approaches, advanced significantly due to the evolution of mass spectrometry. We focus on the current development of the mass spectrometry-based strategy for COVID-19 biomarkers' investigation. Potential application of glycoproteomics approaches and challenges in biomarkers identification are also discussed.
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Affiliation(s)
- Li Zhong
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Zong-Wei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
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3
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Shimazaki H, Ono A, Tsuruga M, Ueki A, Koseki-Kuno S, Toyoda T, Saito K, Sawakami K, Kariya M, Segawa O, Nakamura K, Koizuka M, Kuno A. GlycoBIST: A System for Automatic Glycan Profiling of a Target Protein Using Milli-Bead Array in a Tip. ACTA ACUST UNITED AC 2020; 99:e103. [PMID: 32073758 DOI: 10.1002/cpps.103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Lectin is a biomolecule that recognizes a specific part of glycans and, thus, has been used widely as a probe for glycoprotein analysis. Owing to the wide repertoire in nature combined with the recent two decades of advances in microarray technology, the multiplexed use of lectins has been widely used for glycan profiling of endogenous proteins. Because protein glycosylation is recognized as being biologically important and is expected to be a reliable disease marker, lectin microarray analysis with highly sensitive detection has been used to discover disease-relevant glycosylation alterations. However, the conventional system is limited to research purposes; thus, its implementation in clinical settings is warranted. Here, we provide an automatic glycan profiling method using GlycoBIST. A unique array format is used for 10-plexed lectin-glycoprotein interaction analysis on 1-mm-sized beads, which are arranged vertically in a capillary-shaped plastic tip. Using a one-boxed autopipetting machine, the whole process (including interaction, washing, and detection) is performed automatically and serially, resulting in reproducible measurements. In this article, a typical method for glycan profiling of a purified glycoprotein and the fabrication of GlycoBIST tips is explained. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Fabrication of a GlycoBIST tip Basic Protocol 2: Automatic profiling of a target glycoprotein using GlycoBIST.
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Affiliation(s)
- Hiroko Shimazaki
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Ayaka Ono
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Masako Tsuruga
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Aya Ueki
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Shiori Koseki-Kuno
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takako Toyoda
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Kozue Saito
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | | | - Minoru Kariya
- Precision System Science, Kamihongou, Matsudo, Chiba, Japan
| | - Osamu Segawa
- Precision System Science, Kamihongou, Matsudo, Chiba, Japan
| | | | | | - Atsushi Kuno
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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4
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Verhelst X, Dias AM, Colombel JF, Vermeire S, Van Vlierberghe H, Callewaert N, Pinho SS. Protein Glycosylation as a Diagnostic and Prognostic Marker of Chronic Inflammatory Gastrointestinal and Liver Diseases. Gastroenterology 2020; 158:95-110. [PMID: 31626754 DOI: 10.1053/j.gastro.2019.08.060] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/03/2019] [Accepted: 08/23/2019] [Indexed: 12/16/2022]
Abstract
Glycans are sequences of carbohydrates that are added to proteins or lipids to modulate their structure and function. Glycans modify proteins required for regulation of immune cells, and alterations have been associated with inflammatory conditions. For example, specific glycans regulate T-cell activation, structures, and functions of immunoglobulins; interactions between microbes and immune and epithelial cells; and malignant transformation in the intestine and liver. We review the effects of protein glycosylation in regulation of gastrointestinal and liver functions, and how alterations in glycosylation serve as diagnostic or prognostic factors, or as targets for therapy.
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Affiliation(s)
- Xavier Verhelst
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Ana M Dias
- Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | | | - Severine Vermeire
- Translational Research in Gastrointestinal Disorders, Department of Clinical and Experimental Medicine, Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Hans Van Vlierberghe
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Nico Callewaert
- Vlaams Instituut voor Biotechnologie-UGent Center for Medical Biotechnology, Gent, Belgium
| | - Salomé S Pinho
- Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; Institute for Research and Innovation in Health, University of Porto, Porto, Portugal; Medical Faculty, University of Porto, Porto, Portugal.
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5
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Vermassen T, Callewaert N, Rottey S, Delanghe JR. Prostate Protein N-Glycosylation Profiling by Means of DNA Sequencer-Assisted Fluorophore-Assisted Carbohydrate Electrophoresis. Methods Mol Biol 2019; 1972:235-250. [PMID: 30847796 DOI: 10.1007/978-1-4939-9213-3_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA sequencer-assisted fluorophore-assisted carbohydrate electrophoresis allows for accurate profiling of the asparagine-linked (N-) glycosylation patterns, a posttranslational modification present on many soluble and membrane proteins. This technique has been extensively tested to identify N-glycosylation patterns associated with serum proteins. Here we describe the use of DNA sequencer-assisted fluorophore-assisted carbohydrate electrophoresis to identify the N-glycosylation patterns of prostate proteins in urine.
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Affiliation(s)
- Tijl Vermassen
- Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
- Drug Research Unit Ghent, Ghent University Hospital, Ghent, Belgium
| | | | - Sylvie Rottey
- Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
- Drug Research Unit Ghent, Ghent University Hospital, Ghent, Belgium
| | - Joris R Delanghe
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium.
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6
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Tozawa-Ono A, Kubota M, Honma C, Nakagawa Y, Yokomichi N, Yoshioka N, Tsuda C, Ohara T, Koizumi H, Suzuki N. Glycan profiling using formalin-fixed, paraffin-embedded tissues: Hippeastrum hybrid lectin is a sensitive biomarker for squamous cell carcinoma of the uterine cervix. J Obstet Gynaecol Res 2017; 43:1326-1334. [DOI: 10.1111/jog.13359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/06/2017] [Accepted: 03/20/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Akiko Tozawa-Ono
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Manabu Kubota
- Department of Pathology; St. Marianna University School of Medicine; Miyamae, Kawasaki Japan
| | - Chika Honma
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Yuko Nakagawa
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Noriyuki Yokomichi
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Norihito Yoshioka
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Chiharu Tsuda
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Tatsuru Ohara
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
| | - Hirotaka Koizumi
- Department of Pathology; St. Marianna University School of Medicine; Miyamae, Kawasaki Japan
| | - Nao Suzuki
- Department of Obstetrics and Gynecology; St. Marianna University School of Medicine; Miyamae Kawasaki Japan
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7
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Bythell BJ, Abutokaikah MT, Wagoner AR, Guan S, Rabus JM. Cationized Carbohydrate Gas-Phase Fragmentation Chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:688-703. [PMID: 27896699 DOI: 10.1007/s13361-016-1530-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 05/04/2023]
Abstract
We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms. Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies. Graphical Abstract ᅟ.
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Affiliation(s)
- Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA.
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Ashley R Wagoner
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Jordan M Rabus
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
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8
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Zou X, Yoshida M, Nagai-Okatani C, Iwaki J, Matsuda A, Tan B, Hagiwara K, Sato T, Itakura Y, Noro E, Kaji H, Toyoda M, Zhang Y, Narimatsu H, Kuno A. A standardized method for lectin microarray-based tissue glycome mapping. Sci Rep 2017; 7:43560. [PMID: 28262709 PMCID: PMC5337905 DOI: 10.1038/srep43560] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/25/2017] [Indexed: 01/12/2023] Open
Abstract
The significance of glycomic profiling has been highlighted by recent findings that structural changes of glycans are observed in many diseases, including cancer. Therefore, glycomic profiling of the whole body (glycome mapping) under different physiopathological states may contribute to the discovery of reliable biomarkers with disease-specific alterations. To achieve this, standardization of high-throughput and in-depth analysis of tissue glycome mapping is needed. However, this is a great challenge due to the lack of analytical methodology for glycans on small amounts of endogenous glycoproteins. Here, we established a standardized method of lectin-assisted tissue glycome mapping. Formalin-fixed, paraffin-embedded tissue sections were prepared from brain, liver, kidney, spleen, and testis of two C57BL/6J mice. In total, 190 size-adjusted fragments with different morphology were serially collected from each tissue by laser microdissection and subjected to lectin microarray analysis. The results and subsequent histochemical analysis with selected lectins were highly consistent with previous reports of mass spectrometry-based N- and/or O-glycome analyses and histochemistry. This is the first report to look at both N- and O-glycome profiles of various regions within tissue sections of five different organs. This simple and reproducible mapping approach is also applicable to various disease model mice to facilitate disease-related biomarker discovery.
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Affiliation(s)
- Xia Zou
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan.,Ministry of Education, Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Maki Yoshida
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Chiaki Nagai-Okatani
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Jun Iwaki
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Atsushi Matsuda
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Binbin Tan
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan.,Ministry of Education, Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kozue Hagiwara
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Takashi Sato
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Yoko Itakura
- Research Team for Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - Erika Noro
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Hiroyuki Kaji
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Masashi Toyoda
- Research Team for Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - Yan Zhang
- Ministry of Education, Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hisashi Narimatsu
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Atsushi Kuno
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
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9
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Rabus JM, Abutokaikah MT, Ross RT, Bythell BJ. Sodium-cationized carbohydrate gas-phase fragmentation chemistry: influence of glycosidic linkage position. Phys Chem Chem Phys 2017; 19:25643-25652. [DOI: 10.1039/c7cp04738j] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Gas-phase structure and fragmentation chemistries of isomeric sodium-cationized sugars.
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Affiliation(s)
- Jordan M. Rabus
- Department of Chemistry and Biochemistry
- University of Missouri
- St. Louis
- USA
| | | | - Reginald T. Ross
- Department of Chemistry and Biochemistry
- University of Missouri
- St. Louis
- USA
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10
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Huang Y, Dodds ED. Ion-neutral collisional cross sections of carbohydrate isomers as divalent cation adducts and their electron transfer products. Analyst 2016. [PMID: 26225371 DOI: 10.1039/c5an01093d] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the gravity of glycoscience continues to amass, a commensurate demand for rapid, sensitive, and structurally comprehensive glycoanalytical tools has arisen. Among the most elusive but desirable analytical capabilities is the ability to expeditiously and unambiguously detect, distinguish, and resolve carbohydrates that differ only in their constitutional isomerism and/or stereoisomerism. While ion mobility spectrometry (IMS) has proven a highly promising tool for such analyses, the facility of this method to discriminate larger oligosaccharides is still somewhat limited. In an effort to expand the capabilities of IMS to discriminate among carbohydrate isomers, the present investigation was focused on IMS studies of four trisaccharide isomers, four pentasaccharide isomers, and two hexasaccharide isomers, each as group II metal ion adducts and their corresponding gas-phase electron transfer (ET) products. These studies were also evaluated in the context of previously investigated group I metal ion adducts of the same saccharides. The orientationally averaged ion-neutral collisional cross sections (CCSs) of the various carbohydrate/metal ion adducts were found to be dependent on the structures of specific carbohydrate isomers, sensitive to the electronic characteristics of the bound cation, and responsive to the attachment of an additional electron (in the case of divalent metal ion adducts). Overall, these results underscore the utility of metal ions for probing carbohydrate structure in concert with IMS, and the capacity of gas-phase ion chemistry to expand the menu of such probes.
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Affiliation(s)
- Yuting Huang
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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11
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Defaus S, Gupta P, Andreu D, Gutiérrez-Gallego R. Mammalian protein glycosylation--structure versus function. Analyst 2015; 139:2944-67. [PMID: 24779027 DOI: 10.1039/c3an02245e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates fulfil many common as well as extremely important functions in nature. They show a variety of molecular displays--e.g., free mono-, oligo-, and polysaccharides, glycolipids, proteoglycans, glycoproteins, etc.--with particular roles and localizations in living organisms. Structure-specific peculiarities are so many and diverse that it becomes virtually impossible to cover them all from an analytical perspective. Hence this manuscript, focused on mammalian glycosylation, rather than a complete list of analytical descriptors or recognized functions for carbohydrate structures, comprehensively reviews three central issues in current glycoscience, namely (i) structural analysis of glycoprotein glycans, covering both classical and novel approaches for teasing out the structural puzzle as well as potential pitfalls of these processes; (ii) an overview of functions attributed to carbohydrates, covering from monosaccharide to complex, well-defined epitopes and full glycans, including post-glycosylational modifications, and (iii) recent technical advances allowing structural identification of glycoprotein glycans with simultaneous assignation of biological functions.
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Affiliation(s)
- S Defaus
- Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
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12
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Rana S, Le NDB, Mout R, Duncan B, Elci SG, Saha K, Rotello VM. A Multichannel Biosensor for Rapid Determination of Cell Surface Glycomic Signatures. ACS CENTRAL SCIENCE 2015; 1:191-197. [PMID: 26405691 PMCID: PMC4571165 DOI: 10.1021/acscentsci.5b00126] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Indexed: 05/03/2023]
Abstract
Cell surface glycosylation serves a fundamental role in dictating cell and tissue behavior. Cell surface glycomes differ significantly, presenting viable biomarkers for identifying cell types and their states. Glycoprofiling is a challenging task, however, due to the complexity of the constituent glycans. We report here a rapid and effective sensor for surface-based cell differentiation that uses a three-channel sensor produced by noncovalent conjugation of a functionalized gold nanoparticle (AuNP) and fluorescent proteins. Wild-type and glycomutant mammalian cells were effectively stratified using fluorescence signatures obtained from a single sensor element. Blinded unknowns generated from the tested cell types were identified with high accuracy (44 out of 48 samples), validating the robustness of the multichannel sensor. Notably, this selectivity-based high-throughput sensor differentiated between cells, employing a nondestructive protocol that required only a single well of a microplate for detection.
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Affiliation(s)
- Subinoy Rana
- Department
of Chemistry, University of Massachusetts
Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ngoc D. B. Le
- Department
of Chemistry, University of Massachusetts
Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
| | - Rubul Mout
- Department
of Chemistry, University of Massachusetts
Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
| | - Bradley Duncan
- Department
of Chemistry, University of Massachusetts
Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
| | - S. Gokhan Elci
- Department
of Chemistry, University of Massachusetts
Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
| | - Krishnendu Saha
- Department
of Chemistry, University of Massachusetts
Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
| | - Vincent M. Rotello
- Department
of Chemistry, University of Massachusetts
Amherst, 710 North Pleasant
Street, Amherst, Massachusetts 01003, United States
- E-mail:
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13
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Huang Y, Dodds ED. Discrimination of Isomeric Carbohydrates as the Electron Transfer Products of Group II Cation Adducts by Ion Mobility Spectrometry and Tandem Mass Spectrometry. Anal Chem 2015; 87:5664-8. [PMID: 25955237 DOI: 10.1021/acs.analchem.5b00759] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The rapid and unambiguous distinction of isomeric carbohydrate structures persists as a tremendous analytical challenge. This paper reports the first exploitation of carbohydrate/metal ion interactions in concert with gas-phase ion chemistry to improve discrimination of oligosaccharide isomers by both ion mobility spectrometry and tandem mass spectrometry. This is demonstrated for two isomeric pentasaccharides and two isomeric hexasaccharides, each studied in an underivatized form as their calcium ion adducts, barium ion adducts, and gas-phase electron transfer products thereof. With appropriate selection of the charge carrier, transfer of a single electron to the carbohydrate metal ion adducts resulted in isomer-distinguishing shifts in their ion/neutral collision cross sections and the appearance of unique features in their vibrational activation/dissociation spectra. These findings suggest novel and elegant gas-phase strategies for rapid differentiation of isomeric oligosaccharides.
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Affiliation(s)
- Yuting Huang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Eric D Dodds
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
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14
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010. MASS SPECTROMETRY REVIEWS 2015; 34:268-422. [PMID: 24863367 PMCID: PMC7168572 DOI: 10.1002/mas.21411] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 05/07/2023]
Abstract
This review is the sixth update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.
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Affiliation(s)
- David J. Harvey
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordOX1 3QUUK
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15
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Futsukaichi T, Etoh T, Nakajima K, Daa T, Shiroshita H, Shiraishi N, Kitano S, Inomata M. Decreased expression of Bauhinia purpurea lectin is a predictor of gastric cancer recurrence. Surg Today 2015; 45:1299-306. [PMID: 25753302 DOI: 10.1007/s00595-015-1127-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/21/2014] [Indexed: 02/06/2023]
Abstract
PURPOSE Molecular markers as indicators for gastric cancer recurrence are urgently required. The aim of this study was to identify lectins that can be used to predict gastric cancer recurrence after gastrectomy. METHODS We created lectin expression profiles by microarray analysis for 60 patients, who underwent surgery for gastric cancer at the Oita University Hospital between January, 2005 and December, 2007. Lectin expression and clinicopathological factors in patients who suffered gastric cancer recurrence and those who did not were compared by univariate and multivariate analyses. RESULTS Thirteen lectins showed a significant increase in binding to cancer tissues, whereas 11 lectins showed a significant decrease in binding to cancer tissues, when compared with binding to normal epithelia. Multivariate analysis revealed that lymph node metastasis and low Bauhinia purpurea lectin (BPL)-binding signals were independent predictive factors for recurrence. All patients with low BPL expression had significantly worse relapse-free survival than those with high BPL expression. CONCLUSIONS Our results using a novel lectin microarray system provide the first solid evidence that BPL expression is a predictor of gastric cancer recurrence.
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Affiliation(s)
- Takuro Futsukaichi
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Hasama-machi, Yufu, Oita, 879-5593, Japan.
| | - Tsuyoshi Etoh
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Hasama-machi, Yufu, Oita, 879-5593, Japan.
| | - Kentaro Nakajima
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Tsutomu Daa
- Department of Diagnostic Pathology, Oita University Faculty of Medicine, Oita, Japan
| | - Hidefumi Shiroshita
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Norio Shiraishi
- Center for Community Medicine, Oita University Faculty of Medicine, Oita, Japan
| | | | - Masafumi Inomata
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, Hasama-machi, Yufu, Oita, 879-5593, Japan
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16
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Hennig R, Rapp E, Kottler R, Cajic S, Borowiak M, Reichl U. N-Glycosylation Fingerprinting of Viral Glycoproteins by xCGE-LIF. Methods Mol Biol 2015; 1331:123-43. [PMID: 26169738 DOI: 10.1007/978-1-4939-2874-3_8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The ongoing threat of pathogens, increasing resistance against antibiotics, and the risk of fast spreading of infectious diseases in a global community resulted in an intensified development of vaccines. Antigens used for vaccination comprise a wide variety of macromolecules including glycoproteins, lipopolysaccharides, and complex carbohydrates. For all of these antigens the sugar composition plays a crucial role for immunogenicity and protective efficacy of the vaccine. Here, we provide a protocol for N-glycosylation fingerprinting utilizing high performance multiplexed capillary gel electrophoresis with laser-induced fluorescence detection (xCGE-LIF) technology. The method described, enables to analyze the N-glycosylation of specific proteins out of a complex sample or even the total of all N-glycans contained in such a sample. The protocol is exemplarily demonstrated for N-glycosylation fingerprinting of cell culture-derived influenza A and B viruses and their major antigens, the membrane glycoproteins hemagglutinin and neuraminidase.
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Affiliation(s)
- René Hennig
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse1, 39106, Magdeburg, Germany
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17
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Nakajima K, Inomata M, Iha H, Hiratsuka T, Etoh T, Shiraishi N, Kashima K, Kitano S. Establishment of new predictive markers for distant recurrence of colorectal cancer using lectin microarray analysis. Cancer Med 2014; 4:293-302. [PMID: 25355679 PMCID: PMC4329012 DOI: 10.1002/cam4.342] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 07/16/2014] [Accepted: 08/15/2014] [Indexed: 01/05/2023] Open
Abstract
We evaluated the clinical benefits of novel predictive markers for distant recurrence with colorectal cancer using lectin microarray analysis of cell surface glycan modifications. Glycoproteins were extracted from formalin-fixed, paraffin-embedded tumor specimens and normal epithelium from 53 consecutive curatively resected stage I–III colorectal cancer cases and then subjected to lectin microarray to obtain lectin–glycan interaction (LGI) values. In addition, clinicopathological factors associated with distant recurrence were identified. LGI values that were associated with distant recurrence were validated with an additional 55 curatively resected stage II colorectal cancer cases. LGI values for Agaricus bisporus (ABA) lectin, prominent in cancer tissues, were statistically associated with distant recurrence. ABA lectin staining exhibited strikingly intense signals in the cytoplasm and apical surfaces of cancer cells, while weak staining was observed in the supranuclear regions of normal epithelium. This ABA tumor/normal LGI ratio may be a new predictive biomarker for distant recurrence of curatively resected colorectal cancer.
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Affiliation(s)
- Kentaro Nakajima
- Department of Gastrointestinal and Pediatric Surgery, Oita University Faculty of Medicine, Hasama-machi, Oita, Japan
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18
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Schwedler C, Kaup M, Weiz S, Hoppe M, Braicu EI, Sehouli J, Hoppe B, Tauber R, Berger M, Blanchard V. Identification of 34 N-glycan isomers in human serum by capillary electrophoresis coupled with laser-induced fluorescence allows improving glycan biomarker discovery. Anal Bioanal Chem 2014; 406:7185-93. [PMID: 25234305 DOI: 10.1007/s00216-014-8168-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 02/06/2023]
Abstract
Alterations in glycosylation have been observed in many human diseases and specific changes in glycosylation have been proposed as relevant diagnostic information. Capillary electrophoresis coupled with laser-induced fluorescence (CE-LIF) is a robust method to quantify desialylated N-glycans that are labeled with 8-aminopyrene-1,3,6-trisulfonic acid prior to analysis. To date, only a maximum of 12 glycan structures, the most abundant ones, have been identified by CE-LIF to characterize glycome modulations of total serum in the course of the diseases. In most forms of cancer, findings using CE-LIF were limited to the increase of triantennary structures carrying a Lewis(x) epitope. In this work, we identified 32 linkage and positional glycan isomers in healthy human serum using exoglycosidase digestions as well as standard glycoproteins, for which we report the assignment of novel structures. It was possible to identify and quantify 34 glycan isomers in the serum of primary epithelial ovarian cancer patients (EOC). Reduced levels of diantennary structures and of high-mannose 5 were statistically significant in the EOC samples, and also, elevated branching as well as increased antennary fucosylation were observed. For the first time, we could demonstrate that not only antennary fucosylation was of relevance in tetraantennary structures but also core-fucosylated tetraantennary N-glycans were statistically increased in EOC patients. The results of the current study provide an improved dataset to be used in glycan biomarker discovery.
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Affiliation(s)
- Christian Schwedler
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité Medical University, Augustenburger Platz 1, 13353, Berlin, Germany
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19
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Mu B, Zhang J, McNicholas TP, Reuel NF, Kruss S, Strano MS. Recent advances in molecular recognition based on nanoengineered platforms. Acc Chem Res 2014; 47:979-88. [PMID: 24467652 DOI: 10.1021/ar400162w] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nanoparticles and nanoengineered platforms have great potential for technologies involving biomoleuclar detection or cell-related biosensing, and have provided effective chemical interfaces for molecular recognition. Typically, chemists work on the modification of synthetic polymers or macromolecules, which they link to the nanoparticles by covalent or noncovalent approaches. The motivation for chemical modification is to enhance the selectivity and sensitivity, and to improve the biocompatibility for the in vivo applications. In this Account, we present recent advances in the development and application of chemical interfaces for molecular recognition for nanoparticles and nanoengineered platforms, in particular single-walled carbon nanotubes (SWNTs). We discuss emerging approaches for recognizing small molecules, glycosylated proteins, and serum biomarkers. For example, we compare and discuss detection methods for ATP, NO, H2O2, and monosaccharides for recent nanomaterials. Fluorometric detection appears to have great potential for quantifying concentration gradients and determining their location in living cells. For macromolecular detection, new methods for glycoprofiling using such interfaces appear promising, and benefit specifically from the potential elimination of cumbersome labeling and liberation steps during conventional analysis of glycans, augmenting the currently used mass spectrometry (MS), capillary electrophoresis (CE), and liquid chromatography (LC) methods. In particular, we demonstrated the great potential of fluorescent SWNTs for glycan-lectin interactions sensing. In this case, SWNTs are noncovalently functionalized to introduce a chelated nickel group. This group provides a docking site for the His-tagged lectin and acts as the signal modulator. As the nickel proximity to the SWNT surface changes, the fluorescent signal is increased or attenuated. When a free glycan or glycosylated probe interacts with the lectin, the signal increases and they are able to obtain loading curves similar to surface plasmon resonance measurements. They demonstrate the sensitivity and specificity of this platform with two higher-affined glycan-lectin pairs: fucose (Fuc) to PA-IIL and N-acetylglucosamine (GlcNAc) to GafD. Lastly, we discuss how developments in protein biomarker detection in general are benefiting specifically from label-free molecular recognition. Electrical field effect transistors, chemi-resistive and fluorometric nanosensors based on various nanomaterials have demonstrated substantial progress in recent years in addressing this challenging problem. In this Account, we compare the balance between sensitivity, selectivity, and nonspecific adsorption for various applications. In particular, our group has utilized SWNTs as fluorescence sensors for label-free protein-protein interaction measurements. In this assay, we have encapsulated each nanotube in a biocompatible polymer, chitosan, which has been further modified to conjugate nitrilotriacetic acid (NTA) groups. After Ni(2+) chelation, NTA Ni(2+) complexes bind to his-tagged proteins, resulting in a local environment change of the SWNT array, leading to optical fluorescence modulation with detection limit down to 100 nM. We have further engineered the platform to monitor single protein binding events, with an even lower detection limit down to 10 pM.
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Affiliation(s)
- Bin Mu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jingqing Zhang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas P. McNicholas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nigel F. Reuel
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sebastian Kruss
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael S. Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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20
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Adaptive immune activation: glycosylation does matter. Nat Chem Biol 2014; 9:776-84. [PMID: 24231619 DOI: 10.1038/nchembio.1403] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 10/22/2013] [Indexed: 12/13/2022]
Abstract
Major histocompatibility complex (MHC) class I and II are glycoproteins that can present antigenic peptides at the cell surface for recognition and activation of circulating T lymphocytes. Here, the importance of the modification of protein antigens by glycans on cellular uptake, proteolytic processing, presentation by MHC and subsequent T-cell priming is reviewed. Antigen glycosylation is important for a number of diseases and vaccine design. All of the key proteins involved in antigen recognition and the orchestration of downstream effector functions are glycosylated. The influence of protein glycosylation on immune function and disease is covered.
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21
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Hirabayashi J, Kuno A, Tateno H. Development and Applications of the Lectin Microarray. Top Curr Chem (Cham) 2014; 367:105-24. [DOI: 10.1007/128_2014_612] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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22
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Yodoshi M, Ikeda N, Yamaguchi N, Nagata M, Nishida N, Kakehi K, Hayakawa T, Suzuki S. A novel condition for capillary electrophoretic analysis of reductively aminated saccharides without removal of excess reagents. Electrophoresis 2013; 34:3198-205. [DOI: 10.1002/elps.201200612] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 09/02/2013] [Accepted: 09/05/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Masahiro Yodoshi
- Faculty of Pharmaceutical Sciences; Kinki University; Kowakae; Higashi-Osaka Osaka Japan
| | - Natsumi Ikeda
- Faculty of Pharmaceutical Sciences; Kinki University; Kowakae; Higashi-Osaka Osaka Japan
| | - Naoko Yamaguchi
- Faculty of Pharmaceutical Sciences; Kinki University; Kowakae; Higashi-Osaka Osaka Japan
| | - Mana Nagata
- Faculty of Pharmaceutical Sciences; Kinki University; Kowakae; Higashi-Osaka Osaka Japan
| | - Noriaki Nishida
- Faculty of Pharmaceutical Sciences; Kinki University; Kowakae; Higashi-Osaka Osaka Japan
| | - Kazuaki Kakehi
- Faculty of Pharmaceutical Sciences; Kinki University; Kowakae; Higashi-Osaka Osaka Japan
| | - Takao Hayakawa
- Faculty of Pharmaceutical Sciences; Kinki University; Kowakae; Higashi-Osaka Osaka Japan
| | - Shigeo Suzuki
- Faculty of Pharmaceutical Sciences; Kinki University; Kowakae; Higashi-Osaka Osaka Japan
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23
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Huang Y, Dodds ED. Ion mobility studies of carbohydrates as group I adducts: isomer specific collisional cross section dependence on metal ion radius. Anal Chem 2013; 85:9728-35. [PMID: 24033309 DOI: 10.1021/ac402133f] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Carbohydrates play numerous critical roles in biological systems. Characterization of oligosaccharide structures is essential to a complete understanding of their functions in biological processes; nevertheless, their structural determination remains challenging in part due to isomerism. Ion mobility spectrometry provides the means to resolve gas phase ions on the basis of their shape-to-charge ratios, thus providing significant potential for separation and differentiation of carbohydrate isomers. Here, we report on the determination of collisional cross sections for four groups of isomeric carbohydrates (including five isomeric disaccharides, four isomeric trisaccharides, two isomeric pentasaccharides, and two isomeric hexasaccharides) as their group I metal ion adducts (i.e., [M + Li](+), [M + Na](+), [M + K](+), [M + Rb](+), and [M + Cs](+)). In all, 65 collisional cross sections were measured, the great majority of which have not been previously reported. As anticipated, the collisional cross sections of the carbohydrate metal ion adducts generally increase with increasing metal ion radius; however, the collisional cross sections were found to scale with the group I cation size in isomer specific manners. Such measurements are of substantial analytical value, as they illustrate how the selection of charge carrier influences carbohydrate ion mobility determinations. For example, certain pairs of isomeric carbohydrates assume unique collisional cross sections upon binding one metal ion, but not another. On the whole, these data suggest a role for the charge carrier as a probe of carbohydrate structure and thus have significant implications for the continued development and application of ion mobility spectrometry for the distinction and resolution of isomeric carbohydrates.
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Affiliation(s)
- Yuting Huang
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
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24
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Mitra I, Alley WR, Goetz JA, Vasseur JA, Novotny MV, Jacobson SC. Comparative profiling of N-glycans isolated from serum samples of ovarian cancer patients and analyzed by microchip electrophoresis. J Proteome Res 2013; 12:4490-6. [PMID: 23984816 DOI: 10.1021/pr400549e] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ovarian cancer is the fifth leading cause of cancer-related mortalities for women in the United States and the most lethal gynecological cancer. Aberrant glycosylation has been linked to several human diseases, including ovarian cancer, and accurate measurement of changes in glycosylation may provide relevant diagnostic and prognostic information. In this work, we used microchip electrophoresis coupled with laser-induced fluorescence detection to determine quantitative differences among the N-glycan profiles of control individuals and late-stage recurrent ovarian cancer patients prior to and after an experimental drug treatment that combined docetaxel and imatinib mesylate. N-Glycans were enzymatically released from 5-μL aliquots of serum samples, labeled with the anionic fluorescent tag, 8-aminopyrene-1,3,6-trisulfonic acid, and analyzed on microfluidic devices. A 22-cm long separation channel, operated at 1250 V/cm, generated analysis times less than 100 s, separation efficiencies up to 8 × 10(5) plates (3.6 × 10(6) plates/m), and migration time reproducibilities better than 0.1% relative standard deviation after peak alignment. Principal component analysis (PCA) and analysis of variance (ANOVA) tests showed significant differences between the control and both pre- and post-treatment cancer samples and subtle differences between the pre- and post-treatment cancer samples. Area-under-the-curve (AUC) values from receiver operating characteristics (ROC) tests were used to evaluate the diagnostic merit of N-glycan peaks, and specific N-glycan peaks used in combination provided AUCs > 0.90 (highly accurate test) when the control and pretreatment cancer samples and control and post-treatment samples were compared.
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Affiliation(s)
- Indranil Mitra
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
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25
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Everest-Dass AV, Kolarich D, Campbell MP, Packer NH. Tandem mass spectra of glycan substructures enable the multistage mass spectrometric identification of determinants on oligosaccharides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:931-939. [PMID: 23592194 DOI: 10.1002/rcm.6527] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 01/29/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Glycosylation of proteins and lipids affects many biological processes, such as host-pathogen interactions, cell communication, and initiation of the immune responses. Terminal glycan substructures, or determinants, often govern the function or recognition of the carrier glycoconjugate and modulate these processes. In this study we describe a strategy using multistage mass spectrometry to identify and confirm these glycan substructures. METHODS An online tandem mass spectrometry (MS(2)) spectral fragment library of glycan substructures that typically occur at the non-reducing terminus of glycoconjugates was created to enable the easier identification and confirmation of glycan determinants on oligosaccharides released from glycoproteins. Oligosaccharides were separated by porous graphitized carbon capillary chromatography and analysed by ion trap MS. Candidate product ions that constitute the glycan substructure mass were identified in the MS(2) product ion spectrum, and used as the precursor ion for subsequent MS(3) fragmentation. The resulting MS(3) spectrum was matched against the MS(2) spectral fragment library to identify the glycan substructure(s) that comprise the parent oligosaccharide. RESULTS Thirty biologically important terminal glycan determinants commonly observed on glycoconjugates were fragmented by positive and negative ion mass spectrometry and the MS(2) product ion masses manually annotated and stored in the UniCarb-DB online database. Negative ion tandem mass spectra were especially useful in assigning isobaric glycan structures. We have applied this strategy for the identification of the sulphation, blood group antigens and sialic acid linkages on complex N-and O-glycans released from glycoproteins. CONCLUSIONS We show the potential of these glycan substructure MS(2) spectra in the negative ionization mode to facilitate the assignment of determinants on N- and O-linked glycans released from glycoproteins. Comparing the structural feature ions of known glycan reference substructures assists in the annotation of complex glycan product ion spectra, and can remove the need for other orthogonal confirmation analyses such as sequential glycosidase digestion.
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Affiliation(s)
- Arun V Everest-Dass
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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26
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Reuel NF, Mu B, Zhang J, Hinckley A, Strano MS. Nanoengineered glycan sensors enabling native glycoprofiling for medicinal applications: towards profiling glycoproteins without labeling or liberation steps. Chem Soc Rev 2013; 41:5744-79. [PMID: 22868627 DOI: 10.1039/c2cs35142k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanoengineered glycan sensors may help realize the long-held goal of accurate and rapid glycoprotein profiling without labeling or glycan liberation steps. Current methods of profiling oligosaccharides displayed on protein surfaces, such as liquid chromatography, mass spectrometry, capillary electrophoresis, and microarray methods, are limited by sample pretreatment and quantitative accuracy. Microarrayed platforms can be improved with methods that better estimate kinetic parameters rather than simply reporting relative binding information. These quantitative glycan sensors are enabled by an emerging class of nanoengineered materials that differ in their mode of signal transduction from traditional methods. Platforms that respond to mass changes include a quartz crystal microbalance and cantilever sensors. Electronic response can be detected from electrochemical, field effect transistor, and pore impedance sensors. Optical methods include fluorescent frontal affinity chromatography, surface plasmon resonance methods, and fluorescent carbon nanotubes. After a very brief primer on glycobiology and its connection to medicine, these emerging systems are critically reviewed for their potential use as core sensors in future glycoprofiling tools.
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Affiliation(s)
- Nigel F Reuel
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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27
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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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28
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SUZUKI S. Recent Developments in Liquid Chromatography and Capillary Electrophoresis for the Analysis of Glycoprotein Glycans. ANAL SCI 2013; 29:1117-28. [DOI: 10.2116/analsci.29.1117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Hayes CA, Doohan R, Kirkley D, Leister K, Harhen B, Savage AV, Karlsson NG. Cross validation of liquid chromatography-mass spectrometry and lectin array for monitoring glycosylation in fed-batch glycoprotein production. Mol Biotechnol 2012; 51:272-82. [PMID: 22048797 DOI: 10.1007/s12033-011-9465-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycosylation analysis of recombinant glycoproteins is of importance for the biopharmaceutical industry and the production of glycoprotein pharmaceuticals. A commercially available lectin array technology was evaluated for its ability to present a reproducible fingerprint of a recombinant CTLY4-IgG fusion glycoprotein expressed in large scale CHO-cell fermentation. The glycosylation prediction from the array was compared to traditional negative mode capillary LC-MS of released oligosaccharides. It was shown that both methods provide data that allow samples to be distinguished by their glycosylation pattern. This included information about sialylation, the presence of reducing terminal galactose β1-, terminal N-acetylglucosamine β1-, and antennary distribution. With both methods it was found that a general trend of increased sialylation was associated with an increase of the antenna and reduced amount of terminal galactose β1-, while N-acetylglucosamine β1- was less affected. LC-MS, but not the lectin array, provided valuable information about the sialic acid isoforms present, including N-acetylneuraminic acid, N-glycolylneuraminic acid and their O-acetylated versions. Detected small amounts of high-mannose structures by LC-MS correlated with the detection of the same epitope by the lectin array.
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Zhao SS, Zhong X, Tie C, Chen DD. Capillary electrophoresis-mass spectrometry for analysis of complex samples. Proteomics 2012; 12:2991-3012. [DOI: 10.1002/pmic.201200221] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/10/2012] [Accepted: 07/18/2012] [Indexed: 12/20/2022]
Affiliation(s)
- Shuai Sherry Zhao
- Department of Chemistry; University of British Columbia; Vancouver BC Canada
| | - Xuefei Zhong
- Department of Chemistry; University of British Columbia; Vancouver BC Canada
| | - Cai Tie
- Department of Chemistry; University of British Columbia; Vancouver BC Canada
| | - David D.Y. Chen
- Department of Chemistry; University of British Columbia; Vancouver BC Canada
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31
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Nishijima Y, Toyoda M, Yamazaki-Inoue M, Sugiyama T, Miyazawa M, Muramatsu T, Nakamura K, Narimatsu H, Umezawa A, Mikami M. Glycan profiling of endometrial cancers using lectin microarray. Genes Cells 2012; 17:826-36. [DOI: 10.1111/gtc.12003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 07/25/2012] [Indexed: 12/11/2022]
Affiliation(s)
| | - Masashi Toyoda
- Tokyo Metropolitan Institute of Gerontology; 35-2 Sakaecho; Itabashi-ku; Tokyo; 173-0015; Japan
| | - Mayu Yamazaki-Inoue
- Department of Reproductive Biology; National Research Institute for Child Health and Development; 2-10-1 Okura; Setagaya-ku; Tokyo; 157-8535; Japan
| | - Taro Sugiyama
- Department of Obstetrics and Gynecology, Specialized Clinical Science; Tokai University School of Medicine; 143 Shimokasuya; Isehara-shi; Kanagawa; 259-1193; Japan
| | - Masaki Miyazawa
- Department of Obstetrics and Gynecology, Specialized Clinical Science; Tokai University School of Medicine; 143 Shimokasuya; Isehara-shi; Kanagawa; 259-1193; Japan
| | - Toshinari Muramatsu
- Department of Obstetrics and Gynecology, Specialized Clinical Science; Tokai University School of Medicine; 143 Shimokasuya; Isehara-shi; Kanagawa; 259-1193; Japan
| | - Kyoko Nakamura
- Department of Reproductive Biology; National Research Institute for Child Health and Development; 2-10-1 Okura; Setagaya-ku; Tokyo; 157-8535; Japan
| | - Hisashi Narimatsu
- Research Center for Medical Glycoscience; National Institute of Advanced Industrial Science and Technology; Central-2; 1-1-1, Umezono; Tsukuba; Ibaraki; 305-8568; Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology; National Research Institute for Child Health and Development; 2-10-1 Okura; Setagaya-ku; Tokyo; 157-8535; Japan
| | - Mikio Mikami
- Department of Obstetrics and Gynecology, Specialized Clinical Science; Tokai University School of Medicine; 143 Shimokasuya; Isehara-shi; Kanagawa; 259-1193; Japan
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32
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Jeong HJ, Kim YG, Yang YH, Kim BG. High-throughput quantitative analysis of total N-glycans by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chem 2012; 84:3453-60. [PMID: 22455307 DOI: 10.1021/ac203440c] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate and reproducible quantification of glycans from protein drugs has become an important issue for quality control of therapeutic proteins in biopharmaceutical and biotechnology industries. Mass spectrometry is a promising tool for both qualitative and quantitative analysis of glycans owing to mass accuracy, efficiency, and reproducibility, but it has been of limited success in quantitative analysis for sialylated glycans in a high-throughput manner. Here, we present a solid-phase permethylation-based total N-glycan quantitative method that includes N-glycan releasing, purification, and derivatization on a 96-well plate platform. The solid-phase neutralization enabled us to perform reliable absolute quantification of the acidic N-glycans as well as neutral N-glycans from model glycoproteins (i.e., chicken ovalbumin and porcine thyroglobulin) by only using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Furthermore, low-abundance sialylated N-glycans from human serum prostate specific antigen (PSA), an extremely valuable prostate cancer marker, were initially quantified, and their chemical compositions were proposed. Taken together, these results demonstrate that our all-inclusive glycan preparation method based on a 96-well plate platform may contribute to the precise and reliable qualitative and quantitative analysis of glycans.
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Affiliation(s)
- Hee-Jin Jeong
- School of Chemical and Biological Engineering in College of Engineering, Seoul National University, Shillim-dong, Seoul, 151-742, Korea
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Robinson LN, Artpradit C, Raman R, Shriver ZH, Ruchirawat M, Sasisekharan R. Harnessing glycomics technologies: integrating structure with function for glycan characterization. Electrophoresis 2012; 33:797-814. [PMID: 22522536 PMCID: PMC3743516 DOI: 10.1002/elps.201100231] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Glycans, or complex carbohydrates, are a ubiquitous class of biological molecule which impinge on a variety of physiological processes ranging from signal transduction to tissue development and microbial pathogenesis. In comparison to DNA and proteins, glycans present unique challenges to the study of their structure and function owing to their complex and heterogeneous structures and the dominant role played by multivalency in their sequence-specific biological interactions. Arising from these challenges, there is a need to integrate information from multiple complementary methods to decode structure-function relationships. Focusing on acidic glycans, we describe here key glycomics technologies for characterizing their structural attributes, including linkage, modifications, and topology, as well as for elucidating their role in biological processes. Two cases studies, one involving sialylated branched glycans and the other sulfated glycosaminoglycans, are used to highlight how integration of orthogonal information from diverse datasets enables rapid convergence of glycan characterization for development of robust structure-function relationships.
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Affiliation(s)
- Luke N. Robinson
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Charlermchai Artpradit
- Program in Applied Biological Sciences: Environmental Health, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Rahul Raman
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Zachary H. Shriver
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Mathuros Ruchirawat
- Program in Applied Biological Sciences: Environmental Health, Chulabhorn Graduate Institute, Bangkok, Thailand
- Laboratory of Environmental Toxicology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Ram Sasisekharan
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
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Farwanah H, Kolter T. Lipidomics of glycosphingolipids. Metabolites 2012; 2:134-64. [PMID: 24957371 PMCID: PMC3901200 DOI: 10.3390/metabo2010134] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/27/2012] [Accepted: 01/30/2012] [Indexed: 01/14/2023] Open
Abstract
Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed.
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Affiliation(s)
- Hany Farwanah
- Life and Medical Sciences Institute (LiMES), Membrane Biology and Lipid Biochemistry Unit, c/o Kekulé-Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk Str. 1, D-53121 Bonn, Germany.
| | - Thomas Kolter
- Life and Medical Sciences Institute (LiMES), Membrane Biology and Lipid Biochemistry Unit, c/o Kekulé-Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk Str. 1, D-53121 Bonn, Germany.
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35
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Glycomics: An Overview of the Complex Glycocode. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 749:1-13. [DOI: 10.1007/978-1-4614-3381-1_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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36
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Fry S, Afrough B, Leathem A, Dwek M. Lectin array-based strategies for identifying metastasis-associated changes in glycosylation. Methods Mol Biol 2012; 878:267-272. [PMID: 22674140 DOI: 10.1007/978-1-61779-854-2_18] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Since 2005, lectin microarray technology has emerged as a relatively simple yet powerful technique for the comprehensive analysis of glycoprotein glycosylation. Lectin microarrays represent a new analytical method that can be used to explore the human glycome, a unique source of markers of diseases including cancer. The lectin microarray technology is a sensitive tool with the potential to allow high-throughput analysis of cancer-associated changes in glycosylation. This chapter describes the generation of a lectin-binding signature associated with metastatic primary breast tumours that have been resected, fixed, and embedded in paraffin. Procedures concerning sample and lectin microarray preparation are explained, alongside experimental considerations and approaches to data analysis.
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Affiliation(s)
- Simon Fry
- Department of Molecular and Applied Biosciences, School of Life Sciences, University of Westminster, London, UK
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37
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Hexapeptide library as a universal tool for sample preparation in protein glycosylation analysis. J Proteomics 2011; 75:1515-28. [PMID: 22154983 DOI: 10.1016/j.jprot.2011.11.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/14/2011] [Accepted: 11/21/2011] [Indexed: 11/21/2022]
Abstract
Recent analytical advancements allow for large-scale glycomics and glycan-biomarker research with N-glycans released from complex protein mixtures of e.g. plasma with a wide range of protein concentrations. Protein enrichment techniques to obtain samples with a better representation of low-abundance proteins are hardy applied. In this study, hexapeptide ligands previously described for enrichment of low-abundance proteins in proteomics are evaluated for glycan analysis. A repeatable on-bead glycan release strategy was developed, and glycans were analyzed using capillary sieving electrophoresis on a DNA analyzer. Binding of proteins to the hexapeptide library occurred via the protein backbone. At neutral pH no discrimination between protein glycoforms was observed. Interestingly, glycan profiles of plasma with and without hexapeptide library enrichment revealed very similar patterns, despite the vast changes in protein concentrations in the samples. The most significant differences in glycosylation profiles were ascribed to a reduction in immunoglobulin-derived glycans. These results suggest that specific and sensitive biomarkers will be hard to access on the full plasma level using protein enrichment in combination with glycan analysis. Instead, fractionation techniques or profiling strategies on the glycopeptide level after enrichment are proposed for in-depth glycoproteomics research.
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38
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Thimiri Govinda Raj DB, Ghesquière B, Tharkeshwar AK, Coen K, Derua R, Vanderschaeghe D, Rysman E, Bagadi M, Baatsen P, De Strooper B, Waelkens E, Borghs G, Callewaert N, Swinnen J, Gevaert K, Annaert W. A novel strategy for the comprehensive analysis of the biomolecular composition of isolated plasma membranes. Mol Syst Biol 2011; 7:541. [PMID: 22027552 PMCID: PMC3261717 DOI: 10.1038/msb.2011.74] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 09/07/2011] [Indexed: 02/07/2023] Open
Abstract
We manufactured a novel type of lipid-coated superparamagnetic nanoparticles that allow for a rapid isolation of plasma membranes (PMs), enabling high-resolution proteomic, glycomic and lipidomic analyses of the cell surface. We used this technology to characterize the effects of presenilin knockout on the PM composition of mouse embryonic fibroblasts. We found that many proteins are selectively downregulated at the cell surface of presenilin knockout cells concomitant with lowered surface levels of cholesterol and certain sphingomyelin species, indicating defects in specific endosomal transport routes to and/or from the cell surface. Snapshots of N-glycoproteomics and cell surface glycan profiling further underscored the power and versatility of this novel methodology. Since PM proteins provide many pathologically relevant biomarkers representing two-thirds of the currently used drug targets, this novel technology has great potential for biomedical and pharmaceutical applications.
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Affiliation(s)
- Deepak B Thimiri Govinda Raj
- Department of Molecular and Developmental Genetics (VIB11), Laboratory for Membrane Trafficking and Center for Human Genetics (KULeuven), Gasthuisberg O&N4, Leuven, Belgium
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39
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Vivekanandan-Giri A, Slocum JL, Buller CL, Basrur V, Ju W, Pop-Busui R, Lubman DM, Kretzler M, Pennathur S. Urine glycoprotein profile reveals novel markers for chronic kidney disease. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:214715. [PMID: 22091387 PMCID: PMC3196258 DOI: 10.1155/2011/214715] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 07/30/2011] [Indexed: 11/18/2022]
Abstract
Chronic kidney disease (CKD) is a significant public health problem, and progression to end-stage renal disease leads to dramatic increases in morbidity and mortality. The mechanisms underlying progression of disease are poorly defined, and current noninvasive markers incompletely correlate with disease progression. Therefore, there is a great need for discovering novel markers for CKD. We utilized a glycoproteomic profiling approach to test the hypothesis that the urinary glycoproteome profile from subjects with CKD would be distinct from healthy controls. N-linked glycoproteins were isolated and enriched from the urine of healthy controls and subjects with CKD. This strategy identified several differentially expressed proteins in CKD, including a diverse array of proteins with endopeptidase inhibitor activity, protein binding functions, and acute-phase/immune-stress response activity supporting the proposal that inflammation may play a central role in CKD. Additionally, several of these proteins have been previously linked to kidney disease implicating a mechanistic role in disease pathogenesis. Collectively, our observations suggest that the human urinary glycoproteome may serve as a discovery source for novel mechanism-based biomarkers of CKD.
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Affiliation(s)
| | - Jessica L. Slocum
- Division of Nephrology, University of Michigan, Ann Arbor, MI 48105, USA
| | - Carolyn L. Buller
- Division of Nephrology, University of Michigan, Ann Arbor, MI 48105, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan, Ann Arbor, MI 48105, USA
| | - Wenjun Ju
- Division of Nephrology, University of Michigan, Ann Arbor, MI 48105, USA
| | - Rodica Pop-Busui
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48105, USA
| | - David M. Lubman
- Department of Pathology, University of Michigan, Ann Arbor, MI 48105, USA
- Department of Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48105, USA
- Department of Surgery, University of Michigan, Ann Arbor, MI 48105, USA
| | - Matthias Kretzler
- Division of Nephrology, University of Michigan, Ann Arbor, MI 48105, USA
- Department of Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48105, USA
| | - Subramaniam Pennathur
- Division of Nephrology, University of Michigan, Ann Arbor, MI 48105, USA
- Department of Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48105, USA
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40
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Jacobs PP, Sackstein R. CD44 and HCELL: preventing hematogenous metastasis at step 1. FEBS Lett 2011; 585:3148-58. [PMID: 21827751 DOI: 10.1016/j.febslet.2011.07.039] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 07/21/2011] [Indexed: 12/23/2022]
Abstract
Despite great strides in our knowledge of the genetic and epigenetic changes underlying malignancy, we have limited information on the molecular basis of metastasis. Over 90% of cancer deaths are caused by spread of tumor cells from a primary site to distant organs and tissues, highlighting the pressing need to define the molecular effectors of cancer metastasis. Mounting evidence suggests that circulating tumor cells (CTCs) home to specific tissues by hijacking the normal leukocyte trafficking mechanisms. Cancer cells characteristically express CD44, and there is increasing evidence that hematopoietic cell E-/L-selectin ligand (HCELL), a sialofucosylated glycoform of CD44, serves as the major selectin ligand on cancer cells, allowing interaction of tumor cells with endothelium, leukocytes, and platelets. Here, we review the structural biology of CD44 and of HCELL, and present current data on the function of these molecules in mediating organ-specific homing/metastasis of CTCs.
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Affiliation(s)
- Pieter P Jacobs
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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41
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Mittermayr S, Bones J, Doherty M, Guttman A, Rudd PM. Multiplexed analytical glycomics: rapid and confident IgG N-glycan structural elucidation. J Proteome Res 2011; 10:3820-9. [PMID: 21699237 DOI: 10.1021/pr200371s] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
N-glycans attached to the C(H)2 domains of the Fc or the antigen binding regions of IgG play an important role in stabilizing and modulating antibody activity. Exhaustive elucidation of 32 IgG N-glycans using a combination of weak anion exchange enrichment and exoglycosidase array digestion with subsequent profiling exceeded 48 h. Pursuing increased throughput and associated structural annotation confidence, we compared the 1.7 μm hydrophilic interaction phase for UPLC with CE-LIF for the rapid and comprehensive characterization of N-glycans released from healthy human serum polyclonal IgG. Combination of the data individually generated using each technique demonstrated that complete structural annotation was possible within a total analysis time of 20 min due to the advantageous orthogonality of the separation mechanisms. The parallel use of both analytical techniques provides a powerful platform for rapid and comprehensive analysis of IgG N-glycosylation present on therapeutic antibodies or on antibodies of biomedical or pathological significance.
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Affiliation(s)
- Stefan Mittermayr
- NIBRT Dublin-Oxford Glycobiology Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
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42
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Glycobiomarkers by glycoproteomics and glycan profiling (glycomics): emergence of functionality. Biochem Soc Trans 2011; 39:399-405. [PMID: 21265812 DOI: 10.1042/bst0390399] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycans stand out from all classes of biomolecules because of their unsurpassed structural complexity. This is generated by variability in anomeric status of the glycosidic bond and its linkage points, ring size, potential for branching and introduction of diverse site-specific substitutions. What poses an enormous challenge for analytical processing is, at the same time, the basis for the fingerprint-like glycomic profiles of glycoconjugates and cells. What's more, the glycosylation machinery is sensitive to disease manifestations, earning glycan assembly a reputation as a promising candidate to identify new biomarkers. Backing this claim for a perspective in clinical practice are recent discoveries that even seemingly subtle changes in the glycan structure of glycoproteins, such as a N-glycan core substitution by a single sugar moiety, have far-reaching functional consequences. They are brought about by altering the interplay between the glycan and (i) its carrier protein and (ii) specific receptors (lectins). Glycan attachment thus endows the protein with a molecular switch and new recognition sites. Co-ordinated regulation of glycan display and presentation of the cognate lectin, e.g. in cancer growth regulation exerted by a tumour suppressor, further exemplifies the broad functional dimension inherent to the non-random shifts in glycosylation. Thus studies on glycobiomarkers converge with research on how distinct carbohydrate determinants are turned into bioactive signals.
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43
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Fry SA, Afrough B, Lomax-Browne HJ, Timms JF, Velentzis LS, Leathem AJC. Lectin microarray profiling of metastatic breast cancers. Glycobiology 2011; 21:1060-70. [PMID: 21507904 DOI: 10.1093/glycob/cwr045] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Altered protein glycosylation compared with the disease-free state is a universal feature of cancer cells. It has long been established that distinct glycan structures are associated with specific forms of cancer, but far less is known about the complete array of glycans associated with certain tumors. The cancer glycome has great potential as a source of biomarkers, but progress in this field has been hindered by a lack of available techniques for the elucidation of disease-associated glycosylation. In the present study, lectin microarrays consisting of 45 lectins with different binding preferences covering N- and O-linked glycans were coupled with evanescent-field activated fluorescent detection in the glycomic analysis of primary breast tumors and the serum and urine of patients with metastatic breast cancer. A single 50 µm section of a primary breast tumor or <1 µL of breast cancer patient serum or urine was sufficient to detect glycosylation alterations associated with metastatic breast cancer, as inferred from lectin-binding patterns. The high-throughput, sensitive and relatively simple nature of the simultaneous analysis of N- and O-linked glycosylation following minimal sample preparation and without the need for protein deglycosylation makes the lectin microarray analysis described a valuable tool for discovery phase glycomic profiling.
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Affiliation(s)
- Simon A Fry
- Breast Cancer Research Group, EGA Institute for Women's Health, University College London, London WC1E 6BT, UK.
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44
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von der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR, Dell A, Dwek RA, Ernst B, Fogh R, Frank M, Geyer H, Geyer R, Harrison MJ, Henrick K, Herget S, Hull WE, Ionides J, Joshi HJ, Kamerling JP, Leeflang BR, Lütteke T, Lundborg M, Maass K, Merry A, Ranzinger R, Rosen J, Royle L, Rudd PM, Schloissnig S, Stenutz R, Vranken WF, Widmalm G, Haslam SM. EUROCarbDB: An open-access platform for glycoinformatics. Glycobiology 2011; 21:493-502. [PMID: 21106561 PMCID: PMC3055595 DOI: 10.1093/glycob/cwq188] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/03/2010] [Accepted: 11/03/2010] [Indexed: 01/03/2023] Open
Abstract
The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.
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Affiliation(s)
| | - Ana Ardá Freire
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Dennis Blank
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | - Matthew P Campbell
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Alessio Ceroni
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - David R Damerell
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Anne Dell
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Raymond A Dwek
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Beat Ernst
- Department of Pharmaceutical Science, University of Basel, BaselSwitzerland
| | - Rasmus Fogh
- European Bioinformatics Institute, Hinxton, UK
| | - Martin Frank
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Hildegard Geyer
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | - Rudolf Geyer
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | | | - Kim Henrick
- European Bioinformatics Institute, Hinxton, UK
| | - Stefan Herget
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - William E Hull
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | | | - Hiren J Joshi
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
- European Bioinformatics Institute, Hinxton, UK
| | - Johannis P Kamerling
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Bas R Leeflang
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Thomas Lütteke
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | | | - Kai Maass
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | | | - René Ranzinger
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Jimmy Rosen
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Louise Royle
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Pauline M Rudd
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Siegfried Schloissnig
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Roland Stenutz
- Organic Chemistry, Stockholm University, Stockholm, Sweden
| | | | - Göran Widmalm
- Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Stuart M Haslam
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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45
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Pabst M, Altmann F. Glycan analysis by modern instrumental methods. Proteomics 2011; 11:631-43. [PMID: 21241022 DOI: 10.1002/pmic.201000517] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/02/2010] [Accepted: 11/03/2010] [Indexed: 12/23/2022]
Abstract
The oligosaccharides attached to proteins or lipids are among the most challenging analytical tasks due to their complexity and variety. Knowing the genes and enzymes responsible for their biosynthesis, a large but not unlimited number of different structures and isomers of such glycans can be imagined. Understanding of the biological role of structural variations requires the ability to unambiguously determine the identity and quantity of all glycan species. Here, we examine, which analytical strategies - with a certain high-throughput potential - may come near this ideal. After an expose of the relevant techniques, we try to depict how analytical raw data are translated into structural assignments using retention times, mass and fragment spectra. A method's ability to discriminate between the many conceivable isomeric structures together with the time, effort and sample amount needed for that purpose is suggested as a criterion for the comparative assessment of approaches and their evolutionary stages.
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Affiliation(s)
- Martin Pabst
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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46
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Vanderschaeghe D, Szekrényes A, Wenz C, Gassmann M, Naik N, Bynum M, Yin H, Delanghe J, Guttman A, Callewaert N. High-throughput profiling of the serum N-glycome on capillary electrophoresis microfluidics systems: toward clinical implementation of GlycoHepatoTest. Anal Chem 2011; 82:7408-15. [PMID: 20684520 DOI: 10.1021/ac101560a] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We developed a 3 h procedure for preparing serum N-glycans and labeling them with 8-aminopyrene-1,3,6-trisulfonic acid (APTS) by sequential addition of reagents to the serum and incubation in a polymerase chain reaction (PCR) thermocycler. Moreover, we succeeded in analyzing these samples by capillary electrophoresis on three commercial microfluidics-based platforms: the MCE-202 MultiNA, the 2100 Bioanalyzer, and a modified prototype of the eGene system which were originally designed for nucleic acid separation and detection. Although these instruments use short separation channels, our technical improvements made it possible to reliably measure the N-glycans constituting GlycoHepatoTest. This test comprises a panel of biomarkers that allows follow-up of liver fibrosis patients starting from the early stage. In this way and for the first time, we demonstrate a clinical glycomics assay on an affordable, robust platform so that clinical chemistry laboratories can exploit glycomics in the diagnosis and monitoring of chronic liver disease. Another potential application is the rapid screening of the N-glycosylation of recombinant glycoproteins produced for pharmaceutical use.
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Affiliation(s)
- Dieter Vanderschaeghe
- Unit for Molecular Glycobiology, Department for Molecular Biomedical Research, VIB, Technologiepark 927, B-9052 Ghent, Belgium
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47
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Rakus JF, Mahal LK. New technologies for glycomic analysis: toward a systematic understanding of the glycome. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:367-392. [PMID: 21456971 DOI: 10.1146/annurev-anchem-061010-113951] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Carbohydrates are the most difficult class of biological molecules to study by high-throughput methods owing to the chemical similarities between the constituent monosaccharide building blocks, template-less biosynthesis, and the lack of clearly identifiable consensus sequences for the glycan modification of cohorts of glycoproteins. These molecules are crucial for a wide variety of cellular processes ranging from cell-cell communication to immunity, and they are altered in disease states such as cancer and inflammation. Thus, there has been a dedicated effort to develop glycan analysis into a high-throughput analytical field termed glycomics. Herein we highlight major advances in applying separation, mass spectrometry, and microarray methods to the fields of glycomics and glycoproteomics. These new analytical techniques are rapidly advancing our understanding of the importance of glycosylation in biology and disease.
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Affiliation(s)
- John F Rakus
- Department of Chemistry, New York University, New York, New York 10003, USA.
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48
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Cortes DF, Kabulski JL, Lazar AC, Lazar IM. Recent advances in the MS analysis of glycoproteins: Capillary and microfluidic workflows. Electrophoresis 2011; 32:14-29. [PMID: 21171110 PMCID: PMC3717299 DOI: 10.1002/elps.201000394] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/21/2010] [Accepted: 09/21/2010] [Indexed: 12/26/2022]
Abstract
Recent developments in bioanalytical instrumentation, MS detection, and computational data analysis approaches have provided researchers with capabilities for interrogating the complex cellular glycoproteome, to help gain a better insight into the cellular and physiological processes that are associated with a disease and to facilitate the efforts centered on identifying disease-specific biomarkers. This review describes the progress achieved in the characterization of protein glycosylation by using advanced capillary and microfluidic MS technologies. The major steps involved in large-scale glycoproteomic analysis approaches are discussed, with special emphasis given to workflows that have evolved around complex MS detection functions. In addition, quantitative analysis strategies are assessed, and the bioinformatics aspects of glycoproteomic data processing are summarized. The developments in commercial and custom fabricated microfluidic front-end platforms to ESI- and MALDI-MS instrumentation, for addressing major challenges in carbohydrate analysis such as sensitivity, throughput, and ability to perform structural characterization, are further evaluated and illustrated with relevant examples.
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Affiliation(s)
- Diego F. Cortes
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
| | - Jarod L. Kabulski
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
| | | | - Iulia M. Lazar
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
- Department of Biological Sciences, Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
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49
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Hart GW, Copeland RJ. Glycomics hits the big time. Cell 2010; 143:672-6. [PMID: 21111227 DOI: 10.1016/j.cell.2010.11.008] [Citation(s) in RCA: 499] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 10/27/2010] [Accepted: 11/02/2010] [Indexed: 10/18/2022]
Abstract
Cells run on carbohydrates. Glycans, sequences of carbohydrates conjugated to proteins and lipids, are arguably the most abundant and structurally diverse class of molecules in nature. Recent advances in glycomics reveal the scope and scale of their functional roles and their impact on human disease.
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Affiliation(s)
- Gerald W Hart
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21205-2185, USA.
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50
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Lazar IM, Lazar AC, Cortes DF, Kabulski JL. Recent advances in the MS analysis of glycoproteins: Theoretical considerations. Electrophoresis 2010; 32:3-13. [PMID: 21171109 DOI: 10.1002/elps.201000393] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 01/19/2023]
Abstract
Protein glycosylation is involved in a broad range of biological processes that regulate protein function and control cell fate. As aberrant glycosylation has been found to be implicated in numerous diseases, the study and large-scale characterization of protein glycosylation is of great interest not only to the biological and biomedical research community, but also to the pharmaceutical and biotechnology industry. Due to the complex chemical structure and differing chemical properties of the protein/peptide and glycan moieties, the analysis and structural characterization of glycoproteins has been proven to be a difficult task. Large-scale endeavors have been further limited by the dynamic outcome of the glycosylation process itself, and, occasionally, by the low abundance of glycoproteins in biological samples. Recent advances in MS instrumentation and progress in miniaturized technologies for sample handling, enrichment and separation, have resulted in robust and compelling analysis strategies that effectively address the challenges of the glycoproteome. This review summarizes the key steps that are involved in the development of efficient glycoproteomic analysis methods, and the latest innovations that led to successful strategies for the characterization of glycoproteins and their corresponding glycans. As a follow-up to this work, we review innovative capillary and microfluidic-MS workflows for the identification, sequencing and characterization of glycoconjugates.
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Affiliation(s)
- Iulia M Lazar
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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