Special Issue "Glycomics and Glycoproteomics"

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A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: closed (20 September 2012)

Special Issue Editor

Guest Editor
Dr. Yehia Mechref (Website)

Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
Interests: Analytical and Bioanalytical methods, Chemical Separation, Glycomics, Glycoproeomics, Proteomics

Special Issue Information

Dear Colleagues,

The importance of posttranslational modifications in modulating the activities and functions of proteins in health and disease is illustrated by the fact that no more than 30,000-50,000 proteins are encoded by the human genome.  The importance of protein glycosylation has been reflected in the fact that cell-cell interactions involve sugar-sugar, or sugar-protein specific recognition.  Consequently, aberrant glycosylation has now been recognized as the attribute of many mammalian diseases, including hereditary disorders, immune deficiencies, neurodegenerative diseases, cardiovascular disease, and cancer.  This special issue will focus on detailing the emerging trends in glycomics and glycoproteomics allowing better understanding of the biological roles of glycans and glycoproteins.

This special issue will consider research papers focused on the analysis and characterization of glycans and glycoproteins to allow better understanding of their biological roles. Novel liquid phase separation methods (HPLC, Nano-LC, gel electrophoresis, CE, CEC, microchip, and microfluidics) combined with all kinds of detection including on line and off line mass spectrometry and laser-induced fluorescence detection or any other type of detection are of high interest for this issue. Papers describing novel sample derivatization, preparation/concentration ,or any enrichment approaches will be considered for publication in this issue.

Dr. Yehia Mechref
Guest Editor

Keywords

  • glycomics
  • glycoproteomics
  • LC-MS/MS
  • capillary electrophoresis
  • CE-MS
  • lectin affinity chromatography
  • glycoprotein enrichment
  • computational approaches
  • data interpretation

Published Papers (5 papers)

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Research

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Open AccessArticle Comparative Analysis of End Point Enzymatic Digests of Arabino-Xylan Isolated from Switchgrass (Panicum virgatum L) of Varying Maturities using LC-MSn
Metabolites 2012, 2(4), 959-982; doi:10.3390/metabo2040959
Received: 14 September 2012 / Revised: 30 October 2012 / Accepted: 9 November 2012 / Published: 19 November 2012
Cited by 3 | PDF Full-text (683 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Switchgrass (Panicum virgatum L., SG) is a perennial grass presently used for forage and being developed as a bioenergy crop for conversion of cell wall carbohydrates to biofuels. Up to 50% of the cell wall associated carbohydrates are xylan. SG was [...] Read more.
Switchgrass (Panicum virgatum L., SG) is a perennial grass presently used for forage and being developed as a bioenergy crop for conversion of cell wall carbohydrates to biofuels. Up to 50% of the cell wall associated carbohydrates are xylan. SG was analyzed for xylan structural features at variable harvest maturities. Xylan from each of three maturities was isolated using classical alkaline extraction to yield fractions (Xyl A and B) with varying compositional ratios. The Xyl B fraction was observed to decrease with plant age. Xylan samples were subsequently prepared for structure analysis by digesting with pure endo-xylanase, which preserved side-groups, or a commercial carbohydrase preparation favored for biomass conversion work. Enzymatic digestion products were successfully permethylated and analyzed by reverse-phase liquid chromatography with mass spectrometric detection (RP-HPLC-MSn). This method is advantageous compared to prior work on plant biomass because it avoids isolation of individual arabinoxylan oligomers. The use of RP-HPLC- MSn differentiated 14 structural oligosaccharides (d.p. 3–9) from the monocomponent enzyme digestion and nine oligosaccharide structures (d.p. 3–9) from hydrolysis with a cellulase enzyme cocktail. The distribution of arabinoxylan oligomers varied depending upon the enzyme(s) applied but did not vary with harvest maturity. Full article
(This article belongs to the Special Issue Glycomics and Glycoproteomics)
Open AccessArticle Structural Identification of O-Linked Oligosaccharides Using Exoglycosidases and MSn Together with UniCarb-DB Fragment Spectra Comparison
Metabolites 2012, 2(4), 648-666; doi:10.3390/metabo2040648
Received: 17 July 2012 / Revised: 18 September 2012 / Accepted: 28 September 2012 / Published: 8 October 2012
Cited by 4 | PDF Full-text (796 KB) | HTML Full-text | XML Full-text
Abstract
The availability of specific exoglycosidases alongside a spectral library of O-linked oligosaccharide collision induced dissociation (CID) MS fragments, UniCarb-DB, provides a pathway to make the elucidation of O-linked oligosaccharides more efficient. Here, we advise an approach of exoglycosidase-digestion of O [...] Read more.
The availability of specific exoglycosidases alongside a spectral library of O-linked oligosaccharide collision induced dissociation (CID) MS fragments, UniCarb-DB, provides a pathway to make the elucidation of O-linked oligosaccharides more efficient. Here, we advise an approach of exoglycosidase-digestion of O-linked oligosaccharide mixtures, for structures that do not provide confirmative spectra. The combination of specific exoglycosidase digestion and MS2 matching of the exoglycosidase products with structures from UniCarb-DB, allowed the assignment of unknown structures. This approach was illustrated by treating sialylated core 2 O-linked oligosaccharides, released from the human synovial glycoprotein (lubricin), with a α2–3 specific sialidase. This methodology demonstrated the exclusive 3 linked nature of the sialylation of core 2 oligosaccharides on lubricin. When specific exoglycosidases were not available, MS3 spectral matching using standards was used. This allowed the unusual 4-linked terminal GlcNAc epitope in a porcine stomach to be identified in the GlcNAc1-4Galb1–3(GlcNAcb1-6)GalNAcol structure, indicating the antibacterial epitope GlcNAca1–4. In total, 13 structures were identified using exoglycosidase and MSn, alongside UniCarb-DB fragment spectra comparison. UniCarb-DB could also be used to identify the specificity of unknown exoglycosidases in human saliva. Endogenous salivary exoglycosidase activity on mucin oligosaccharides could be monitored by comparing the generated tandem MS spectra with those present in UniCarb-DB, showing that oral exoglycosidases were dominated by sialidases with a higher activity towards 3-linked sialic acid rather than 6-linked sialic acid. Full article
(This article belongs to the Special Issue Glycomics and Glycoproteomics)

Review

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Open AccessReview Glycomics Approaches for the Bioassay and Structural Analysis of Heparin/Heparan Sulphates
Metabolites 2012, 2(4), 1060-1089; doi:10.3390/metabo2041060
Received: 10 October 2012 / Revised: 13 November 2012 / Accepted: 15 November 2012 / Published: 28 November 2012
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Abstract
The glycosaminoglycan heparan sulphate (HS) has a heterogeneous structure; evidence shows that specific structures may be responsible for specific functions in biological processes such as blood coagulation and regulation of growth factor signalling. This review summarises the different experimental tools and methods [...] Read more.
The glycosaminoglycan heparan sulphate (HS) has a heterogeneous structure; evidence shows that specific structures may be responsible for specific functions in biological processes such as blood coagulation and regulation of growth factor signalling. This review summarises the different experimental tools and methods developed to provide more rapid methods for studying the structure and functions of HS. Rapid and sensitive methods for the facile purification of HS, from tissue and cell sources are reviewed. Data sets for the structural analysis are often complex and include multiple sample sets, therefore different software and tools have been developed for the analysis of different HS data sets. These can be readily applied to chromatographic data sets for the simplification of data (e.g., charge separation using strong anion exchange chromatography and from size separation using gel filtration techniques. Finally, following the sequencing of the human genome, research has rapidly advanced with the introduction of high throughput technologies to carry out simultaneous analyses of many samples. Microarrays to study macromolecular interactions (including glycan arrays) have paved the way for bioassay technologies which utilize cell arrays to study the effects of multiple macromolecules on cells. Glycan bioassay technologies are described in which immobilisation techniques for saccharides are exploited to develop a platform to probe cell responses such as signalling pathway activation. This review aims at reviewing available techniques and tools for the purification, analysis and bioassay of HS saccharides in biological systems using “glycomics” approaches. Full article
(This article belongs to the Special Issue Glycomics and Glycoproteomics)
Open AccessReview Glycomic Expression in Esophageal Disease
Metabolites 2012, 2(4), 1004-1011; doi:10.3390/metabo2041004
Received: 25 September 2012 / Revised: 5 November 2012 / Accepted: 9 November 2012 / Published: 21 November 2012
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Abstract
Glycosylation is among the most common post translation modifications of proteins in humans. Decades of research have demonstrated that aberrant glycosylation can lead to malignant degeneration. Glycoproteomic studies in the past several years have identified techniques that can successfully characterize a glycan [...] Read more.
Glycosylation is among the most common post translation modifications of proteins in humans. Decades of research have demonstrated that aberrant glycosylation can lead to malignant degeneration. Glycoproteomic studies in the past several years have identified techniques that can successfully characterize a glycan or glycan profile associated with a high-grade dysplastic or malignant state. This review summarizes the current glycomic and glycoproteomic literature with specific reference to esophageal cancer. Esophageal adenocarcinoma represents a highly morbid and mortal cancer with a defined progression from metaplasia (Barrett's esophagus) to dysplasia to neoplasia. This disease is highlighted because (1) differences in glycan profiles between the stages of disease progression have been described in the glycoproteomic literature; (2) a glycan biomarker that identifies a given stage may be used as a predictor of disease progression and thus may have significant influence over clinical management; and (3) the differences in glycan profiles between disease and disease-free states in esophageal cancer are more dramatic than in other cancers. Full article
(This article belongs to the Special Issue Glycomics and Glycoproteomics)
Open AccessReview Tumor-Associated Glycans and Their Role in Gynecological Cancers: Accelerating Translational Research by Novel High-Throughput Approaches
Metabolites 2012, 2(4), 913-939; doi:10.3390/metabo2040913
Received: 31 October 2012 / Revised: 8 November 2012 / Accepted: 9 November 2012 / Published: 14 November 2012
Cited by 11 | PDF Full-text (373 KB) | HTML Full-text | XML Full-text
Abstract
Glycans are important partners in many biological processes, including carcinogenesis. The rapidly developing field of functional glycomics becomes one of the frontiers of biology and biomedicine. Aberrant glycosylation of proteins and lipids occurs commonly during malignant transformation and leads to the expression [...] Read more.
Glycans are important partners in many biological processes, including carcinogenesis. The rapidly developing field of functional glycomics becomes one of the frontiers of biology and biomedicine. Aberrant glycosylation of proteins and lipids occurs commonly during malignant transformation and leads to the expression of specific tumor-associated glycans. The appearance of aberrant glycans on carcinoma cells is typically associated with grade, invasion, metastasis and overall poor prognosis. Cancer-associated carbohydrates are mostly located on the surface of cancer cells and are therefore potential diagnostic biomarkers. Currently, there is increasing interest in cancer-associated aberrant glycosylation, with growing numbers of characteristic cancer targets being detected every day. Breast and ovarian cancer are the most common and lethal malignancies in women, respectively, and potential glycan biomarkers hold promise for early detection and targeted therapies. However, the acceleration of research and comprehensive multi-target investigation of cancer-specific glycans could only be successfully achieved with the help of a combination of novel high-throughput glycomic approaches. Full article
(This article belongs to the Special Issue Glycomics and Glycoproteomics)

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