Showing papers on "Glycome published in 2008"

Mammalian glycosylation in immunity

Abstract: This Review discusses how the diversity of glycan structures that are produced in the secretory pathway and are displayed at the cell surface and in extracellular compartments can have both homeostatic and pathogenic effects on the development and function of the mammalian immune system. Glycosylation produces a diverse and abundant repertoire of glycans, which are collectively known as the glycome. Glycans are one of the four fundamental macromolecular components of all cells, and are highly regulated in the immune system. Their diversity reflects their multiple biological functions that encompass ligands for proteinaceous receptors known as lectins. Since the discovery that selectins and their glycan ligands are important for the regulation of leukocyte trafficking, it has been shown that additional features of the vertebrate immune system are also controlled by endogenous cellular glycosylation. This Review focuses on the emerging immunological roles of the mammalian glycome.

Evaluation of the serum N-linked glycome for the diagnosis of cancer and chronic inflammation

Abstract: The identification of serum biomarkers has lead to improvements in the detection and diagnosis of cancer, and combinations of these biomarkers have increased further their sensitivity and specificity. Glycosylation is the most common PTM of secreted proteins and the identification of novel serum glyco-biomarkers has become a topic of increasing interest because the glycan processing pathways are frequently disturbed in cancer cells. A future goal is to combine current biomarkers with glyco-biomarkers to yield further improvements. Well characterised N-glycosylation changes in the serum glycome of cancer patients include changes in the levels of tri- and tetra-antennary glycan structures, sialyl Lewis X epitopes and agalactosylated bi-antennary glycans. Several of these glycosylated markers have been linked to chronic inflammatory diseases, promoting questions about the links between inflammation and cancer. In this review, the glycoproteins which display these glycan epitopes, the glycosyl transferases which can generate them, their potential functions and their use as biomarkers are evaluated.

Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans.

Abstract: There are considerable differences between bacterial and mammalian glycans. In contrast to most eukaryotic carbohydrates, bacterial glycans are often composed of repeating units with diverse functions ranging from structural reinforcement to adhesion, colonization and camouflage. Since bacterial glycans are typically displayed at the cell surface, they can interact with the environment and, therefore, have significant biomedical importance. The sequence characteristics of glycans (monosaccharide composition, modifications, and linkage patterns) for the higher bacterial taxonomic classes have been examined and compared with the data for mammals, with both similarities and unique features becoming evident. Compared to mammalian glycans, the bacterial glycans deposited in the current databases have a more than ten-fold greater diversity at the monosaccharide level, and the disaccharide pattern space is approximately nine times larger. Specific bacterial subclasses exhibit characteristic glycans which can be distinguished on the basis of distinctive structural features or sequence properties. For the first time a systematic database analysis of the bacterial glycome has been performed. This study summarizes the current knowledge of bacterial glycan architecture and diversity and reveals putative targets for the rational design and development of therapeutic intervention strategies by comparing bacterial and mammalian glycans.

Focused glycomic analysis of the N-linked glycan biosynthetic pathway in ovarian cancer.

Abstract: Epithelial ovarian cancer is the deadliest female reproductive tract malignancy in Western countries. Less than 25% of cases are diagnosed when the cancer is confined, however, pointing to the critical need for early diagnostics for ovarian cancer. Identifying the changes that occur in the glycome of ovarian cancer cells may provide an avenue to develop a new generation of potential biomarkers for early detection of this disease. We performed a glycotranscriptomic analysis of endometrioid ovarian carcinoma using human tissue, as well as a newly developed mouse model that mimics this disease. Our results show that the N-linked glycans expressed in both nondiseased mouse and human ovarian tissues are similar; moreover, malignant changes in the expression of N-linked glycans in both mouse and human endometrioid ovarian carcinoma are qualitatively similar. Lectin reactivity was used as a means for rapid validation of glycan structural changes in the carcinomas that were predicted by the glycotranscriptome analysis. Among several changes in glycan expression noted, the increase of bisected N-linked glycans and the transcripts of the enzyme responsible for its biosynthesis, GnT-III, was the most significant. This study provides evidence that glycotranscriptome analysis can be an important tool in identifying potential cancer biomarkers.

An Introduction to Bioinformatics for Glycomics Research

Abstract: Carbohydrates are considered the thirdclass of information-encoding biologicalmacromolecules ‘‘Glycomics,’’ the scientificattempt to characterize and study carbohy-drates, is a rapidly emerging branch ofscience, for which informatics is just begin-ning Glycomics requires sophisticated algo-rithmic approaches Several algorithms andmodels have been developed for glycobiol-ogy research in the past several years Thistutorial will provide a brief introduction tothe field of glycome informatics, which willinclude a primer on glycobiology as well asdescriptions of the algorithms and modelsthat have been developed in this fieldThe four essential molecular buildingblocks of cells are nucleic acids, proteins,lipids, and carbohydrates, often referred toas glycans Nucleotide and protein sequenc-es are at the heart of nearly all bioinfor-matics applications and research, whereasglycan and lipid structures have been widelyneglected in bioinformatics However, gly-cans are the most abundant and structurallydiverse biopolymers formed in natureBound to proteins, as glycoproteins, theyare known to affectthefunctions of proteinsMore than half of all protein sequencesdeposited in the SWISS-PROT databankinclude potential glycosylation sites and thusmay be glycoproteins Based on an analysisof well-annotated and characterized glyco-proteins inSWISS-PROT,itwas concludedthat more than half of all proteins areglycosylated [1]The development and use of informaticstools and databases for glycobiology andglycomics research has increased consider-ably in recent years However, the generaldevelopment in this field can still beconsidered as being in its infancy whencompared to the genomics and proteomicsareas In terms of bioinformatics in glyco-biology, there are several paths of researchthat are currently in progress The develop-ment of algorithms to reliably support thecharacterization of glycan structures forhigh-throughput applications is the mostimmediate demand of the glycomics com-munity Additionally, several major glyco-related projects (Consortium for FunctionalGlycomics [2], KEGG Glycan [3], GLY-COSCIENCESde [4]) are maturing andprovide well-structured glyco-related datathat are awaiting data mining and analysisWith the exciting new developments incarbohydrate arrays and automated MSannotation, the analysis of the glycome hasreached a new level of sophistication, whichrequires broader informatics support Thistutorial aims to give an overview of thecurrent status of carbohydrate databases, thenewest analytical techniques, as well as theinformatics needed for rapid progress inglycomics research

Fucosylated glycoproteins as markers of liver disease

Abstract: Changes in N-linked glycosylation are known to occur during the development of various diseases. For example, increased branching of oligosaccharides has been associated with cancer metastasis and has been correlated to tumor progression in human cancers of the breast, colon and melanomas. Increases in core fucosylation have also been associated with the development of hepatocellular carcinoma (HCC). Recently, changes in both the total serum glycome and the glycosylation of specific IgG molecules have been observed in people with liver fibrosis and cirrhosis. The mechanisms by which changes in glycosylation are observed and their use as biomarkers of disease will be discussed.

Characterizing the glycome of the mammalian immune system

Abstract: The outermost layer of all immune cells, the glycocalyx, is composed of a complex mixture of glycoproteins, glycolipids and lectins, which specifically recognize particular glycan epitopes. As the glycocalyx is the cell's primary interface with the external environment many biologically significant events can be attributed to glycan recognition. For this reason the rapidly expanding glycomics field is being increasingly recognized as an important component in our quest to better understand the functioning of the immune system. In this review, we highlight the current status of immune cell glycomics, with particular attention being paid to T- and B-lymphocytes and dendritic cells. We also describe the strategies and methodologies used to define immune cell glycomes.

Glycomics: towards bioinformatic approaches to understanding glycosylation.

Abstract: Cell surface glycoconjugates control a variety of biological events including cell differentiation, homing to specific tissues, cell adhesion, virus/cell recognition and immunological recognition. The heterogeneity and diversity of these molecules present a challenge to understanding both their functions and how those functions are encoded. Advances in biotechnology have led to new methods for genome and proteome study that allow for the analysis of the entire genetic or protein content of a cell. Efforts towards the systematic study of the variations in cellular glycoconjugates are, in contrast, in their infancy. Recent advances in glycosylation related technology have begun to open up the possibility of exploring both the structure and the functions of the glycome in a systematic manner. This review focuses on the latest mass spectrometry, microarray-based and computational technologies for glycomics.

Design of recombinant antibody microarrays for cell surface membrane proteomics

Abstract: Generating proteomic maps of membrane proteins, common targets for therapeutic interventions and disease diagnostics, has turned out to be a major challenge. Antibody-based microarrays are among the novel rapidly evolving proteomic technologies that may enable global proteome analysis to be performed. Here, we have designed the first generation of a scaleable human recombinant scFv antibody microarray technology platform for cell surface membrane proteomics as well as glycomics targeting intact cells. The results showed that rapid and multiplexed profiling of the cell surface proteome (and glycome) could be performed in a highly specific and sensitive manner and that differential expression patterns due to external stimuli could be monitored.

The Potentials of Glycomics in Biomarker Discovery

Abstract: Glycans have unique characteristics that are significantly different from nucleic acids and proteins in terms of biosynthesis, structures, and functions Moreover, their isomeric nature and the complex linkages between residues have made glycan analysis a challenging task Disease development and progression are usually associated with alternations in glycosylation on tissue proteins and/or blood proteins Glycans released from tissue/blood proteins hence provide a valuable source of biomarkers In this postgenome era, glycomics is an emerging research field Glycome refers to a repertoire of glycans in a tissue/cell type, while glycomics is the study of glycome In the past few years, attempts have been made to develop novel methodologies for quantitative glycomic profiling and to identify potential glycobiomarkers It can be foreseen that glycomics holds the promise for biomarker discovery This review provides an overview of the unique features of glycans and the historical applications of such features to biomarker discovery The concept of glycomics and its recent advancement and future prospective in biomarker research are reviewed Above all, there is no doubt that glycomics is gaining momentum in biomarker research

Human total serum N-glycome.

Abstract: The human total serum N-glycome (TSNG) is the representation of the serum glycoproteins N-glycosylation. The study of N-glycosylation in clinical biochemistry laboratories is emerging as a new assay for diagnosis of congenital and acquired diseases. This review describes the N-glycosylation of serum glycoproteins and its contribution to the serum N-glycome, the different protocols allowing the achievement of an N-glycosylation profile, the variations of this profile in diseases, and finally the perspective of applications of the TSNG in the exploration of congenital disorders of glycosylation (CDG), hepatic cirrhosis, inflammatory disorders, autoimmune diseases, and cancers.

A Single Caenorhabditis elegans Golgi Apparatus-Type Transporter of UDP-Glucose, UDP-Galactose, UDP-N-Acetylglucosamine, and UDP-N-Acetylgalactosamine†

Abstract: The genome of Caenorhabditis elegans encodes for 18 putative nucleotide sugar transporters even though its glycome only contains 7 different monosaccharides To understand the biological significance of this phenomenon, we have begun a systematic substrate characterization of the above putative transporters and have determined that the gene ZK8969 encodes a Golgi apparatus transporter for UDP-glucose, UDP-galactose, UDP-N-acetylglucosamine, and UDP-N-acetylgalactosamine This is the first tetrasubstrate nucleotide sugar transporter characterized for any organism and is also the first nonplant transporter for UDP-glucose Evidence for the above substrate specificity and substrate transport saturation kinetics was obtained by expression of ZK8969 in Saccharomyces cerevisiae followed by Golgi enriched vesicle isolation and assays in vitro Further evidence for UDP-glucose transport was obtained by expression of ZK 8969 in Giardia lamblia, an organism recently characterized as having endogenous transport a

Toward cancer biomarker discovery using the glycomics approach.

Abstract: Following on from genomics and proteomics, glycomics has become one of the most important research fields in recent years. The techniques for glycomics are rather complicated as compared to those for genomics and proteomics because glycans are very heterogeneous and there are no amplifying or cloning techniques such as those for PCR or molecular cloning, nor are there any synthesizers or sequencers such as those for DNA and proteins. As a result scientists in the other research fields feel it is difficult to become involved in this field and they have not paid attention to the significance of glycans. However, in the postgenomic era, the significance of posttranslational modification of proteins is gaining significance as more than 50% of proteins are glycosylated and it is impossible for us to understand the protein functions without knowing the glycan functions. Owing to the development of mass spectrometry, NMR, and HPLC/CE, although expensive, scientists are finding it easier to analyze glycan structures. Moreover, glycoscience including glycobiology and glycotechnology is expanding enormously these days. I would like to mention some examples in medical science. Influenza drugs are neuraminidase inhibitors which inhibit growth of the influenza virus, and at the early stage of infectious diseases some bacteria, bacterial toxins and viruses bind firstly to glycans of infected cells. There are more than 30 congenital disorders of glycosylation (CDG), and more than 60 glycosyltransferase gene KO mice have been developed. Interesting phenotypic changes in the mice have been reported in relation to human diseases. Under inflammatory conditions and/or in the process of cancer metastasis, specific glycans of leukocytes, platelets and cancer cells bind specific adhesion molecules, such as selectin with a lectin motif in the endothelial cells which accelerate rolling of cells and cancer metastasis. Antibody therapies against various cancers, such as breast cancer and non-Hodgkin’s lymphoma, are being widely used at present and most of them involve antibodies raised against cell surface receptors such as growth factor receptors. If fucoyslation (a1,6-fucosylation of innermost GlcNAc residues in glycoproteins) is absent in the IgG1 molecules of the above antibodies, the antibodies will facilitate the binding of the FcgIIIa receptor of NK cells or mononuclear cells to their Fc portion of IgG1, and activate those cells and destroy the tumor cells. This is called antibody-dependent cellular cytotoxity (ADCC). The ADCC of antibodies without core fucose is increased up to 50–100-fold as compared to that of ones with core fucose. In August 2002 we launched the HGPI (Human Glycome/Proteomics Initiative) under HUPO (Taniguchi, N., Mol Cell Proteomics 2008, 7, 626–627) and so far two pilot studies involving N-glycan analysis headed by Wada (Wada, EDITORIAL

Liquid Chromatography/Mass Spectrometry (LC/MS)-Based Glycoproteomics Technologies for Cancer Biomarker Discovery

Abstract: Biomarker discovery is a major objective of clinical proteomics; molecular biomarkers allow for detection of early-stage human diseases, especially cancer, and for monitoring their progression and/or regression after treatment. Biomarkers also help to elucidate the pathology of disease and its diagnosis, drug discovery, and toxicology. Glycans are ideal candidates for biomarkers because (1) glycoconjugates are localized on the cell surface and in the secretions such as plasma, (2) their structures are frequently and drastically changed during normal and aberrant cell differentiation, and (3) different cell types express different glycan signatures. Certain serodiagnostic glycoconjugate markers, such as carcinoembryonic antigen (CEA), are currently available; however, comprehensive glycome analysis has yet to be performed, mainly because of the difficulties of isolating and structurally analyzing complex glycans. Large-scale glycoprotein analysis, termed glycoproteomics, has the potential to effectively trace cellular glycoproteins and therefore to search for new serodiagnostic biomarkers. In this review, we describe current mass spectrometry-based glycoproteomics technologies. Quantitative “shotgun” proteomics analyses of glycopeptides captured from complex biological mixtures such as plasma, coupled with advanced glycome technologies, enhance our knowledge of protein glycosylation and facilitate discovery of new biomarkers for human diseases.

Analysis of Oligosaccharides by Capillary Electrophoresis

Abstract: Carbohydrate analysis has a special feature which should be capable of high-resolution separation, because oligosaccharides derived from glycoconjugates are usually composed of a complex mixture of carbohydrates including isomers and homologues. Capillary electrophoresis (CE) is one of the most powerful techniques in terms of resolving power and is applied to the analysis of various carbohydrates from glycoconjugates. A combination of CE and laser-induced fluorescence (LIF) detection enables to detect even fmol (10−15 mol) to amol (10−18 mol) of carbohydrates. Multiplexed CE systems and multichannel microfluidic devices have been developed for high-throughput research and are applied to clinical analysis of serum glycome.

Functional remodeling of the cardiac glycome throughout the developing myocardium

Abstract: Montpetit, Marty L., "Functional remodeling of the cardiac glycome throughout the developing myocardium" (2008). Graduate Theses and Dissertations. DEDICATION In loving memory of my father, Louis Montpetit. ACKNOWLEDGEMENTS This dissertation would not have been completed without the love and support of my family. I would like to give special thanks to my wife, Alison, for her support throughout this process and helping me to see the bigger picture of life. I would also like to thank my parents, the late Louis Montpetit and Mary Lou and Joseph Budek, and my sister, Marla, for their love and continued encouragement I extend the deepest thanks to Eric S. Bennett, Ph.D. for all the effort he has put forth to help me succeed. I could not have asked for a more supportive mentor. I appreciate the time invested and insight provided by my committee members: I would like to thank all those who have worked with me in the lab:

High Throughput Screening of Glyco-biomarkers Using Plexera's Lectin Array and SPRi Platform, PlexArray®

Abstract: Lectins are glycan-binding proteins that are important to many cellular functions such as cell adhesion, blood glycoprotein regulation, and innate immunity. The glycoform recognition function is essential in leading the immune system to remove pathogenic glycoproteins. Detailed studies of glycan structures are necessary to fully describe the glycome and the post-translational proteome and promise to play an major role in biomarker discovery. Glycosylation, the covalent attachment of carbohydrate groups (glycans), is the most common, yet structurally complex, of the post-translational modifications that occur naturally in proteins. Dysregulation of glycosylation is associated with a wide range of diseases including diabetes, cardiovascular disease, and cancer. For diagnosis, aberrant glycosylation has long been recognized as a hallmark of cancer with notable protein markers such as CA 19-9 consisting of glycan epitopes. More recently, specific cancer-induced glycoforms of classical serum proteins such as haptoglobin and transferrin have been observed and can potentially serve as markers for the physiological effects of the disease. Contact: cro@plexera.com, http://www.plexera.com