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Insights of New Tools in Glycomics Research Denong Wang1 * and Srinubabu Gedela2,3

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Insights of New Tools in Glycomics Research Denong Wang1 * and Srinubabu Gedela2,3 Journal of Proteomics & Bioinformatics - Open Access Editorial JPB/Vol.1/November 2008 Insights of New Tools In Glycomics Research Denong Wang1 * and Srinubabu Gedela2,3 1Stanford Tumor Glycome Laboratory, Stanford University School of Medicine, Beckman Center, Rm B006, 279 Campus Drive, Stanford, CA 94305-5120, USA 2Center for Biotechnology & International Center for Bioinformatics, Andhra University College of Engineering, Visakhapatnam-530003, India. 3Institute of Glycoproteomics & Systems Biology, Andhra Pradesh, India *Corresponding authors: Denong Wang, Stanford Tumor Glycome Laboratory, Stanford University School of Medicine, Beckman Center, Rm B006, 279 Campus Drive, Stanford, CA 94305-5120, USA, E-mail: [email protected] Srinubabu Gedela: [email protected] Received November 01, 2008; Accepted November 04, 2008; Published November 05, 2008 Citation: Denong W, Srinubabu G (2008) Insights of New tools in Glycomics Research. J Proteomics Bioinform 1: 374-378. doi:10.4172/jpb.1000046 Copyright: © 2008 Denong W, Srinubabu G. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Since the origin of Journal of Proteomics & Bioinformatics the equivalence of papers published from different –omics disciplines is steadfast. The present editorial describes the new tools in glycomics research. -omics era Completion of the genome sequencing projects not only on the outer surfaces of the majority of viral, bacterial, pro- provides insight into the complex origin, history and related- tozoan and fungal pathogens. Many sugar structures are ness of the species, but also helps in understanding molecu- pathogen-specific, which makes them important molecular lar pathology of genetic diseases. Unrevealing of the reper- targets for pathogen recognition, diagnosis of infectious dis- toire of genes in an organism opens the door to the universe eases, and vaccine development. of Proteomics and Glycomics diversities and to the new levels of understanding of the complexity of living species. Altered glycosylations are associated with many human diseases. Structural and functional changes of glycans may The “omics” are usually named based on its main mo- thus serve as biomarkers of tumors, some type of cancers, lecular target, such as Genomics for the Genomes, peripheral vascular diseases, coronary artery diseases, in- Proteomics for the Proteomes, and Glycomics targets the flammation, diabetes mellitus and associated complications universe of sugar chains and carbohydrate-containing mac- (microvascular-nephropathy, retinopathy and neuropathy; romolecules. There is, however, no boundary among “omics” macrovascular-stroke, cardiomyopathy and stroke). Aug- in exploring the mysteries of lives. Instead, there is increas- mented acquaintances on disease associated alterations in ing need of integrated studies of living organisms. Systems glycosylation tessellations and its data integration with Biology & Medicine emerged to accommodate with these proteome, genome and transcriptome endows new intrinsic new developments. biomedical insights and thus, far-reaching peradventures diagnostic application (preventions, early stage identifica- Glycomics is Complementary to Other –omics tion and cure) as well as for the new therapeutic discovery. Carbohydrates are prominently displayed on the surfaces Identification of glycan markers for pathological condi- of cells and present in many secretory proteins in bodily tions is, thus, one of the major jaunts for glycomics re- fluids. Expression of complex carbohydrates by human cells search. To let this area of postgenomics research with fo- are characteristically associated with the stages or steps of cus on new tools and technologies, scientists and scholars embryonic development, cell differentiation, as well as trans- must be attracted, and they should be trained in this highly formation of normal cells to abnormally differentiated tu- bustling area of research that crosses the barriers between mor cells. Sugar moieties are also abundantly expressed various disciplines. J Proteomics Bioinform Volume 1(8) : 374-378 (2008) - 374 ISSN:0974-276X JPB, an open access journal Journal of Proteomics & Bioinformatics - Open Access Editorial JPB/Vol.1/November 2008 Emerging High-throughput Glycomics Tools glycan binding proteins mediate cell communication. Data towards achieving this goal is compiled in the CFG data- Biophysical, biochemical and classical immunological base, which can be accessed at methods have proven very valuable in studying carbohy- <www.functionalglycomics.org>. Among the resources as drate-carbohydrate and carbohydrate-protein interactions. services offered by the CFG to its investigators are glycan They were, however, designed to monitor carbohydrate- analysis, glyco-gene microarray, mouse knockout strains, based molecular recognition on a one-by-one basis and have mouse phenotype analysis, carbohydrate compounds, and limited analytical power or throughput in practical applica- glycan microarrays for screening the specificity of glycan tions. In the past few years, a number of experimental ap- binding proteins, including recent development of CFG proaches have been developed to fill this gap. Glycans pro- pathogen carbohydrate arrays. A challenging issue is to se- filing and sequencing with MALDI-MS, MALDI-FTMS, lect and obtain glycans of highest priority to the community CID MS/MS and MALDI-TOF-MS are developed for high since over 8800 structures are reported in the Bacterial throughput structural characterization of glycomes. Ad- Carbohydrate Structure Database (www.glyco.ac.ru/bcsdb/ vances in the development of microarray-based approaches start.shtml). are poised to accelerate progress towards better understand- ing of the roles of carbohydrates in biology and medicine. Analogous to CFG in US, there is emerging of consor- Carbohydrate microarrays, lectin & antibody arrays, tiums of glycobiologists in various countries worldwide: (http:/ neoglycolipid (NGL) technology coupled with mass spec- /www.functionalglycomics.org/static/consortium/ trometry for carbohydrate ligand discovery, fluorescent links2Website.shtml) neoglycoconjugate probes, and aminoglycoside antibiotic microarrays are among the many new tools becoming avail- Tumor Glycome Laboratories of the NIH Alliance of able to glycobiologists. Glycobiologists for Detection of Cancer and Cancer Risk In spite of their technological differences, the microarray- based technologies are all solid phase binding assays for Numerous studies comparing normal and tumor cells have carbohydrates and their interaction with other biological shown that changes in glycan structures on the cell corre- molecules. They share a number of common characteris- late with cancer development. Compared to molecular pro- tics and technical advantages. First, they contain the ca- teins, molecular glycans are extremely abundant and recent pacity to display a large panel of carbohydrates in a limited advances in technology have now allowed the effective chip space. Second, each carbohydrate is spotted in an systematic study of these structures. In late 2007, the Na- amount that is much smaller than that required for a con- tional Cancer Institute launched a new initiative to discover, ventional molecular or immunological assay. Thus, the develop, and clinically validate cancer biomarkers based on bioarray platform makes effective use of carbohydrate sub- complex carbohydrate structures attached to proteins and stances. Third, they have high detection sensitivity. The lipids. (http://prevention.cancer.gov/programs-resources/ microarray-based assays have higher detection sensitivity groups/cb/programs/glycome). than most conventional molecular and immunological as- says. This characteristic is attributed to the fact that the Seven Tumor Glycome Laboratories have been funded to binding of a molecule in a solution phase to an immobilized search for glycan-based biomarkers for breast, ovarian, lung, micro-spot of ligand in the solid phase has minimal reduc- prostate, and pancreatic cancers and melanoma. NCI’s tion of the molar concentration of the molecule in solution. Tumor Glycome Laboratories are the principal component Therefore, in a microarray assay, it is much easier to have of the new trans-NIH Alliance of Glycobiologists for De- binding equilibrium take place and result is high sensitivity. tection of Cancer and cancer Risk. The other members of Different platforms of microarrays are technically comple- the Alliance are the Consortium for Functional Glycomics mentary and helpful for addressing many of problems in the supported by the National Institute of General Medical Sci- glycomics research. ences and the Glycomics and Glycotechnology Resource Centers supported by the National Center for Research Consortium for Functional Glycomics Resources. The Consortium for Functional Glycomics (CFG) has taken Integrating Data solid steps in facilitating key areas of glycomics research. One of the goals of CFG is to define paradigms by which The challenge for -omics is to tackle the problem of frag- mentation of knowledge by integrating the many sources of J Proteomics Bioinform Volume 1(8) : 374-378 (2008) - 375 ISSN:0974-276X JPB, an open access journal Journal of Proteomics & Bioinformatics - Open Access Editorial JPB/Vol.1/November 2008 heterogeneous information into a systematic
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