The Second Golden Age of Glycomics: From Functional Glycomics to Clinical Applications
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or a long time, the glycan modifications of complex molecules that give rise to glycoproteins, glycolipids, proteoglycans, and glycosylphosphatidylinositol (known as GPI) anchors have been considered to be simply “decorations” that confer no functionality. It has now become clear, however, that glycans have structural and functional roles that are crucial to the functions of many glycoconjugates. Glycomics, which is the study of the biological role of carbohydrates, is a new research field, and understanding the glycome is a much bigger challenge than determining the genome or proteome. This is because of the heterogeneity that arises from the complexity of glycan-processing pathways, which are sensitive to genetic and environmental factors. Functional glycomics, which focuses on glycan structure and function, has attracted considerable attention within the life sciences. A growing body of evidence indicates that oligosaccharides in glycoconjugates are associated with various diseases and conditions, including inflammation, immune diseases, neuromuscular diseases, cancer, and metabolic syndromes. Functional glycomics aims to identify disease-related glycoproteins and characterize the function of sugar chains that play a pivotal role in these studies. Translational research, which bridges glycomics at the bench with the diagnostics and biological drugs at the bedside, has been pursued, and some advances are currently being applied to clinical fields. Glycosylation processing is catalyzed by glycosyltransferases, which constitute ∼0.1% of the genome. Glycosylation is one of the most abundant posttranslational modifications of proteins. In eukaryotes, >50% of the proteins are glycosylated. Therefore, the complete characterization and identification of protein functions is impossible without knowledge of glycan functions. During the past decade, most of the known glycosyltransferase genes have been cloned and characterized. Functional glycomics, in which knockout and transgenic animals are used to manipulate the glycosyltransferase genes and thus remodel the glycans, has opened a new avenue for the exploration of glycan function and, simultaneously, has provided a means to identify some of the target proteins on which specific glycans reside. In parallel with the above research strategies, the development of MS, HPLC, CE, and NMR, as well as peptide, antibody, lectin, and aptamer arrays, has made it possible to analyze or profile glycan structures to facilitate the identification of cancer biomarkers. Most of the cancer biomarkers that are in use today are glycoproteins or glycolipids, and they are analyzed by classical ELISA with monoclonal antibodies whose epitope is raised against a protein moiety. Moreover, the measurement is based on the 10.1021/pr801057j
© 2009 American Chemical Society
quantitative analysis of the changes in the total levels of glycoproteins in serum of patients with cancer and does not necessarily reflect the qualitative changes in glycan portions because of aberrant glycosylation in glycoproteins secreted by the cancer. Therefore, distinguishing between cancer and benign diseases, including inflammatory diseases, is problematic. Thus, no biomarkers are available for the early detection of cancer. Current markers provide information for monitoring the disease before and after an operation and for monitoring recurrence of the disease. R-fetoprotein (AFP) is an oncofetal protein and is normally produced in embryonic tissues only and not in adult livers. However, yolk sac tumors and hepatocellular carcinoma (HCC) tissues produce AFP, which is a well-known biomarker for HCC. The measurement of AFP as a cancer biomarker is somewhat limited because its levels also are increased in patients with hepatitis and liver cirrhosis. It is known that the core fucosylation of AFP (fucosylated AFP, designated as the L3 fraction) measured with antibodies and lectins is the best approved marker in patients with HCC. Fucosylated AFP was approved as a biomarker for HCC by the U.S. Food and Drug Administration in 2006. The AFP L3 fractions contain core fucosylated AFP and appear in serum at the stage of liver cirrhosis, before the onset of HCC. The measurement is based on the capture of the L3 fraction with a monoclonal antibody against AFP and a lectin that preferentially recognizes the core fucosylation. The recent development of NMR, HPLC coupled with exoglycosidase digestions, and MS has permitted many glycans to be structurally characterized, and some of these techniques are now coupled with computer-assisted data analysis and are relatively easy for scientists who are not familiar with glycan structures to use. For clinical application, a cancer biomarker discovered with glycomics techniques provides a promising tool for the early detection of cancer or a diagnosis at a precancerous stage. Prostate cancer, ovarian cancer, gall bladder cancer, and pancreatic cancer also are difficult to detect in patients whose disease is at an early stage. The glycomics approach for identifying and characterizing glycan changes of serum proteins constitutes a promising strategy for the discovery of cancer biomarkers and glycotherapeutics in the future. It is also known that IgG1-carrying nonfucosylated glycans can enhance the activity of FcRIII-dependent antibodydependent cellular cytotoxicity, and this is important in the design of therapeutics against cancer. Glycans also are candidates for the preparation of vaccines for the treatment of infectious diseases and cancer. In addition, glycans have been important targets in immune response and transplantation studies in which specific glycan structures have been shown to be responsible for transplant rejection. Journal of Proteome Research • Vol. 8, No. 2, 2009 425
This special issue includes papers that cover various areas that have been of intense research interest in glycomics. These include the development of new analytical methods for characterization of complex glycan structures. Such methods include new separation techniques and chromatography for analysis of glycans, glycopeptides, and glycoproteins. The development of such separation methods has been key to the analysis of this complex problem. Other papers deal with novel MS methods for structural analysis or combinations of separations and MS. Other technologies presented herein include the use of microarrays such as lectin, glycan, and glycoprotein and glycopeptide arrays. These methods have provided a high-throughput means to screen large numbers of glycan structures in marker studies. Other papers describe applications of these technologies to biological or clinical problems. Monitoring glycans in body fluids for cancer and other diseases also is of great interest. These applications represent an exciting future for this field and portend well for a high level of activity in a field intimately involved in the biology of living organisms.
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NAOYUKI TANIGUCHI Endowed Chair Professor, Osaka University, Program Director, RIKEN Advanced Science Institute (Japan) WILLIAM HANCOCK Professor of Chemistry and Bradstreet Chair in Bioanalytical Chemistry, Barnett Institute of Chemical and Biological Analysis and Northeastern University DAVID M. LUBMAN Maude T. Lane Professor of Surgical Immunology, University of Michigan Medical Center PAULINE M. RUDD NIBRT Professor of Glycobiology, National Institute for Bioprocessing Research and Training, Dublin-Oxford Glycobiology Laboratory, Conway Institute, and University College Dublin
