Mass Spectrometry Based Glycoproteomics—From a Proteomics Perspective
2010; Elsevier BV; Volume: 10; Issue: 1 Linguagem: Inglês
10.1074/mcp.r110.003251
ISSN1535-9484
AutoresSheng Pan, Ru Chen, Ruedi Aebersold, Teresa A. Brentnall,
Tópico(s)Mass Spectrometry Techniques and Applications
ResumoGlycosylation is one of the most important and common forms of protein post-translational modification that is involved in many physiological functions and biological pathways. Altered glycosylation has been associated with a variety of diseases, including cancer, inflammatory and degenerative diseases. Glycoproteins are becoming important targets for the development of biomarkers for disease diagnosis, prognosis, and therapeutic response to drugs. The emerging technology of glycoproteomics, which focuses on glycoproteome analysis, is increasingly becoming an important tool for biomarker discovery. An in-depth, comprehensive identification of aberrant glycoproteins, and further, quantitative detection of specific glycosylation abnormalities in a complex environment require a concerted approach drawing from a variety of techniques. This report provides an overview of the recent advances in mass spectrometry based glycoproteomic methods and technology, in the context of biomarker discovery and clinical application. Glycosylation is one of the most important and common forms of protein post-translational modification that is involved in many physiological functions and biological pathways. Altered glycosylation has been associated with a variety of diseases, including cancer, inflammatory and degenerative diseases. Glycoproteins are becoming important targets for the development of biomarkers for disease diagnosis, prognosis, and therapeutic response to drugs. The emerging technology of glycoproteomics, which focuses on glycoproteome analysis, is increasingly becoming an important tool for biomarker discovery. An in-depth, comprehensive identification of aberrant glycoproteins, and further, quantitative detection of specific glycosylation abnormalities in a complex environment require a concerted approach drawing from a variety of techniques. This report provides an overview of the recent advances in mass spectrometry based glycoproteomic methods and technology, in the context of biomarker discovery and clinical application. With recent advances in proteomics, analytical and computational technologies, glycoproteomics—the global analysis of glycoproteins—is rapidly emerging as a subfield of proteomics with high biological and clinical relevance. Glycoproteomics integrates glycoprotein enrichment and proteomics technologies to support the systematic identification and quantification of glycoproteins in a complex sample. The recent development of these techniques has stimulated great interest in applying the technology in clinical translational studies, in particular, protein biomarker research. While glycomics is the study of glycome (repertoire of glycans), glycoproteomics focuses on studying the profile of glycosylated proteins, i.e. the glycoproteome, in a biological system. Considerable work has been done to characterize the sequences and primary structure of the glycan moieties attached to proteins (1.Cooper C.A. Harrison M.J. Wilkins M.R. Packer N.H. GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources.Nucleic Acids Res. 2001; 29: 332-335Crossref PubMed Scopus (84) Google Scholar, 2.Rudd P.M. Dwek R.A. Glycosylation: heterogeneity and the 3D structure of proteins.Crit. Rev. Biochem. Mol. Biol. 1997; 32: 1-100Crossref PubMed Google Scholar, 3.Rudd P.M. Guile G.R. Küster B. Harvey D.J. Opdenakker G. Dwek R.A. 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The potentials of glycomics in biomarker discovery.Clin. Proteom. 2008; 4: 67-79Crossref Google Scholar, 8.Shriver Z. Raguram S. Sasisekharan R. Glycomics: a pathway to a class of new and improved therapeutics.Nat. Rev. Drug Discov. 2004; 3: 863-873Crossref PubMed Scopus (181) Google Scholar, 9.Sierpina V.S. Murray R.K. Glyconutrients: the state of the science and the impact of glycomics.Explore (NY). 2006; 2: 488-494Crossref PubMed Scopus (5) Google Scholar, 10.Taniguchi N. Toward cancer biomarker discovery using the glycomics approach.Proteomics. 2008; 8: 3205-3208Crossref PubMed Scopus (21) Google Scholar). In contrast, this review is focused on recent developments in glycoproteomic techniques and their unique application and technical challenge to biomarker discovery. Most secretory and membrane-bound proteins produced by mammalian cells contain covalently linked glycans with diverse structures (2.Rudd P.M. Dwek R.A. Glycosylation: heterogeneity and the 3D structure of proteins.Crit. Rev. Biochem. Mol. Biol. 1997; 32: 1-100Crossref PubMed Google Scholar). The glycosylation form of a glycoprotein is highly specific at each glycosylation site and generally stable for a given cell type and physiological state. However, the glycosylation form of a protein can be altered significantly because of changes in cellular pathways and processes resulting from diseases, such as cancer, inflammation, and neurodegeneration. Such disease-associated alterations in glycoproteins can happen in one or both of two ways: 1) protein glycosylation sites are either hypo, hyper, or newly glycosylated and/or; 2) the glycosylation form of the attached carbohydrate moiety is altered. In fact, altered glycosylation patterns have long been recognized as hallmarks in cancer progression, in which tumor-specific glycoproteins are actively involved in neoplastic progression and metastasis (5.Kobata A. Altered glycosylation of surface glycoproteins in tumor cells and its clinical application.Pigment Cell Res. 1989; 2: 304-308Crossref PubMed Google Scholar, 6.Kobata A. Amano J. Altered glycosylation of proteins produced by malignant cells, and application for the diagnosis and immunotherapy of tumours.Immunol. Cell Biol. 2005; 83: 429-439Crossref PubMed Scopus (208) Google Scholar, 11.Dennis J.W. Granovsky M. Warren C.E. Glycoprotein glycosylation and cancer progression.Biochim. Biophys. Acta. 1999; 1473: 21-34Crossref PubMed Scopus (580) Google Scholar, 12.Ono M. Hakomori S. Glycosylation defining cancer cell motility and invasiveness.Glycoconj. J. 2004; 20: 71-78Crossref PubMed Scopus (114) Google Scholar). Sensitive detection of such disease-associated glycosylation changes and abnormalities can provide a unique avenue to develop glycoprotein biomarkers for diagnosis and prognosis. In addition, intervention in the glycosylation and carbohydrate-dependent cellular pathways represent a potential new modality for cancer therapies (6.Kobata A. Amano J. Altered glycosylation of proteins produced by malignant cells, and application for the diagnosis and immunotherapy of tumours.Immunol. Cell Biol. 2005; 83: 429-439Crossref PubMed Scopus (208) Google Scholar, 11.Dennis J.W. Granovsky M. Warren C.E. Glycoprotein glycosylation and cancer progression.Biochim. Biophys. Acta. 1999; 1473: 21-34Crossref PubMed Scopus (580) Google Scholar, 13.Vlad A.M. Finn O.J. Glycoprotein tumor antigens for immunotherapy of breast cancer.Breast Dis. 2004; 20: 73-79Crossref PubMed Scopus (25) Google Scholar). Table I lists some of the FDA approved cancer biomarkers (14.Ludwig J.A. Weinstein J.N. Biomarkers in cancer staging, prognosis and treatment selection.Nat. Rev. Cancer. 2005; 5: 845-856Crossref PubMed Scopus (1180) Google Scholar, 15.Polanski M. Anderson N.L. A list of candidate cancer biomarkers for targeted proteomics.Biomark. Insights. 2007; 1: 1-48PubMed Google Scholar) that are glycosylated proteins or protein complexes.Table IListing of some of the US Food and Drug Administration (FDA) approved cancer biomarkersProtein targetGlycosylationDetectionSourceDiseaseClinical biomarkerα-FetoproteinYesGlycoproteinSerumNonseminomatous testicular cancerDiagnosisHuman chorionic gonadotropin-βYesGlycoproteinSerumTesticular cancerDiagnosisCA19–9YesCarbohydrateSerumPancreatic cancerMonitoringCA125YesGlycoproteinSerumOvarian cancerMonitoringCEA (carcinoembryonic antigen)YesProteinSerumColon cancerMonitoringEpidermal growth factor receptorYesProteinTissueColon cancerTherapy selectionKITYesProtein (IHC)TissueGastrointestinal (GIST) cancerDiagnosis/Therapy selectionThyroglobulinYesProteinSerumThyroid cancerMonitoringPSA-prostate-specific antigen (Kallikrein 3)YesProteinSerumProstate cancerScreening/Monitoring/DiagnosisCA15–3YesGlycoproteinSerumBreast cancerMonitoringCA27–29YesGlycoproteinSerumBreast cancerMonitoringHER2/NEUYesProtein (IHC), ProteinTissue, SerumBreast cancerPrognosis/Therapy selection/MonitoringFibrin/FDP-fibrin degradation proteinYesProteinUrineBladder cancerMonitoringBTA-bladder tumour-associated antigen (Complement factor H related protein)YesProteinUrineBladder cancerMonitoringCEA and mucin (high molecular weight)YesProtein (Immunofluorescence)UrineBladder cancerMonitoring Open table in a new tab Protein biomarker development is a complex and challenging task. The criteria and approach applied for developing each individual biomarker can vary, depending on the purpose of the biomarker and the performance requirement for its clinical application (16.Hartwell L. Mankoff D. Paulovich A. Ramsey S. Swisher E. Cancer biomarkers: a systems approach.Nat. Biotechnol. 2006; 24: 905-908Crossref PubMed Scopus (145) Google Scholar, 17.Pepe M.S. Etzioni R. Feng Z. Potter J.D. Thompson M.L. Thornquist M. Winget M. Yasui Y. Phases of biomarker development for early detection of cancer.J. Natl. Cancer Inst. 2001; 93: 1054-1061Crossref PubMed Google Scholar). In general, it has been suggested that the preclinical exploratory phase of protein biomarker development can be technically defined into four stages (18.Rifai N. Gillette M.A. Carr S.A. Protein biomarker discovery and validation: the long and uncertain path to clinical utility.Nat. Biotechnol. 2006; 24: 971-983Crossref PubMed Scopus (1238) Google Scholar), including initial discovery of differential proteins; testing and selection of qualified candidates; verification of a subset of candidates; assay development and pre-clinical validation of potential biomarkers. Thanks to recent technological advances, mass spectrometry based glycoproteomics is now playing a major role in the initial phase of discovering aberrant glycoproteins associated with a disease. Glycoprotein enrichment techniques, coupled with multidimensional chromatographic separation and high-resolution mass spectrometry have greatly enhanced the analytical dynamic range and limit of detection for glycoprotein profiling in complex samples such as plasma, serum, other bodily fluids, or tissue. In addition, candidate-based quantitative glycoproteomics platforms have been introduced recently, allowing targeted detection of glycoprotein candidates in complex samples in a multiplexed fashion, providing a complementary tool for glycoprotein biomarker verification in addition to antibody based approaches. It is clear that glycoproteomics is gaining momentum in biomarker research. Glycoproteomic analysis is complicated not only by the variety of carbohydrates, but also by the complex linkage of the glycan to the protein. Glycosylation can occur at several different amino acid residues in the protein sequence. The most common and widely studied forms are N-linked and O-linked glycosylation. O-linked glycans are linked to the hydroxyl group on serine or threonine residues. N-linked glycans are attached to the amide group of asparagine residues in a consensus Asn-X-Ser/Thr sequence (X can be any amino acid except proline) (19.Bause E. Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes.Biochem. J. 1983; 209: 331-336Crossref PubMed Scopus (499) Google Scholar). Other known, but less well studied forms of glycosylation include glycosylphosphatidylinositol anchors attached to protein carboxyl terminus, C-glycosylation that occurs on tryptophan residues (20.Wei X. Li L. Comparative glycoproteomics: approaches and applications.Brief. Funct. Genomic. Proteomic. 2009; 8: 104-113Crossref PubMed Scopus (42) Google Scholar), and S-linked glycosylation through a sulfur atom on cysteine or methionine (21.Floyd N. Vijayakrishnan B. Koeppe J.R. Davis B.G. Thiyl glycosylation of olefinic proteins: S-linked glycoconjugate synthesis.Angew. Chem. Int. Ed Engl. 2009; 48: 7798-7802Crossref PubMed Scopus (0) Google Scholar, 22.Lote C.J. Weiss J.B. Identification in urine of a low-molecular-weight highly polar glycopeptide containing cysteinyl-galactose.Biochem. J. 1971; 123: 25PCrossref PubMed Google Scholar). Our following discussion is focused on glycoproteomic analysis of the most common N-linked and O-linked glycoproteins. A comprehensive analysis of glycoproteins in a complex biological sample requires a concerted approach. Although the specific methods for sample preparation can be different for different types of samples (e.g. plasma, serum, tissue, and cell lysate), a glycoproteomics pipeline typically consists of glycoprotein or glycopeptide enrichment, multidimensional protein or peptide separation, tandem mass spectrometric analysis, and bioinformatic data interpretation. For glycoprotein-based enrichment methods, proteolytic digestion can be performed before or after glycan cleavage, depending on the specific workflow and enrichment methods used. For glycopeptide enrichment, proteolytic digestion is typically performed before the isolation step so that glycopeptides, instead of glycoproteins, can be captured. For quantitative glycoproteomics profiling, additional steps, such as differential stable isotope labeling of the sample and controls, are required. Fig. 1 illustrates the general strategy for an integrated glycoproteomics analysis. Glycoproteins or glycopeptides can be effectively enriched using a variety of techniques (see below). Following the enrichment step, the workflow then splits into two directions: glycan analysis and glycoprotein analysis. The strategies for glycan analysis have been discussed in several reviews and will not be covered in this report. For glycoprotein analysis, bottom-up workflows (“shotgun proteomics”—peptide based proteomics analysis) (23.Aebersold R. Mann M. Mass spectrometry-based proteomics.Nature. 2003; 422: 198-207Crossref PubMed Scopus (5191) Google Scholar) are still most common, providing not only detailed information of a glycoprotein profile, but also the specific mapping of glycosylation sites. It is notable that the reliable analysis of mass spectrometric data in glycoproteomic studies largely relies on bioinformatic tools and glyco-related databases that are available. An increasing number of algorithms and databases for glycan analysis have been developed and well documented in several recent reviews (24.Aoki-Kinoshita K.F. An introduction to bioinformatics for glycomics research.PLoS. Comput. Biol. 2008; 4: e1000075Crossref PubMed Scopus (0) Google Scholar, 25.von der Lieth C.W. Lütteke T. Frank M. The role of informatics in glycobiology research with special emphasis on automatic interpretation of MS spectra.Biochim. Biophys. Acta. 2006; 1760: 568-577Crossref PubMed Scopus (57) Google Scholar, 26.North S.J. Hitchen P.G. Haslam S.M. Dell A. Mass spectrometry in the analysis of N-linked and O-linked glycans.Curr. Opin. Struct. Biol. 2009; 19: 498-506Crossref PubMed Scopus (164) Google Scholar). For glycoprotein and glycopeptide sequence analysis, a large number of well-characterized and annotated glycoproteins can be found in the UniProt Knowledgebase. In addition, many glycopeptide mass spectra are now available in the continually expanding PeptideAtlas library (27.Deutsch E.W. Lam H. Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.EMBO Rep. 2008; 9: 429-434Crossref PubMed Scopus (414) Google Scholar), which stores millions of high-resolution peptide fragment ion mass spectra acquired from a variety of biological and clinical samples for peptide and protein identification. Ultimately, all the data obtained from different aspects of the workflow need to be merged and interpreted in an integrated fashion so that the full extent of glycosylation changes associated with a particular biological state can be better revealed. To the best of our knowledge, the complete glycoform analysis of any glycoprotein in a specific cell type under any specific condition has not yet been accomplished for any glycoprotein with multiple glycosylation sites. Current technology can define the glycan compliment and profile the glycoproteins, but is not capable of putting them together to define the molecular species present. To date, such integrated studies still remain highly challenging, even with advanced tandem mass spectrometry technologies and growing bioinformatic resources (26.North S.J. Hitchen P.G. Haslam S.M. Dell A. Mass spectrometry in the analysis of N-linked and O-linked glycans.Curr. Opin. Struct. Biol. 2009; 19: 498-506Crossref PubMed Scopus (164) Google Scholar, 28.Tajiri M. Yoshida S. Wada Y. 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