Towards an integrated proteomic and glycomic approach to finding cancer biomarkers
Tóm tắt
Advances in mass spectrometry have had a great impact on the field of proteomics. A major challenge of proteomic analysis has been the elucidation of glycan modifications of proteins in complex proteomes. Glycosylation is the most structurally elaborate and diverse type of protein post-translational modification and, because of this, proteomics and glycomics have largely developed independently. However, given that such a large proportion of proteins contain glycan modifications, and that these may be important for their function or may produce biologically relevant protein variation, a convergence of the fields of glycomics and proteomics would be highly desirable. Here we review the current status of glycoproteomic efforts, focusing on the identification of glycoproteins as cancer biomarkers.
Tài liệu tham khảo
Apweiler R, Hermjakob H, Sharon N: On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim Biophys Acta. 1999, 1473: 4-8.
Hakomori S: Tumor-associated carbohydrate antigens. Annu Rev Immunol. 1984, 2: 103-126.
Dube DH, Bertozzi CR: Glycans in cancer and inflammation - potential for therapeutics and diagnostics. Nat Rev Drug Discov. 2005, 4: 477-488.
Feizi T: Carbohydrate antigens in human cancer. Cancer Surv. 1985, 4: 245-269.
Hollingsworth MA, Swanson BJ: Mucins in cancer: protection and control of the cell surface. Nat Rev Cancer. 2004, 4: 45-60.
Bast RC, Klug TL, St John E, Jenison E, Niloff JM, Lazarus H, Berkowitz RS, Leavitt T, Griffiths CT, Parker L, Zurawski VR, Knapp RC: A radioimmunoassay using a monoclonal antibody to monitor the course of epithelial ovarian cancer. NEJM. 1983, 309: 883-887.
Yin BW, Lloyd KO: Molecular cloning of the CA125 ovarian cancer antigen: identification as a new mucin, MUC16. J Biol Chem. 2001, 276: 27371-27375.
Koprowski H, Steplewski Z, Mitchell K, Herlyn M, Herlyn D, Fuhrer P: Colorectal carcinoma antigens detected by hybridoma antibodies. Somatic Cell Genet. 1979, 5: 957-971.
Sawabu N, Watanabe H, Yamaguchi Y, Ohtsubo K, Motoo Y: Serum tumor markers and molecular biological diagnosis in pancreatic cancer. Pancreas. 2004, 28: 263-267.
Magnani J, Nilsson B, Brockhaus M: The antigen of a tumor-specific monoclonal antibody is a ganglioside containing sialylated lacto-N-fucopentaose II. Fed Proc. 1982, 41: 898-
Burchell JM, Mungul A, Taylor-Papadimitriou J: O-linked glycosylation in the mammary gland: changes that occur during malignancy. J Mammary Gland Biol Neoplasia. 2001, 6: 355-364.
Colcher D, Hand PH, Nuti M, Schlom J: A spectrum of monoclonal-antibodies reactive with human mammary-tumor cells. Proc Natl Acad Sci USA. 1981, 78: 3199-3203.
States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM: Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol. 2006, 24: 333-338.
Kirmiz C, Li B, An HJ, Clowers BH, Chew HK, Lam KS, Ferrige A, Alecio R, Borowsky AD, Sulaimon S, Lebrilla CB, Miyamoto S: A serum glycomics approach to breast cancer biomarkers. Mol Cell Proteomics. 2007, 6: 43-55.
Cho W, Jung K, Regnier FE: Use of glycan targeting antibodies to identify cancer-associated glycoproteins in plasma of breast cancer patients. Anal Chem. 2008, 80: 5286-5292.
Abbott KL, Aoki K, Lim JM, Porterfield M, Johnson R, O'Regan RM, Wells L, Tiemeyer M, Pierce M: Targeted glycoproteomic identification of biomarkers for human breast carcinoma. J Proteome Res. 2008, 7: 1470-1480.
Abd Hamid UM, Royle L, Saldova R, Radcliffe CM, Harvey DJ, Storr SJ, Pardo M, Antrobus R, Chapman CJ, Zitzmann N, Robertson JF, Dwek RA, Rudd PM: A strategy to reveal potential glycan markers from serum glycoproteins associated with breast cancer progression. Glycobiology. 2008, 18: 1105-1118.
Kyselova Z, Mechref Y, Kang P, Goetz JA, Dobrolecki LE, Sledge GW, Schnaper L, Hickey RJ, Malkas LH, Novotny MV: Breast cancer diagnosis and prognosis through quantitative measurements of serum glycan profiles. Clin Chem. 2008, 54: 1166-1175.
Goldman R, Ressom HW, Varghese RS, Goldman L, Bascug G, Loffredo CA, Abdel-Hamid M, Gouda I, Ezzat S, Kyselova Z, Mechref Y, Novotny MV: Detection of hepatocellular carcinoma using glycomic analysis. Clin Cancer Res. 2009, 15: 1808-1813.
Jung KY, Cho WR, Regnier FE: Glycoproteomics of plasma based on narrow selectivity lectin affinity chromatography. J Proteome Res. 2009, 8: 643-650.
Madera M, Mann B, Mechref Y, Novotny MV: Efficacy of glycoprotein enrichment by microscale lectin affinity chromatography. J Sep Sci. 2008, 31: 2722-2732.
Kullolli M, Hancock WS, Hincapie M: Preparation of a high-performance multilectin affinity chromatography (HP-M-LAC) adsorbent for the analysis of human plasma glycoproteins. J Sep Sci. 2008, 31: 2733-2739.
Lee YC, Block G, Chen H, Folch-Puy E, Foronjy R, Jalili R, Jendresen CB, Kimura M, Kraft E, Lindemose S, Lu J, McLain T, Nutt L, Ramon-Garcia S, Smith J, Spivak A, Wang ML, Zanic M, Lin SH: One-step isolation of plasma membrane proteins using magnetic beads with immobilized concanavalin A. Protein Expr Purif. 2008, 62: 223-229.
Qiu RQ, Regnier FE: Use of multidimensional lectin affinity chromatography in differential glycoproteomics. Anal Chem. 2005, 77: 2802-2809.
Ralin DW, Dultz SC, Silver JE, Travis JC, Kullolli M, Hancock WS, Hincapie M: Kinetic analysis of glycoprotein-lectin interactions by label-free internal reflection ellipsometry. Clin Proteomics. 2008, 1-2: 37-46.
Mechref Y, Madera M, Novotny MV: Glycoprotein enrichment through lectin affinity techniques. Methods Mol Biol. 2008, 424: 373-396.
Calvano CD, Zambonin CG, Jensen ON: Assessment of lectin and HILIC based enrichment protocols for characterization of serum glycoproteins by mass spectrometry. J Proteomics. 2008, 71: 304-317.
Wang Y, Ao X, Vuong H, Konanur M, Miller FR, Goodison S, Lubman DM: Membrane glycoproteins associated with breast tumor cell progression identified by a lectin affinity approach. J Proteome Res. 2008, 7: 4313-4325.
Zhao J, Simeone DM, Heidt D, Anderson MA, Lubman DM: Comparative serum glycoproteomics using lectin selected sialic acid glycoproteins with mass spectrometric analysis: Application to pancreatic cancer serum. J Proteome Res. 2006, 5: 1792-1802.
Sumi S, Arai K, Kitahara S, Yoshida K: Serial lectin affinity chromatography demonstrates altered asparagine-linked sugar-chain structures of prostate-specific antigen in human prostate carcinoma. J Chromatogr B Biomed Sci Appl. 1999, 727: 9-14.
Qiu R, Regnier FE: Comparative glycoproteomics of N-linked complex-type glycoforms containing sialic acid in human serum. Anal Chem. 2005, 77: 7225-7231.
Yang ZP, Hancock WS: Approach to the comprehensive analysis of glycoproteins isolated from human serum using a multilectin affinity column. J Chromatogr A. 2004, 1053: 79-88.
Lundquist JJ, Toone EJ: The cluster glycoside effect. Chem Rev. 2002, 102: 555-578.
Yang Z, Harris LE, Palmer-Toy DE, Hancock WS: Multilectin affinity chromatography for characterization of multiple glycoprotein biomarker candidates in serum from breast cancer patients. Clin Chem. 2006, 52: 1897-1905.
White KY, Rodemich L, Nyalwidhe JO, Comunale MA, Clements MA, Lance RS, Schellhammer PF, Mehta AS, Semmes OJ, Drake RR: Glycomic characterization of prostate-specific antigen and prostatic acid phosphatase in prostate cancer and benign disease seminal plasma fluids. J Proteome Res. 2009, 8: 620-630.
Nakano M, Nakagawa T, Ito T, Kitada T, Hijioka T, Kasahara A, Tajiri M, Wada Y, Taniguchi N, Miyoshi E: Site-specific analysis of N-glycans on haptoglobin in sera of patients with pancreatic cancer: a novel approach for the development of tumor markers. Int J Cancer. 2008, 122: 2301-2309.
Miyoshi E, Nakano M: Fucosylated haptoglobin is a novel marker for pancreatic cancer: Detailed analyses of oligosaccharide structures. Proteomics. 2008, 8: 3257-3262.
Narisada M, Kawamoto S, Kuwamoto K, Moriwaki K, Nakagawa T, Matsumoto H, Asahi M, Koyama N, Miyoshi E: Identification of an inducible factor secreted by pancreatic cancer cell lines that stimulates the production of fucosylated haptoglobin in hepatoma cells. Biochem Biophys Res Commun. 2008, 377: 792-796.
Okuyama N, Ide Y, Nakano M, Nakagawa T, Yamanaka K, Moriwaki K, Murata K, Ohigashi H, Yokoyama S, Eguchi H, Ishikawa O, Ito T, Kato M, Kasahara A, Kawano S, Gu J, Taniguchi N, Miyoshi E: Fucosylated haptoglobin is a novel marker for pancreatic cancer: a detailed analysis of the oligosaccharide structure and a possible mechanism for fucosylation. Int J Cancer. 2006, 118: 2803-2808.
Hanash SM, Pitteri SJ, Faca VM: Mining the plasma proteome for cancer biomarkers. Nature. 2008, 452: 571-579.
Wu SL, Kim J, Bandle RW, Liotta L, Petricoin E, Karger BL: Dynamic profiling of the post-translational modifications and interaction partners of epidermal growth factor receptor signaling after stimulation by epidermal growth factor using extended range proteomic analysis (ERPA). Mol Cell Proteomics. 2006, 5: 1610-1627.
Hirabayashi J: Concept, strategy and realization of lectin-based glycan profiling. J Biochem. 2008, 144: 139-147.
Chen SM, LaRoche T, Hamelinck D, Bergsma D, Brenner D, Simeone D, Brand RE, Haab BB: Multiplexed analysis of glycan variation on native proteins captured by antibody microarrays. Nat Methods. 2007, 4: 437-444.
Li C, Simeone DM, Brenner DE, Anderson MA, Shedden KA, Ruffin MT, Lubman DM: Pancreatic cancer serum detection using a lectin/glyco-antibody array method. J Proteome Res. 2009, 8: 483-492.
Uchiyama N, Kuno A, Tateno H, Kubo Y, Mizuno M, Noguchi M, Hirabayashi J: Optimization of evanescent-field fluorescence-assisted lectin microarray for high-sensitivity detection of monovalent oligosaccharides and glycoproteins. Proteomics. 2008, 8: 3042-3050.
Kuno A, Uchiyama N, Koseki-Kuno S, Ebe Y, Takashima S, Yamada M, Hirabayashi J: Evanescent-field fluorescence-assisted lectin microarray: a new strategy for glycan profiling. Nat Methods. 2005, 2: 851-856.
Carlsson J, Aqvist J: Absolute and relative entropies from computer simulation with applications to ligand binding. J Phys Chem B. 2005, 109: 6448-6456.
Leerapun A, Suravarapu SV, Bida JP, Clark RJ, Sanders EL, Mettler TA, Stadheim LM, Aderca I, Moser CD, Nagorney DM, LaRusso NF, de Groen PC, Menon KV, Lazaridis KN, Gores GJ, Charlton MR, Roberts RO, Therneau TM, Katzmann JA, Roberts LR: The utility of Lens culinaris agglutinin-reactive alpha-fetoprotein in the diagnosis of hepatocellular carcinoma: evaluation in a United States referral population. Clin Gastroenterol Hepatol. 2007, 5: 394-402. quiz 267.,
Zhang H, Loriaux P, Eng J, Campbell D, Keller A, Moss P, Bonneau R, Zhang N, Zhou Y, Wollscheid B, Cooke K, Yi EC, Lee H, Peskind ER, Zhang J, Smith RD, Aebersold R: UniPep - a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biol. 2006, 7: R73-
Clowers BH, Dodds ED, Seipert RR, Lebrilla CB: Site determination of protein glycosylation based on digestion with immobilized nonspe-cific proteases and Fourier transform ion cyclotron resonance mass spectrometry. J Proteome Res. 2007, 6: 4032-4040.
Hulsmeier AJ, Paesold-Burda P, Hennet T: N-glycosylation site occupancy in serum glycoproteins using multiple reaction monitoring liquid chromatographymass spectrometry. Mol Cell Proteomics. 2007, 6: 2132-2138.
Hagglund P, Matthiesen R, Elortza F, Hojrup P, Roepstorff P, Jensen ON, Bunkenborg J: An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins. J Proteome Res. 2007, 6: 3021-3031.
Wu SL, Huhmer AF, Hao Z, Karger BL: On-line LC-MS approach combining collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced species for the trace-level characterization of proteins with post-translational modifications. J Proteome Res. 2007, 6: 4230-4244.
Kaji H, Yamauchi Y, Takahashi N, Isobe T: Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site-specific stable isotope tagging. Nat Protoc. 2006, 1: 3019-3027.
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R: The International Protein Index: an integrated database for proteomics experiments. Proteomics. 2004, 4: 1985-1988.
