Application of microarrays for deciphering the structure and function of the human glycome

Molecular and Cellular Proteomics

Volumn 12, Issue 4, 2013, Pages 902-912

  Smith, David F ^a   Cummings, Richard D ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; GALECTIN 2; GALECTIN 4; GALECTIN 8; GLYCAN; MONOCLONAL ANTIBODY;

ACETYLATION; ADAPTIVE IMMUNITY; ALGORITHM; AMINATION; ANTIBODY SPECIFICITY; BIOINFORMATICS; CELL SURFACE; ELECTRONICS; GENOMICS; GLYCOBIOLOGY; GLYCOCALYX; GLYCOSYLATION; HIGH THROUGHPUT SEQUENCING; HUMAN; INNATE IMMUNITY; MOLECULAR WEIGHT; NONHUMAN; OZONOLYSIS; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN HYDROLYSIS; PROTEIN LOCALIZATION; PROTEIN METHYLATION; PROTEIN MICROARRAY; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; TERMINAL SEQUENCE;

ANIMALS; CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; GLYCOMICS; HUMANS; MICROARRAY ANALYSIS; MILK, HUMAN; MOLECULAR SEQUENCE DATA; POLYSACCHARIDES; PROTEIN BINDING;

EID: 84875993339     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.R112.027110     Document Type: Review

References (97)

1. Mechref, Y., Hu, Y., Garcia, A., and Hussein, A. (2012) Identifying cancer biomarkers by mass spectrometry-based glycomics. Electrophoresis 33, 1755-1767
2. North, S. J., Chalabi, S., Sutton-Smith, M., Dell, A., and Haslam, S. M. (2009) in Handbook of Glycomics (Cummings, R. D., and Pierce, J. M., eds) Academic Press, San Diego pp. 263-327
3. Zoldoš, V., Novokmet, M., Bečeheli, I., and Lauc, G. (2013) Genomics and epigenomics of the human glycome. Glycoconj. J. 30, 41-50
4. Cummings, R. D. (2009) The repertoire of glycan determinants in the human glycome. Mol. Biosyst. 5, 1087-1104
5. Wuhrer, M. (2013) Glycomics using mass spectrometry. Glycoconj. J. 30, 11-22
6. Robinson, L. N., Artpradit, C., Raman, R., Shriver, Z. H., Ruchirawat, M., and Sasisekharan, R. (2012) Harnessing glycomics technologies: integrating structure with function for glycan characterization. Electrophoresis 33, 797-814
7. Ito, S. (1969) Structure and function of the glycocalyx. Fed. Proc. 28, 12-25
8. Lee, G. M., Johnstone, B., Jacobson, K., and Caterson, B. (1993) The dynamic structure of the pericellular matrix on living cells. J. Cell Biol. 123, 1899-1907
9. Weinbaum, S., Tarbell, J. M., and Damiano, E. R. (2007) The structure and function of the endothelial glycocalyx layer. Annu. Rev. Biomed. Eng. 9, 121-167
10. Schachter, H., and Freeze, H. H. (2009) Glycosylation diseases: quo vadis? Biochim. Biophys. Acta 1792, 925-930
11. Narimatsu, H., Sawaki, H., Kuno, A., Kaji, H., Ito, H., and Ikehara, Y. (2010) A strategy for discovery of cancer glyco-biomarkers in serum using newly developed technologies for glycoproteomics. FEBS J. 277, 95-105
12. Nairn, A. V., and Moremen, K. W. (2009) in Handbook of Glycomics (Cum- mings, R. D., and Pierce, J. M., eds) pp. 95-136, Academic Press, San Diego
13. Hollenberg, M. D., Fishman, P. H., Bennett, V., and Cuatrecasas, P. (1974) Cholera toxin and cell growth: role of membrane gangliosides. Proc. Natl. Acad. Sci. U.S.A. 71, 4224-4228
14. Varki, A., and Gagneux, P. (2012) Multifarious roles of sialic acids in immu- nity. Ann. N.Y. Acad. Sci. 1253, 16-36
15. Paulson, J. C., Sadler, J. E., and Hill, R. L. (1979) Restoration of specific myxovirus receptors to asialoerythrocytes by incorporation of sialic acid with pure sialyltransferases. J. Biol. Chem. 254, 2120-2124
16. Imberty, A., and Varrot, A. (2008) Microbial recognition of human cell surface glycoconjugates. Curr. Opin. Struct. Biol. 18, 567-576
17. Viswanathan, K., Chandrasekaran, A., Srinivasan, A., Raman, R., Sasisekharan, V., and Sasisekharan, R. (2010) Glycans as receptors for influenza pathogenesis. Glycoconj. J. 27, 561-570
18. Burger, M. M. (1969) A difference in the architecture of the surface mem- brane of normal and virally transformed cells. Proc. Natl. Acad. Sci. U.S.A. 62, 994-1001
19. Hakomori, S. (1984) Tumor-associated carbohydrate antigens. Annu. Rev. Immunol. 2, 103-126
20. Raman, R., Raguram, S., Venkataraman, G., Paulson, J. C., and Sasisekha- ran, R. (2005) Glycomics: an integrated systems approach to structure-function relationships of glycans. Nat. Methods 2, 817-824
21. Hirabayashi, J., Arata, Y., and Kasai, K. (2001) Glycome project: concept, strategy, and preliminary application to Caenorhabditis elegans. Proteomics 1, 295-303
22. Gabius, H. J. (2011) Glycobiomarkers by glycoproteomics and glycan pro- filing (glycomics): emergence of functionality. Biochem. Soc. Trans. 39, 399-405
23. Doherty, M., McManus, C. A., Duke, R., and Rudd, P. M. (2012) High throughput quantitative N-glycan analysis of glycoproteins. Methods Mol. Biol. 899, 293-313
24. Rakus, J. F., and Mahal, L. K. (2011) New technologies for glycomic analysis: toward a systematic understanding of the glycome. Annu. Rev. Anal. Chem. 4, 367-392
25. Esposito, D., Hurevich, M., Castagner, B., Wang, C. C., and Seeberger, P. H. (2012) Automated synthesis of sialylated oligosaccharides. Beilstein. J. Org. Chem. 8, 1601-1609
26. Hsu, C. H., Hung, S. C., Wu, C. Y., and Wong, C. H. (2011) Toward automated oligosaccharide synthesis. Angew. Chem. Int. Ed. Engl. 50, 11872-11923
27. North, S. J., Hitchen, P. G., Haslam, S. M., and Dell, A. (2009) Mass spectrometry in the analysis of N-linked and O-linked glycans. Curr. Opin. Struct. Biol. 19, 498-506
28. Leymarie, N., and Zaia, J. (2012) Effective use of mass spectrometry for glycan and glycopeptide structural analysis. Anal. Chem. 84, 3040-3048
29. Nairn, A. V., Aoki, K., dela Rosa, M., Porterfield, M., Lim, J. M., Kulik, M., Pierce, J. M., Wells, L., Dalton, S., Tiemeyer, M., and Moremen, K. W. (2012) Regulation of glycan structures in murine embryonic stem cells: combined transcript profiling of glycan-related genes and glycan structural analysis. J. Biol. Chem. 287, 37835-37856
30. Antonopoulos, A., North, S. J., Haslam, S. M., and Dell, A. (2011) Glyco- sylation of mouse and human immune cells: insights emerging from N-glycomics analyses. Biochem. Soc. Trans. 39, 1334-1340
31. Goldberg, D., Sutton-Smith, M., Paulson, J., and Dell, A. (2005) Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra. Proteomics 5, 865-875
32. Pang, P. C., Chiu, P. C., Lee, C. L., Chang, L. Y., Panico, M., Morris, H. R., Haslam, S. M., Khoo, K. H., Clark, G. F., Yeung, W. S., and Dell, A. (2011) Human sperm binding is mediated by the sialyl-Lewis(x) oligosaccharide on the zona pellucida. Science 333, 1761-1764
33. Kannagi, R. (2007) Carbohydrate antigen sialyl Lewis a-its pathophysiolog- ical significance and induction mechanism in cancer progression. Chang Gung Med. J. 30, 189-209
34. Arend, P. (2011) "Natural" antibodies and histo-blood groups in biological development with respect to histo-blood group A. A perspective review. Immunobiology 216, 1318-1321
35. Miyagawa, S., Ueno, T., Nagashima, H., Takama, Y., and Fukuzawa, M. (2012) Carbohydrate antigens. Curr. Opin. Organ Transplant. 17, 174-179
36. Merkle, R. K., and Cummings, R. D. (1987) Lectin affinity chromatography of glycopeptides. Methods Enzymol. 138, 232-259
37. Cummings, R. D. (1994) Use of lectins in analysis of glycoconjugates. Methods Enzymol. 230, 66-86
38. Hirabayashi, J., Kuno, A., and Tateno, H. (2011) Lectin-based structural glycomics: a practical approach to complex glycans. Electrophoresis 32, 1118-1128
39. Mahal, L. K. (2008) Glycomics: toward bioinformatic approaches to under- standing glycosylation. Anticancer Agents Med. Chem. 8, 37-51
40. Fanayan, S., Hincapie, M., and Hancock, W. S. (2012) Using lectins to harvest the plasma/serum glycoproteome. Electrophoresis 33, 1746-1754
41. Patnaik, S. K., and Stanley, P. (2006) Lectin-resistant CHO glycosylation mutants. Methods Enzymol. 416, 159-182
42. Novotny, M. V., Alley, W. R., Jr., and Mann, B. F. (2013) Analytical glyco- biology at high sensitivity: current approaches and directions. Glycoconj. J. 30, 89-117
43. Kato, K. (2012) Structural glycomic approaches to molecular recognition events on cell surfaces. Adv. Exp. Med. Biol. 749, 15-32
44. Ruhaak, L. R., and Lebrilla, C. B. (2012) Advances in analysis of human milk oligosaccharides. Adv. Nutr. 3, 406S-414S
45. Fuchs, B. (2012) Analysis of phospholipids and glycolipids by thin-layer chromatography-matrix-assisted laser desorption and ionization mass spectrometry. J. Chromatogr. A 1259, 62-73
46. van Die, I., van Stijn, C. M., Geyer, H., and Geyer, R. (2010) Structural and functional analysis of glycosphingolipids of Schistosoma mansoni. Methods Enzymol. 480, 117-140
47. Song, X., Smith, D. F., and Cummings, R. D. (2012) Nonenzymatic release of free reducing glycans from glycosphingolipids. Anal. Biochem. 429, 82-87
48. Huang, Y., Mechref, Y., and Novotny, M. V. (2001) Microscale nonreductive release of O-linked glycans for subsequent analysis through MALDI mass spectrometry and capillary electrophoresis. Anal. Chem. 73, 6063-6069
49. Bigge, J. C, Patel, T. P., Bruce, J. A., Goulding, P. N., Charles, S. M., and Parekh, R. B. (1995) Nonselective and efficient fluorescent labeling of glycans using 2-aminobenzamide and anthranilic acid. Anal. Biochem. 230, 229-238
50. Song, X., Xia, B., Stowell, S.R., Lasanajak, Y., Smith, D.F., Cummings, R.D. (2009) Novel fluorescent glycan microarray strategy reveals ligands for galectins. Chem. Biol. 16, 36-47
51. Townsend, R. R., Lipniunas, P. H., Bigge, C, Ventom, A., and Parekh, R. (1996) Multimode high-performance liquid chromatography of fluores-cently labeled oligosaccharides from glycoproteins. Anal. Biochem. 239, 200-207
52. Harvey, D. J. (2012) Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2007-2008. Mass Spectrom. Rev. 31, 183-311
53. Jiménez-Barbero, J., Díaz, M. D., and Nieto, P. M. (2008) NMR structural studies of oligosaccharides related to cancer processes. Anticancer Agents Med. Chem. 8, 52-63
54. Imberty, A. (1997) Oligosaccharide structures: theory versus experiment. Curr. Opin. Struct. Biol. 7, 617-623
55. Kondakova, A. N., Novototskaya-Vlasova, K. A., Arbatsky, N. P., Drutskaya, M. S., Shcherbakova, V. A., Shashkov, A. S., Gilichinsky, D. A., Nedos-pasov, S. A., and Knirel, Y. A. (2012) Structure of the O-specific polysaccharide from the lipopolysaccharide of Psychrobacter cryohalolentis K5(T) containing a 2,3,4-triacetamido-2,3,4-trideoxy-L-arabinose moiety. J. Nat. Prod. 75, 2236-2240
56. Bones, J., Mittermayr, S., O'Donoghue, N., Guttman, A., and Rudd, P. M. (2010) Ultra performance liquid chromatographic profiling of serum N-glycans for fast and efficient identification of cancer-associated alterations in glycosylation. Anal. Chem. 82, 10208-10215
57. Gillmeister, M. P., Tomiya, N., Jacobia, S. J., Lee, Y. C, Gorfien, S. F., and Betenbaugh, M. J. (2009) An HPLC-MALDI MS method for N-glycan analyses using smaller size samples: application to monitor glycan modulation by medium conditions. Glycoconj. J. 26, 1135-1149
58. Goodarzi, M. T., and Turner, G. A. (1998) Reproducible and sensitive determination of charged oligosaccharides from haptoglobin by PNGase F digestion and HPAEC/PAD analysis: glycan composition varies with disease. Glycoconj. J. 15, 469-475
59. Rohrer, J. S., and Townsend, R. R. (1995) Separation of partially desialy- lated branched oligosaccharide isomers containing α(2←3)- and α(2←6)-linked Neu5Ac. Glycobiology 5, 391-395
60. Kawar, Z.S., Johnson, T. K., Natunen, S., Lowe, J. B., and Cummings, R. D. (2008) PSGL-1 from the murine leukocytic cell lineWEHI-3 is enriched for core 2-based O-glycans with sialyl Lewis x antigen. Glycobiology 18, 441-446
61. Wuhrer, M., Koeleman, C. A., and Deelder, A. M. (2009) Two-dimensional HPLC separation with reverse-phase-nano-LC-MS/MS for the characterization of glycan pools after labeling with 2-aminobenzamide. Methods Mol. Biol. 534, 79-91
62. Tomiya, N., Awaya, J., Kurono, M., Endo, S., Arata, Y., and Takahashi, N. (1988) Analyses of N-linked oligosaccharides using a two-dimensional mapping technique. Anal. Biochem. 171, 73-90
63. Hase, S., Ikenaka, K., Mikoshiba, K., and Ikenaka, T. (1988) Analysis of tissue glycoprotein sugar chains by two-dimensional high-performance liquid chromatographic mapping. J. Chromatogr. 434, 51-60
64. Volpi, N., and Maccari, F. (2006) Electrophoretic approaches to the analysis of complex polysaccharides. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 834, 1-13
65. Jackson, P. (1996) The analysis of fluorophore-labeled carbohydrates by polyacrylamide gel electrophoresis. Mol. Biotechnol. 5, 101-123
66. Arnold, J. N., Saldova, R., Galligan, M. C, Murphy, T. B., Mimura-Kimura, Y., Telford, J. E., Godwin, A. K., and Rudd, P. M. (2011) Novel glycan biomarkers for the detection of lung cancer. J. Proteome Res. 10, 1755-1764
67. Cummings, R. D., and Kornfeld, S. (1982) Fractionation of asparagine- linked oligosaccharides by serial lectin-agarose affinity chromatography. A rapid, sensitive, and specific technique. J. Biol. Chem. 257, 11235-11240
68. Osawa, T., and Tsuji, T. (1987) Fractionation and structural assessment of oligosaccharides and glycopeptides by use of immobilized lectins. Annu. Rev. Biochem. 56, 21-42
69. Diaz, S., and Varki, A. (2001) Metabolic radiolabeling of animal cell glyco- conjugates. Curr. Protoc. Mol. Biol. Chapter 17, Unit 17.14
70. Yamashita, K., Mizuochi, T., and Kobata, A. (1982) Analysis of oligosac- charides by gel filtration. Methods Enzymol. 83, 105-126
71. Royle, L, Radcliffe, C. M., Dwek, R. A., and Rudd, P. M. (2006) Detailed structural analysis of N-glycans released from glycoproteins in SDS-PAGE gel bands using HPLC combined with exoglycosidase array digestions. Methods Mol. Biol. 347, 125-143
72. Varki, A., and Kornfeld, S. (1980) Structural studies of phosphorylated high mannose-type oligosaccharides. J. Biol. Chem. 255, 10847-10858
73. Nyame, K., Cummings, R. D., and Damian, R. T. (1988) Characterization of the high mannose asparagine-linked oligosaccharides synthesized by Schistosoma mansoni adult male worms. Mol. Biochem. Parasitol. 28, 265-274
74. Cummings, R. D., and Kornfeld, S. (1982) Characterization of the structural determinants required for the high affinity interaction of asparagine-linked oligosaccharides with immobilized Phaseolus vulgaris leukoagglu-tinating and erythroagglutinating lectins. J. Biol. Chem. 257, 11230-11234
75. Cummings, R. D., Trowbridge, I. S., and Kornfeld, S. (1982) A mouse lymphoma cell line resistant to the leukoagglutinating lectin from Phaseolus vulgaris is deficient in UDP-GlcNAc: α-D-mannoside β1,6 N-acetyl-glucosaminyltransferase. J. Biol. Chem. 257, 13421-13427
76. Granovsky, M., Fata, J., Pawling, J., Muller, W. J., Khokha, R., and Dennis, J. W. (2000) Suppression of tumor growth and metastasis in Mgat5-deficient mice. Nat. Med. 6, 306-312
77. Ahn, Y. H., Lee, J. Y., Lee, J. Y., Kim, Y. S., Ko, J. H., and Yoo, J. S. (2009) Quantitative analysis of an aberrant glycoform of TIMP1 from colon cancer serum by L-PHA-enrichment and SISCAPA with MRM mass spectrometry. J. Proteome Res. 8, 4216-4224
78. Stowell, S. R., Arthur, C. M., Mehta, P., Slanina, K. A., Blixt, O., Leffler, H., Smith, D. F., and Cummings, R. D. (2008) Galectin-1, -2, and -3 exhibit differential recognition of sialylated glycans and blood group antigens. J. Biol. Chem. 283, 10109-10123
79. Stowell, S. R., Arthur, C. M., Dias-Baruffi, M., Rodrigues, L. C, Gourdine, J. P., Heimburg-Molinaro, J., Ju, T., Molinaro, R. J., Rivera-Marrero, C, Xia, B., Smith, D. F., and Cummings, R. D. (2010) Innate immune lectins kill bacteria expressing blood group antigen. Nat. Med. 16, 295-301
80. Xia, B., Kawar, Z. S., Ju, T., Alvarez, R. A., Sachdev, G. P., and Cummings, R. D. (2005) Versatile fluorescent derivatization of glycans for glycomic analysis. Nat. Methods 2, 845-850
81. de Boer, A. R., Hokke, C. H., Deelder, A. M., and Wuhrer, M. (2007) General microarray technique for immobilization and screening of natural glycans. Anal. Chem. 79, 8107-8113
82. Song, X., Lasanajak, Y., Xia, B., Heimburg-Molinaro, J., Rhea, J. M., Ju, H., Zhao, C, Molinaro, R. J., Cummings, R. D., and Smith, D. F. (2011) Shotgun glycomics: a microarray strategy for functional glycomics. Nat. Methods 8, 85-90
83. Kornfeld, R., and Ferris, C. (1975) Interaction of immunoglobulin glycopep- tides with concanavalin A. J. Biol. Chem. 250, 2614-2619
84. Baenziger, J. U., and Fiete, D. (1979) Structural determinants of conca- navalin A specificity for oligosaccharides. J. Biol. Chem. 254, 2400-2407
85. Shibuya, N., Goldstein, I. J., Broekaert, W. F., Nsimba-Lubaki, M., Peeters, B., and Peumans, W. J. (1987) Fractionation of sialylated oligosaccharides, glycopeptides, and glycoproteins on immobilized elderberry (Sambucus nigra L.) bark lectin. Arch. Biochem. Biophys. 254, 1-8
86. Shibuya, N., Goldstein, I. J., Broekaert, W. F., Nsimba-Lubaki, M., Peeters, B., and Peumans, W. J. (1987) The elderberry (Sambucus nigra L.) bark lectin recognizes the Neu5Ac(α2-6)Gal/GalNAc sequence. J. Biol. Chem. 262, 1596-1601
87. Smith, D. F., Song, X., and Cummings, R. D. (2010) Use of glycan microar- rays to explore specificity of glycan-binding proteins. Methods Enzymol. 480, 417-444
88. Wang, W. C, and Cummings, R. D. (1988) The immobilized leukoagglutinin from the seeds of Maackia amurensis binds with high affinity to complex-type Asn-linked oligosaccharides containing terminal sialic acid-linked α-2,3 to penultimate galactose residues. J. Biol. Chem. 263, 4576-4585
89. Itakura, Y., Nakamura-Tsuruta, S., Kominami, J., Sharon, N., Kasai, K., and Hirabayashi, J. (2007) Systematic comparison of oligosaccharide specificity of Ricinus communis agglutinin I and Erythrina lectins: a search by frontal affinity chromatography. J. Biochem. 142, 459-469
90. Kochibe, N., and Furukawa, K. (1980) Purification and properties of a novel fucose-specific hemagglutinin of Aleuria aurantia. Biochemistry 19, 2841-2846
91. Matsumoto, I., and Osawa, T. (1969) Purification and characterization of an anti-H(O) phytohemagglutinin of Ulex europeus. Biochim. Biophys. Acta 194, 180-189
92. Yu, Y., Mishra, S., Song, X., Lasanajak, Y., Bradley, K. C, Tappert, M. M., Air, G. M., Steinhauer, D. A., Halder, S., Cotmore, S., Tattersall, P., Agbandje-McKenna, M., Cummings, R. D., and Smith, D. F. (2012) Functional glycomic analysis of human milk glycans reveals the presence of virus receptors and embryonic stem cell biomarkers. J. Biol. Chem. 287, 44784-44799
93. Niñonuevo, M. R., and Lebrilla, C. B. (2009) Mass spectrometric methods for analysis of oligosaccharides in human milk. Nutr. Rev. 67, S216-S226
94. Natunen, S., Satomaa, T., Pitkänen, V., Salo, H., Mikkola, M., Natunen, J., Otonkoski, T., and Valmu, L. (2011) The binding specificity of the marker antibodies Tra-1-60 and Tra-1-81 reveals a novel pluripotency-associated type 1 lactosamine epitope. Glycobiology 21, 1125-1130
95. Wu, S., Tao, N., German, J. B., Grimm, R., and Lebrilla, C. B. (2010) Development of an annotated library of neutral human milk oligosaccharides. J. Proteome Res. 9, 4138-4151
96. Kobata, A. (2010) Structures and application of oligosaccharides in human milk. Proc. Jpn. Acad. Ser. B, Phys. Biol. Sci. 86, 731-747
97. Cholleti, S. R., Agravat, S., Morris, T., Saltz, J. H., Song, X., Cummings, R. D., and Smith, D. F. (2012) Automated motif discovery from glycan array data. Omics 16, 497-512