Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures

PLoS Computational Biology

Volumn 9, Issue 1, 2013, Pages

  Bennun, Sandra V ^a,b,d   Yarema, Kevin J ^c   Betenbaugh, Michael J ^a   Krambeck, Frederick J ^a,b  

^a Johns Hopkins University   (United States)

^b ReacTech Inc   (United States)

^c Johns Hopkins University   (United States)

^d SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOLOGY; ENZYMES; GENE EXPRESSION; POLYSACCHARIDES;

CANCER PROGRESSION; ENZYMES ACTIVITY; GLYCANS; GLYCOFORMS; GLYCOMES; GLYCOSYLATIONS; MASS SPECTRAL; N-GLYCOSYLATION; TRANSCRIPTOMES; TRANSCRIPTOMICS;

GLYCOSYLATION;

ALPHA2 FUC TRANSFERASE; ANDROGEN; BIOLOGICAL MARKER; CELL PROTEIN; GLYCAN; PROTEIN GNTV; TRANSCRIPTOME; TRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; CANCER GROWTH; CARBOHYDRATE ANALYSIS; CELL STRAIN LNCAP; CELL TYPE; CONTROLLED STUDY; ENZYME ACTIVITY; GENE EXPRESSION; GLYCOBIOLOGY; GLYCOSYLATION; HORMONE DEPENDENCE; HUMAN; HUMAN CELL; MALE; MASS SPECTROMETRY; MICROARRAY ANALYSIS; SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

EID: 84873490671     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002813     Document Type: Article

References (43)

1. Sell S, (1990) Cancer-associated carbohydrates identified by monoclonal antibodies. Human Pathology 21: 1003-1019.
2. Hakomori S, (1984) Tumor-associated carbohydrate antigens. Annual Review of Immunology 2: 103-126.
3. Fuster MM, Esko JD, (2005) The sweet and sour of cancer: glycans as novel therapeutic targets. Nature Reviews Cancer 5: 526-542.
4. Tong L, Baskaran G, Jones MB, Rhee JK, Yarema KJ, (2003) Glycosylation changes as markers for the diagnosis and treatment of human disease. Biotechnology & Genetic Engineering Reviews 20: 199-244.
5. Dennis JW, Granovsky M, Warren CE, (1999) Glycoprotein glycosylation and cancer progression. Biochimica Et Biophysica Acta-General Subjects 1473: 21-34.
6. Arenas MI, Romo E, de Gaspar I, de Bethencourt FR, Sanchez-Chapado M, et al. (1999) A lectin histochemistry comparative study in human normal prostate, benign prostatic hyperplasia, and prostatic carcinoma. Glycoconj J 16: 375-382.
7. Martensson S, Bigler SA, Brown M, Lange PH, Brawer MK, et al. (1995) Sialyl-Lewis(x) and related carbohydrate antigens in the prostate. Hum Pathol 26: 735-739.
8. Ohyama C, Hosono M, Nitta K, Oh-eda M, Yoshikawa K, et al. (2004) Carbohydrate structure and differential binding of prostate specific antigen to Maackia amurensis lectin between prostate cancer and benign prostate hypertrophy. Glycobiology 14: 671-679.
9. Prakash S, Robbins PW, (2000) Glycotyping of prostate specific antigen. Glycobiology 10: 173-176.
10. Peracaula R, Tabares G, Royle L, Harvey DJ, Dwek RA, et al. (2003) Altered glycosylation pattern allows the distinction between prostate-specific antigen (PSA) from normal and tumor origins. Glycobiology 13: 457-470.
11. Meany DL, Zhang Z, Sokoll LJ, Zhang H, Chan DW, (2009) Glycoproteomics for Prostate Cancer Detection: Changes in Serum PSA Glycosylation Patterns. J Proteome Res 8: 613-619.
12. Tajiri M, Ohyama C, Wada Y, (2008) Oligosaccharide profiles of the prostate specific antigen in free and complexed forms from the prostate cancer patient serum and in seminal plasma: a glycopeptide approach. Glycobiology 18: 2-8.
13. Zaia J, (2008) Mass Spectrometry and the Emerging Field of Glycomics. Chemistry & Biology 15: 881-892.
14. Packer NH, von der Lieth CW, Aoki-Kinoshita KF, Lebrilla CB, Paulson JC, et al. (2008) Frontiers in glycomics: Bioinformatics and biomarkers in disease- An NIH White Paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11-13,2006). Proteomics 8: 8-20.
15. Joshi HJ, Harrison MJ, Schulz BL, Cooper CA, Packer NH, et al. (2004) Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data. Proteomics 4: 1650-1664.
16. Kawano S, Hashimoto K, Miyama T, Goto S, Kanehisa M, (2005) Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinformatics 21: 3976-3982.
17. Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, et al. (2006) KEGG as a glycome informatics resource. Glycobiology 16: 63R-70R.
18. Suga A, Yamanishi Y, Hashimoto K, Goto S, Kanehisa M, (2007) An improved scoring scheme for predicting glycan structures from gene expression data. Genome Informatics 18: 237-246.
19. Krambeck FJ, Bennun SV, Narang S, Choi S, Yarema KJ, et al. (2009) A mathematical model to derive N-glycan structures and cellular enzyme activities from mass spectrometric data. Glycobiology 19: 1163-1175.
20. Krambeck FJ, Betenbaugh MJ, (2005) A mathematical model of N-linked glycosylation. Biotechnol Bioeng 92: 711-728.
21. Igawa T, Lin FF, Lee MS, Karan D, Batra SK, et al. (2002) Establishment and characterization of androgen-independent human prostate cancer LNCaP cell model. Prostate 50: 222-235.
22. The Consortium for Functional Glycomics. Available: http://functionalglycomics.org.
23. Holmes EH, Greene TG, Tino WT, Boynton AL, Aldape HC, et al. (1996) Analysis of glycosylation of prostate-specific membrane antigen derived from LNCaP cells, prostatic carcinoma tumors, and serum from prostate cancer patients. Prostate Suppl 7: 25-29.
24. Sumi S, Arai K, Kitahara S, Yoshida K, (1999) 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 727: 9-14.
25. Tabares G, Radcliffe CM, Barrabes S, Ramirez M, Aleixandre RN, et al. (2006) Different glycan structures in prostate-specific antigen from prostate cancer sera in relation to seminal plasma PSA. Glycobiology 16: 132-145.
26. Abel PD, Marsh C, Henderson D, Leathem A, Powell PH, et al. (1987) Detection of blood group antigens in frozen sections of prostatic epithelium. Br J Urol 59: 430-435.
27. Vowden P, Lowe AD, Lennox ES, Bleehen NM, (1986) Are blood group isoantigens lost from malignant prostatic epithelium? Immunohistochemical support for the preservation of the H isoantigen. Br J Cancer 53: 307-312.
28. Marker PC, Stephan JP, Lee J, Bald L, Mather JP, et al. (2001) fucosyltransferase1 and H-type complex carbohydrates modulate epithelial cell proliferation during prostatic branching morphogenesis. Dev Biol 233: 95-108.
29. Culig Z, Hittmair A, Hobisch A, Bartsch G, Klocker H, et al. (1998) Expression of Lewis carbohydrate antigens in metastatic lesions from human prostatic carcinoma. Prostate 36: 162-167.
30. Zhang S, Zhang HS, Cordon-Cardo C, Reuter VE, Singhal AK, et al. (1997) Selection of tumor antigens as targets for immune attack using immunohistochemistry: II. Blood group-related antigens. Int J Cancer 73: 50-56.
31. Fukushima K, Satoh T, Baba S, Yamashita K, (2010) alpha1,2-Fucosylated and beta-N-acetylgalactosaminylated prostate-specific antigen as an efficient marker of prostatic cancer. Glycobiology 20: 452-460.
32. Tsui KH, Chang PL, Feng TH, Chung LC, Sung HC, et al. (2008) Evaluating the function of matriptase and N-acetylglucosaminyltransferase V in prostate cancer metastasis. Anticancer Res 28: 1993-1999.
33. Radhakrishnan P, Lin MF, Cheng PW, (2009) Elevated expression of L-selectin ligand in lymph node-derived human prostate cancer cells correlates with increased tumorigenicity. Glycoconjugate Journal 26: 75-81.
34. Young WW Jr, Mills SE, Lippert MC, Ahmed P, Lau SK, (1988) Deletion of antigens of the Lewis a/b blood group family in human prostatic carcinoma. Am J Pathol 131: 578-586.
35. Chandrasekaran EV, Chawda R, Locke RD, Piskorz CF, Matta KL, (2002) Biosynthesis of the carbohydrate antigenic determinants, Globo H, blood group H, and Lewis b: a role for prostate cancer cell alpha 1,2-L-fucosyltransferase. Glycobiology 12: 153-162.
36. Sun XY, Plouzek CA, Henry JP, Wang TT, Phang JM, (1998) Increased UDP-glucuronosyltransferase activity and decreased prostate specific antigen production by biochanin A in prostate cancer cells. Cancer Res 58: 2379-2384.
37. Chouinard S, Barbier O, Belanger A, (2007) UDP-glucuronosyltransferase 2B15 (UGT2B15) and UGT2B17 enzymes are major determinants of the androgen response in prostate cancer LNCaP cells. J Biol Chem 282: 33466-33474.
38. Kanaya J, Takashima M, Koh E, Namiki M, (2003) Androgen-independent growth in LNCaP cell lines and steroid uridine diphosphate-glucuronosyltransferase expression. Asian J Androl 5: 9-13.
39. Jorgensen T, Berner A, Kaalhus O, Tveter KJ, Danielsen HE, et al. (1995) Up-regulation of the oligosaccharide sialyl LewisX: a new prognostic parameter in metastatic prostate cancer. Cancer Res 55: 1817-1819.
40. McNaught AD, (1997) International Union of Pure and Applied Chemistry and International Union of Biochemistry and Molecular Biology- Joint Commission on Biochemical Nomenclature- Nomenclature of carbohydrates (Recommendations 1996) (Reprinted from Pure Appl Chem, vol 68, pg 1919-2008, 1996). Advances in Carbohydrate Chemistry and Biochemistry 52: 43-177.
41. Banin E, Neuberger Y, Altshuler Y, Halevi A, Inbar O, et al. (2002) A novel Linear Code((R)) nomenclature for complex carbohydrates. Trends in Glycoscience and Glycotechnology 14: 127-137.
42. Marquardt DW, (1963) An Algorithm for Least-Squares Estimation of Nonlinear Parameters. Journal of the Society for Industrial and Applied Mathematics 11: 431-441.
43. Williams B, Cornett S, Crecelius A, Caprioli R (2005) An algorithm for baseline correction of MALDI mass spectra. 43rd ACM Southeast Conference, March 18-20, 2005, Kennesaw, GA.