Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer

Molecular and Cellular Proteomics

Volumn 8, Issue 4, 2009, Pages 827-845

  Nibbe, Rod K ^a   Markowitz, Sanford ^a,b   Myeroff, Lois ^a   Ewing, Rob ^a   Chance, Mark R ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TUMOR PROTEIN;

ARTICLE; BIOLOGICAL MODEL; CANCER STAGING; COLON TUMOR; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; PATHOLOGY; PROTEIN BINDING; PROTEOMICS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

COLONIC NEOPLASMS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MODELS, BIOLOGICAL; NEOPLASM PROTEINS; NEOPLASM STAGING; PROTEIN BINDING; PROTEOMICS; RNA, MESSENGER;

EID: 66149156998     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M800428-MCP200     Document Type: Article

References (39)

1. Vidal, M. (2005) Interactome modeling. FEBS Lett. 579, 1834-1838
2. Edelman, E. J., Guinney, J., Chi, J. T., Febbo, P. G., and Mukherjee, S. (2008) Modeling cancer progression via pathway dependencies. PLoS Comput. Biol. 4, e28
3. Auffray, C. (2007) Protein subnetwork markers improve prediction of cancer outcome. Mol. Syst. Biol. 3, 141-142
4. Shoemaker, B. A., and Panchenko, A. R. (2007) Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput. Biol. 3, e42
5. Ries, L. A. G., Melbert, D., Krapcho, M., Mariotto, A., Miller, B. A., Feuer, E. J., Clegg, L, Horner, M. J., Howlader, N., Eisner, M. P., Reichman, M., and Edwards, B. K. (eds) (2007) SEER Cancer Statistics Review, 1975-2004, National Cancer Institute, National Institutes of Health Be-thesda, MD
6. Friedman, D. B., Hill, S., Keller, J. W., Merchant, N. B., Levy, S. E., Coffey, R. J., and Caprioli, R. M. (2004) Proteome analysis of human colon cancer by two-dimensional difference electrophoresis and mass spectrometry. Proteomics 4, 793-811
7. Bi, X., Lin, Q., Foo, T. W., Joshi, S., You, T., Shen, H. M., Ong, C. N., Cheah, P. Y., Eu, K. W., and Hew, C. L. (2006) Proteomic analysis of colorectal cancer reveals alterations in metabolic pathways. Mol. Cell. Proteomics 6, 1119-1130
8. Mazzanti, R., Solazzo, M., Fantappie, O., Elfering, S., Pantaleo, P., Bechi, P., Cianchi, F., Ettl, A., and Giulivi, C. (2006) Differential expression proteomics of human colon cancer. Am. J. Physiol. 290, G1329-G1338
9. Alfonso, P., Nunez, A., Madoz-Gurpide, J., Lombardia, L., Sanchez, A., and Casa, L. (2005) Proteomic expression analysis of colorectal cancer by two-dimensional differential gel electrophoresis. Proteomics 5, 2602-2611
10. Rahman-Roblick, R., Roblick, U. J., Hellman, U., Conrotto, P., Liu, T., Becker, S., Hirschberg, D., Jornvall, H., Auer, G., and Wiman, K. G. (2007) p53 targets identified by protein expression profiling. Proc. Natl. Acad. Sci. U. S. A. 13, 5401-5406
11. Volmer, M. W., Stuhler, K., Zapatka, M., Schoneck, A., Klein-Scory, S., Schmiegel, W., Meyer, H. E., and Schwarte-Waldhoff, I. (2005) Differential proteome analysis of conditioned media to detect Smad4 regulated secreted biomarkers in colon cancer. Proteomics 5, 2587-2601
12. Tan, S., Seow, T. K., Liang, R. C, Koh, S., Lee, C. P., Chung, M. C, and Hooi, S. C. (2002) Proteome analysis of butyrate-treated human colon cancer cells (HT-29). Int. J. Cancer 98, 523-531
13. Ahmed, N., Oliva, K., Wang, Y., Quinn, M., and Rice, G. (2003) Proteomic profiling of proteins associated with urokinase plasminogen activator receptor in a colon cancer cell line using an antisense approach. Proteomics 3, 288-298
14. Ekins, S., Nikolsky, Y., Bugrim, A., Kirillov, E., and Nikolskaya, T. (2006) Pathway mapping tools for analysis of high content data. Methods Mol. Biol. 356, 319-350
15. Chuang, H. Y., Lee, E., Liu, Y. T., Lee, D., and Ideker, T. (2007) Network-based classification of breast cancer metastasis. Mol. Syst. Biol. 3, 140
16. Viswanathan, S., Unlu, M., and Minden, J. S. (2006) Two-dimensional difference gel electrophoresis. Nat. Protoc. 1, 1351-1358
17. Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289-300
18. Williams, A. C, Smartt, H., H-Zadeh, A. M., Macfarlane, M., Paraskeva, C, and Collard, T. J. (2007) Insulin-like growth factor binding protein 3 (IGFBP-3) potentiates TRAIL-induced apoptosis of human colorectal carcinoma cells through inhibition of NF-KB. Cell Death Differ. 14, 137-145
19. Slattery, M. L., Samowitz, W., Curtin, K., Ma, K. N., Hoffman, M., Caan, B., and Neuhausen, S. (2004) Associations among IRS1, IRS2, IGF1, and IGFBP3 genetic polymorphisms and colorectal cancer. Cancer Epidemiol. Biomark. Prev. 13, 1206-1214
20. Stallmach, A., von Lampe, B., Matthes, H., Bornhoft, G., and Riecken, E. O. (1992) Diminished expression of integrin adhesion molecules on human colonic epithelial cells during the benign to malign tumour transformation. Gut 33, 342-346
21. Andreu, P., Colnot, S., Godard, C, Laurent-Puig, P., Lamarque, D., Kahn, A., Perret, C, and Romagnolo, B. (2006) Identification of the IFITM family as a new molecular marker in human colorectal tumors. Cancer Res. 66, 1949-1955
22. Barker, N., Hurlstone, A., Musisi, H., Miles, A., Bienz, M., and Clevers, H. (2001) The chromatin remodeling factor Brg-1 interacts with/3-catenin to promote target gene activation. EMBO J. 20, 4935-4943
23. Kitadai, Y., Sasaki, T., Kuwai, T., Nakamura, T., Bucana, C. D., Hamilton, S. R., and Fidler, I. J. (2006) Expression of activated platelet-derived growth factor receptor in stromal cells of human colon carcinomas is associated with metastatic potential. Int. J. Cancer 119, 2567-2574
24. Izeradjene, K., Douglas, L., Delaney, A., and Houghton, J. A. (2005) Casein kinase II (CK2) enhances death-inducing signaling complex (DISC) activity in TRAIL-induced apoptosis in human colon carcinoma cell lines. Oncogene 24, 2050-2058
25. Tapia, J. C, Torres, V. A., Rodriguez, D. A., Leyton, L., and Quest, A. F. (2006) Casein kinase 2 (CK2) increases survivin expression via enhanced/3-catenin-T cell factor/lymphoid enhancer binding factor dependent transcription. Proc. Natl. Acad. Sci. U. S. A. 103, 15079-15084
26. Mounier, C. M., Wendum, D., Greenspan, E., Flejou, J. F., Rosenberg, D. W., and Lambeau, G. (2008) Distinct expression pattern of the full set of secreted phospholipases A2 in human colorectal adenocarcinomas: sPLA2-III as a biomarker candidate. Br. J. Cancer 98, 587-595
27. Watari, A., Takaki, K., Higashiyama, S., Li, Y., Satomi, Y., Takao, T., Tanemura, A., Yamaguchi, Y., Katayama, I., Shimakage, M., Miyashiro, I., Takami, K., Kodama, K., and Yutsudo, M. (2006) Suppression of tumor-igenicity, but not anchorage independence, of human cancer cells by new candidate tumor suppressor gene CapG. Oncogene 25, 7373-7380
28. Holtrich, U., Wolf, G., Brauninger, A., Karn, T., Bohme, B., Rubsamen-Waigmann, H., and Strebhardt, K. (1994) Induction and down-regulation of PLK, a human serine/threonine kinase expressed in proliferating cells and tumors. Proc. Natl. Acad. Sci. U. S. A 91, 1736-1740
29. Takahashi, T., Sano, B., Nagata, T., Kato, H., Sugiyama, Y., Kunieda, K., Kimura, M., Okano, Y., and Saji, S. (2003) Polo-like kinase 1 (PLK1) is overexpressed in primary colorectal cancers. Cancer Sci. 94, 148-152
30. Weichert, W., Kristiansen, G., Schmidt, M., Gekeler, V., Noske, A., Niesporek, S., Dietel, M., and Denkert, C. (2005) Polo-like kinase 1 expression is a prognostic factor in human colon cancer. World J. Gastroenterol. 11, 5644-5650
31. Schmidt, M., Hofmann, H. P., Sanders, K., Sczakiel, G., Beckers, T. L., and Gekeler, V. (2006) Molecular alterations after Polo-like kinase 1 mRNA suppression versus pharmacologic inhibition in cancer cells. Mol. Cancer Ther. 5, 809-817
32. Greenman, C, Stephens, P., Smith, R., Dalgliesh, G. L., Hunter, C, Bignell, G., Davies, H., Teague, J., Butler, A., Stevens, C, Edkins, S., O'Meara, S., Vastrik, I., Schmidt, E. E., Avis, T., Barthorpe, S., Bhamra, G., Buck, G., Choudhury, B., Clements, J., Cole, J., Dicks, E., Forbes, S., Gray, K., Halliday, K., Harrison, R., Hills, K., Hinton, J., Jenkinson, A., Jones, D., Menzies, A., Mironenko, T., Perry, J., Raine, K., Richardson, D., Shepherd, R., Small, A., Tofts, C, Varian, J., Webb, T., West, S., Widaa, S., Yates, A., Cahill, D. P., Louis, D. N., Goldstraw, P., Nicholson, A. G., Brasseur, F., Looijenga, L., Weber, B. L., Chiew, Y. E., DeFazio, A., Greaves, M. F., Green, A. R., Campbell, P., Birney, E., Easton, D. F., Chenevix-Trench, G., Tan, M. H., Khoo, S. K., Teh, B. T., Yuen, S. T., Leung, S. Y., Wooster, R., Futreal, P. A., and Stratton, M. R. (2007) Patterns of somatic mutation in human cancer genomes. Nature 446, 153-158
33. Chen, Y., Choong, L. Y., Lin, Q., Philp, R., Wong, C. H., Ang, B. K., Tan, Y. L., Loh, M. C, Hew, C. L., Shah, N., Druker, B. J., Chong, P. K., and Lim, Y. P. (2007) Differential expression of novel tyrosine kinase substrates during breast cancer development. Mol. Cell. Proteomics 6, 2072-2087
34. Vogelstein, B., and Kinzler, K. W. (2004) Cancer genes and the pathways they control. Nat. Med. 10, 789-799
35. Zou, T. T., Selaru, F. M., Xu, Y., Shustova, V., Yin, J., Mori, Y., Shibata, D., Sato, F., Wang, S., Olaru, A., Deacu, E., Liu, T. C, Abraham, J. M., and Meltzer, S. J. (2002) Application of cDNA microarrays to generate a molecular taxonomy capable of distinguishing between colon cancer and normal colon. Oncogene 21, 4855-4862
36. Williams, N. S., Gaynor, R. B., Scoggin, S., Verma, U., Gokaslan, T., Simmang, C, Fleming, J., Tavana, D., Frenkel, E., and Becerra, C. (2003) Identification and validation of genes involved in the pathogenesis of colorectal cancer using cDNA microarrays and RNA interference. Clin. Cancer Res. 9, 931-946
37. Wood, L. D., Parsons, D. W., Jones, S., Lin, J., Sjöblom, T., Leary, R. J., Shen, D., Boca, S. M., Barber, T., Ptak, J., Silliman, N., Szabo, S., Dezso, Z., Ustyanksky, V., Nikolskaya, T., Nikolsky, Y., Karchin, R., Wilson, P. A., Kaminker, J. S., Zhang, Z., Croshaw, R., Willis, J., Dawson, D., Shipitsin, M., Willson, J. K., Sukumar, S., Polyak, K., Park, B. H., Pethiyagoda, C. L., Pant, P. V., Ballinger, D. G., Sparks, A. B., Hartigan, J., Smith, D. R., Suh, E., Papadopoulos, N., Buckhaults, P., Markowitz, S. D., Parmigiani, G., Kinzler, K. W., Velculescu, V. E., and Vogelstein, B. (2007) The genomic landscapes of human breast and colorectal cancers. Science 318, 1108-1113
38. Stumpf, M. P., Thorne, T., de Silva, E., Stewart, R., An, H. J., Lappe, M., and Wiuf, C. (2008) Estimating the size of the human interactome. Proc. Natl. Acad. Sci. U. S. A. 105, 6959-6964
39. Marouga, R., David, S., and Hawkins, E. (2005) The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal. Bioanal. Chem. 382, 669-678