Exploring the pathogenesis of renal cell carcinoma: Pathway and bioinformatics analysis of dysregulated genes and proteins

Biological Chemistry

Volumn 390, Issue 2, 2009, Pages 125-135

  Romaschin, Alexander D ^a,b   Youssef, Youssef ^a   Chow, Tsz Fung F ^a   Siu, K W Michael ^c   DeSouza, Leroi V ^c   Honey, R John ^d   Stewart, Robert ^d   Pace, Kenneth T ^d   Yousef, George M ^a,b  

^a ST MICHAEL'S HOSPITAL   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c YORK UNIVERSITY   (Canada)

^d ST MICHAEL'S HOSPITAL   (Canada)

Author keywords

Bioinformatics; Gene ontology (GO) consortium; Kidney cancer; Mammalian target of rapamycin (mTOR); Mass spectrometry; Pathway analysis; Proteomics; Renal cell carcinoma; Tumor markers

Indexed keywords

RAPAMYCIN;

ARTICLE; BIOINFORMATICS; CANCER GROWTH; CLINICAL ASSESSMENT; CLINICAL FEATURE; CONTROLLED STUDY; ELECTRIC POTENTIAL; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; KIDNEY CARCINOMA; PATH ANALYSIS; PATHOGENESIS; PRIORITY JOURNAL; UPREGULATION;

CARCINOMA, RENAL CELL; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; IMMUNOHISTOCHEMISTRY; KIDNEY NEOPLASMS; PROTEIN KINASES; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; TUMOR MARKERS, BIOLOGICAL;

MAMMALIA;

EID: 59949086822     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/BC.2009.013     Document Type: Article

References (64)

1. Belfiore, A. (2007). The role of insulin receptor isoforms and hybrid insulin/IGF-I receptors in human cancer. Curr. Pharm. Des. 13, 671-686.
2. Boer, J.M., Huber, W.K., Sultmann, H., Wilmer, F., von Heydebreck, A., Haas, S., Korn, B., Gunawan, B., Vente, A., Fuzesi, L., et al. (2001). Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array. Genome Res. 11, 1861-1870.
3. Buchner, A., Castro, M., Hennig, A., Popp, T., Assmann, G., Hofstetter, A., Stief, C., and Zimmermann, W. (2007). [Transcriptome analyses in renal cell carcinoma. Combination of laser microdissection and microarrays] (in German). Urologe A 46, 1170-1175.
4. Buller, H.R., van Doormaal, F.F., van Sluis, G.L., and Kamphuisen, P.W. (2007). Cancer and thrombosis: from molecular mechanisms to clinical presentations. J. Thromb. Haemost. 5 (Suppl. 1), 246-254.
5. Chen, Z., Gibson, T.B., Robinson, F., Silvestro, L., Pearson, G., Xu, B., Wright, A., Vanderbilt, C., and Cobb, M.H. (2001). MAP kinases. Chem. Rev. 101, 2449-2476.
6. Cowey, S. and Hardy, R.W. (2006). The metabolic syndrome: a high-risk state for cancer? Am. J. Pathol. 169, 1505-1522.
7. Craven, R.A., Stanley, A.J., Hanrahan, S., Dods, J., Unwin, R., Totty, N., Harnden, P., Eardley, I., Selby, P.J., and Banks, R.E. (2006). Proteomic analysis of primary cell lines identifies protein changes present in renal cell carcinoma. Proteomics 6, 2853-2864.
8. Dennis, G. Jr., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C., and Lempicki, R.A. (2003). DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 4, 3.
9. DeSouza, L., Diehl, G., Rodrigues, M.J., Guo, J., Romaschin, A.D., Colgan, T.J., and Siu, K.W. (2005). Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 4, 377-386.
10. Draghici, S., Khatri, P., Bhavsar, P., Shah, A., Krawetz, S.A., and Tainsky, M.A. (2003). Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res. 31, 3775-3781.
11. Draghici, S., Khatri, P., Tarca, A.L., Amin, K., Done, A., Voichita, C., Georgescu, C., and Romero, R. (2007). A systems biology approach for pathway level analysis. Genome Res. 17, 1537-1545.
12. Faca, V., Krasnoselsky, A., and Hanash, S. (2007). Innovative proteomic approaches for cancer biomarker discovery. Biotechniques 43, 279, 281-3, 285.
13. George, S. and Bukowski, R.M. (2007). Biomarkers in clear cell renal cell carcinoma. Expert. Rev. Anticancer Ther. 7, 1737-1747.
14. Gieseg, M.A., Cody, T., Man, M.Z., Madore, S.J., Rubin, M.A., and Kaldjian, E.P. (2002). Expression profiling of human renal carcinomas with functional taxonomic analysis. BMC Bioinform. 3, 26.
15. Gomez Roman, J.J., Garay, G.O., Saenz, P., Escuredo, K., Sanz, I.C., Gutkind, S., Junquera, C., Simon, L., Martinez, A., Fernandez Luna, J.L., and Val-Bernal, J.F. (2008). Plexin B1 is downregulated in renal cell carcinomas and modulates cell growth. Transl. Res. 151, 134-140.
16. Hanada, K., Perry-Lalley, D.M., Ohnmacht, G.A., Bettinotti, M.P., and Yang, J.C. (2001). Identification of fibroblast growth factor-5 as an overexpressed antigen in multiple human adenocarcinomas. Cancer Res. 61, 5511-5516.
17. Hanna, S.C., Heathcote, S.A., and Kim, W.Y. (2008). mTOR pathway in renal cell carcinoma. Expert. Rev. Anticancer Ther. 8, 283-292.
18. Harris, M.A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R., Eilbeck, K., Lewis, S., Marshall, B., Mungall, C., et al. (2004). The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-D261.
19. He, B., Reguart, N., You, L., Mazieres, J., Xu, Z., Lee, A.Y., Mikami, I., McCormick, F., and Jablons, D.M. (2005). Blockade of Wnt-1 signaling induces apoptosis in human colorectal cancer cells containing downstream mutations. Oncogene 24, 3054-3058.
20. Higgins, J.P., Shinghal, R., Gill, H., Reese, J.H., Terris, M., Cohen, R.J., Fero, M., Pollack, J.R., van de Rijn, M., and Brooks, J.D. (2003). Gene expression patterns in renal cell carcinoma assessed by complementary DNA microarray. Am. J. Pathol. 162, 925-932.
21. Hoehn, W. and Hermanek, P. (1983). Invasion of veins in renal cell carcinoma - frequency, correlation and prognosis. Eur. Urol. 9, 276-280.
22. Hudes, G., Carducci, M., Tomczak, P., Dutcher, J., Figlin, R., Kapoor, A., Staroslawska, E., Sosman, J., McDermott, D., Bodrogi, I., et al. (2007). Temsirolimus, interferon α, or both for advanced renal-cell carcinoma. N. Engl. J. Med. 356, 2271-2281.
23. Hwa, J.S., Kim, H.J., Goo, B.M., Park, H.J., Kim, C.W., Chung, K.H., Park, H.C., Chang, S.H., Kim, Y.W., Kim, D.R., et al. (2006). The expression of ketohexokinase is diminished in human clear cell type of renal cell carcinoma. Proteomics 6, 1077-1084.
24. Kaelin, W.G. Jr. (2003). The von Hippel-Lindau gene, kidney cancer, and oxygen sensing. J. Am. Soc. Nephrol. 14, 2703-2711.
25. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., et al. (2008). KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484.
26. Kassouf, W., Chintharlapalli, S., Abdelrahim, M., Nelkin, G., Safe, S., and Kamat, A.M. (2006). Inhibition of bladder tumor growth by 1, 1-bis(3′-indolyl)-1-(p-substitutedphenyl)methanes: a new class of peroxisome proliferator-activated receptor gamma agonists. Cancer Res. 66, 412-418.
27. Koochekpour, S., Jeffers, M., Wang, P.H., Gong, C., Taylor, G.A., Roessler, L.M., Stearman, R., Vasselli, J.R., Stetler-Stevenson, W.G., Kaelin, W.G. Jr., et al. (1999). The von Hippel-Lindau tumor suppressor gene inhibits hepatocyte growth factor/scatter factor-induced invasion and branching morphogenesis in renal carcinoma cells. Mol. Cell. Biol. 19, 5902-5912.
28. Krizman, D.B., Wagner, L., Lash, A., Strausberg, R.L., and Emmert-Buck, M.R. (1999). The Cancer Genome Anatomy Project: EST sequencing and the genetics of cancer progression. Neoplasia 1, 101-106.
29. Le, J.S., Amy, C., Cazes, A., Monnot, C., Lamande, N., Favier, J., Philippe, J., Sibony, M., Gasc, J.M., Corvol, P., et al. (2003). Angiopoietin-like 4 is a proangiogenic factor produced during ischemia and in conventional renal cell carcinoma. Am. J. Pathol. 162, 1521-1528.
30. Le, S.F., Boulben, S., Le, B.R., Cormier, P., Morales, J., Belle, R., and Mulner-Lorillon, O. (2006). eEF1B: at the dawn of the 21st century. Biochim. Biophys. Acta 1759, 13-31.
31. Lenburg, M.E., Liou, L.S., Gerry, N.P., Frampton, G.M., Cohen, H.T., and Christman, M.F. (2003). Previously unidentified changes in renal cell carcinoma gene expression identified by parametric analysis of microarray data. BMC Cancer 3, 31.
32. Lin, F., Zhang, P.L., Yang, X.J., Prichard, J.W., Lun, M., and Brown, R.E. (2006). Morphoproteomic and molecular concomitants of an overexpressed and activated mTOR pathway in renal cell carcinomas. Ann. Clin. Lab. Sci. 36, 283-293.
33. Liou, L.S., Shi, T., Duan, Z.H., Sadhukhan, P., Der, S.D., Novick, A.A., Hissong, J., Skacel, M., Almasan, A., and DiDonato, J.A. (2004). Microarray gene expression profiling and analysis in renal cell carcinoma. BMC Urol. 4, 9.
34. Lwaleed, B.A., Cooper, A.J., Voegeli, D., and Getliffe, K. (2007). Tissue factor: a critical role in inflammation and cancer. Biol. Res. Nurs. 9, 97-107.
35. Mazurek, S., Boschek, C.B., Hugo, F., and Eigenbrodt, E. (2005). Pyruvate kinase type M2 and its role in tumor growth and spreading. Semin. Cancer Biol. 15, 300-308.
36. Michalik, L., Desvergne, B., and Wahli, W. (2004). Peroxisomeproliferator-activated receptors and cancers: complex stories. Nat. Rev. Cancer 4, 61-70.
37. Mikami, I., You, L., He, B., Xu, Z., Batra, S., Lee, A.Y., Mazieres, J., Reguart, N., Uematsu, K., Koizumi, K., and Jablons, D.M. (2005). Efficacy of Wnt-1 monoclonal antibody in sarcoma cells. BMC Cancer 5, 53.
38. Narbonne, P. and Roy, R. (2008). Genes that affect both cell growth and polarity mediate stem cell quiescence. Front. Biosci. 13, 995-1002.
39. Perego, R.A., Bianchi, C., Corizzato, M., Eroini, B., Torsello, B., Valsecchi, C., Di Fonzo, A., Cordani, N., Favini, P., Ferrero, S., et al. (2005). Primary cell cultures arising from normal kidney and renal cell carcinoma retain the proteomic profile of corresponding tissues. J. Proteome Res. 4, 1503-1510.
40. Perroud, B., Lee, J., Valkova, N., Dhirapong, A., Lin, P.Y., Fiehn, O., Kultz, D., and Weiss, R.H. (2006). Pathway analysis of kidney cancer using proteomics and metabolic profiling. Mol. Cancer 5, 64.
41. Peruzzi, B., Athauda, G., and Bottaro, D.P. (2006). The von Hippel-Lindau tumor suppressor gene product represses oncogenic β-catenin signaling in renal carcinoma cells. Proc. Natl. Acad. Sci. USA 103, 14531-14536.
42. Radulovic, S. and Bjelogrlic, S.K. (2007). Sunitinib, sorafenib and mTOR inhibitors in renal cancer. J. BUON 12 (Suppl. 1), S151-S162.
43. Rae, F.K., Stephenson, S.A., Nicol, D.L., and Clements, J.A. (2000). Novel association of a diverse range of genes with renal cell carcinoma as identified by differential display. Int. J. Cancer 88, 726-732.
44. Rak, J., Yu, J.L., Luyendyk, J., and Mackman, N. (2006). Oncogenes, Trousseau syndrome, and cancer-related changes in the coagulom of mice and humans. Cancer Res. 66, 10643-10646.
45. Sarto, C., Marocchi, A., Sanchez, J.C., Giannone, D., Frutiger, S., Golaz, O., Wilkins, M.R., Doro, G., Cappellano, F., Hughes, G., et al. (1997). Renal cell carcinoma and normal kidney protein expression. Electrophoresis 18, 599-604.
46. Seliger, B., Lichtenfels, R., and Kellner, R. (2003a). Detection of renal cell carcinoma-associated markers via proteome- and other 'ome'-based analyses. Brief. Funct. Genomics Proteomics 2, 194-212.
47. Seliger, B., Menig, M., Lichtenfels, R., Atkins, D., Bukur, J., Halder, T.M., Kersten, M., Harder, A., Ackermann, A., Beck, J., et al. (2003b). Identification of markers for the selection of patients undergoing renal cell carcinoma-specific immunotherapy. Proteomics 3, 979-990.
48. Setlur, S.R., Royce, T.E., Sboner, A., Mosquera, J.M., Demichelis, F., Hofer, M.D., Mertz, K.D., Gerstein, M., and Rubin, M.A. (2007). Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer. Cancer Res. 67, 10296-10303.
49. Shi, T., Dong, F., Liou, L.S., Duan, Z.H., Novick, A.C., and Di-Donato, J.A. (2004). Differential protein profiling in renal-cell carcinoma. Mol. Carcinog. 40, 47-61.
50. Siu, M.K., DeSouza, L., Scorilas, A., Romaschin, A., Honey, J., Stewart, R., Pace, K., Youssef, Y., Chow, F., and Yousef, G. (2008). Differential protein expressions in renal cell carcinoma: new biomarker discovery by mass spectrometry. J. Proteome Res., in press.
51. Sosman, J.A., Puzanov, I., and Atkins, M.B. (2007). Opportunities and obstacles to combination targeted therapy in renal cell cancer. Clin. Cancer Res. 13, 764s-769s.
52. Takahashi, M., Rhodes, D.R., Furge, K.A., Kanayama, H., Kagawa, S., Haab, B.B., and Teh, B.T. (2001). Gene expression profiling of clear cell renal cell carcinoma: gene identification and prognostic classification. Proc. Natl. Acad. Sci. USA 98, 9754-9759.
53. Takayama, T., Mugiya, S., Sugiyama, T., Aoki, T., Furuse, H., Liu, H., Hirano, Y., Kai, F., Ushiyama, T., and Ozono, S. (2006). High levels of thymidine phosphorylase as an independent prognostic factor in renal cell carcinoma. Jpn. J. Clin. Oncol. 36, 564-569.
54. Todorovic-Rakovic, N. (2005). TGF-β 1 could be a missing link in the interplay between ER and HER-2 in breast cancer. Med. Hypoth. 65, 546-551.
55. Turner, K.J., Moore, J.W., Jones, A., Taylor, C.F., Cuthbert-Heavens, D., Han, C., Leek, R.D., Gatter, K.C., Maxwell, P.H., Ratcliffe, P.J., et al. (2002). Expression of hypoxia-inducible factors in human renal cancer: relationship to angiogenesis and to the von Hippel-Lindau gene mutation. Cancer Res. 62, 2957-2961.
56. van Nimwegen, M.J. and van de Water, B. (2007). Focal adhesion kinase: a potential target in cancer therapy. Biochem. Pharmacol. 73, 597-609.
57. van Spronsen, D.J., Mulders, P.F., and de Mulder, P.H. (2005). Novel treatments for metastatic renal cell carcinoma. Crit. Rev. Oncol. Hematol. 55, 177-191.
58. Vastrik, I., D'Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., et al. (2007). Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 8, R39.
59. Vincenzi, B., Schiavon, G., Silletta, M., Santini, D., Perrone, G., Di, M.M., Angeletti, S., Baldi, A., and Tonini, G. (2006). Cell cycle alterations and lung cancer. Histol. Histopathol. 21, 423-435.
60. Wang, X., Beugnet, A., Murakami, M., Yamanaka, S., and Proud, C.G. (2005). Distinct signaling events downstream of mTOR cooperate to mediate the effects of amino acids and insulin on initiation factor 4E-binding proteins. Mol. Cell. Biol. 25, 2558-2572.
61. Yan, Q., Bartz, S., Mao, M., Li, L., and Kaelin, W.G. Jr. (2007). The hypoxia-inducible factor 2α N-terminal and C-terminal transactivation domains cooperate to promote renal tumorigenesis in vivo. Mol. Cell. Biol. 27, 2092-2102.
62. Yao, M., Tabuchi, H., Nagashima, Y., Baba, M., Nakaigawa, N., Ishiguro, H., Hamada, K., Inayama, Y., Kishida, T., Hattori, K., et al. (2005). Gene expression analysis of renal carcinoma: adipose differentiation-related protein as a potential diagnostic and prognostic biomarker for clear-cell renal carcinoma. J. Pathol. 205, 377-387.
63. Yu, J.X., Sieuwerts, A.M., Zhang, Y., Martens, J.W., Smid, M., Klijn, J.G., Wang, Y., and Foekens, J.A. (2007). Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC Cancer 7, 182.
64. Zacharski, L.R., Memoli, V.A., and Rousseau, S.M. (1986). Coagulation-cancer interaction in situ in renal cell carcinoma. Blood 68, 394-399.