Quantitative proteomic analysis reveals potential diagnostic markers and pathways involved in pathogenesis of renal cell carcinoma

Oncotarget

Volumn 5, Issue 2, 2014, Pages 506-518

  White, Nicole M A ^a,b   Masui, Olena ^c   DeSouza, Leroi V ^c   Krakovska, Olga ^c   Metias, Shereen ^a   Romaschin, Alexander D ^a,b   John Honey, R ^d   Stewart, Robert ^d   Pace, Kenneth ^d   Lee, Jason ^d   Jewett, Michael A S ^e   Bjarnason, Georg A ^f   Michael Siu, K W ^c   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)

^e UNIVERSITY HEALTH NETWORK   (Canada)

^f SUNNYBROOK RESEARCH INSTITUTE   (Canada)

Author keywords

Carcinoma; Hsp27; ITRAQ; Kidney cancer; proteomics; Renal cell; Urine markers

Indexed keywords

ALPHA ENOLASE; EARLY PREGNANCY FACTOR; HEAT SHOCK PROTEIN 27; LACTATE DEHYDROGENASE; HSPB1 PROTEIN, HUMAN; TUMOR MARKER; TUMOR PROTEIN;

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FEMALE; GLUCOSE METABOLISM; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; KIDNEY CARCINOMA; KIDNEY PARENCHYMA; LIQUID CHROMATOGRAPHY; MAJOR CLINICAL STUDY; MALE; MOLECULAR DYNAMICS; PATHOGENESIS; POLYMERASE CHAIN REACTION; PROTEIN BLOOD LEVEL; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN SECRETION; PROTEOMICS; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY; WESTERN BLOTTING; BLOOD; CASE CONTROL STUDY; GENE EXPRESSION PROFILING; GENETICS; KIDNEY TUMOR; METABOLISM; PROCEDURES; PROGNOSIS; URINE;

CARCINOMA, RENAL CELL; CASE-CONTROL STUDIES; FEMALE; GENE EXPRESSION PROFILING; HSP27 HEAT-SHOCK PROTEINS; HUMANS; IMMUNOHISTOCHEMISTRY; KIDNEY NEOPLASMS; MALE; NEOPLASM PROTEINS; PROGNOSIS; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 84896696598     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.1529     Document Type: Article

References (35)

1. Lipworth L, Tarone RE, McLaughlin JK. The epidemiology of renal cell carcinoma. J Urol. 2006; 176: 2353-2358.
2. Weiss RH, Lin PY. Kidney cancer: identification of novel targets for therapy. Kidney Int. 2006; 69: 224-232.
3. Feldstein MS, Rhodes DJ, Parker AS, Orford RR, Castle EP. The haphazard approach to the early detection of asymptomatic renal cancer: results from a contemporary executive health programme. BJU Int. 2009; 104: 53-56.
4. Beroukhim R, Brunet JP, Di NA, Mertz KD, Seeley A, Pires MM, Linhart D, Worrell RA, Moch H, Rubin MA, Sellers WR, Meyerson M, Linehan WM, Kaelin WG, Jr., Signoretti S. Patterns of gene expression and copy-number alterations in von-hippel lindau disease-associated and sporadic clear cell carcinoma of the kidney. Cancer Res. 2009; 69: 4674-4681.
5. Girgis AH, Iakovlev VV, Beheshti B, Bayani J, Squire JA, Bui A, Mankaruos M, Youssef Y, Khalil B, Khella HW, Pasic MD, Yousef GM. Multi-level whole genome analysis reveals candidate biomarkers in clear cell renal cell carcinoma. Cancer Res. 2012; 72: 5273-5284.
6. White NM, Yousef GM. Translating molecular signatures of renal cell carcinoma into clinical practice. J Urol. 2011; 186: 9-11.
7. Metias SM, Lianidou E, Yousef GM. MicroRNAs in clinical oncology: at the crossroads between promises and problems. J Clin Pathol. 2009; 62: 771-776.
8. Pavlovich CP, Schmidt LS. Searching for the hereditary causes of renal-cell carcinoma. Nat Rev Cancer. 2004; 4: 381-393.
9. Sarto C, Marocchi A, Sanchez JC, Giannone D, Frutiger S, Golaz O, Wilkins MR, Doro G, Cappellano F, Hughes G, Hochstrasser DF, Mocarelli P. Renal cell carcinoma and normal kidney protein expression. Electrophoresis. 1997; 18: 599-604.
10. DeSouza L, Diehl G, Rodrigues MJ, Guo J, Romaschin AD, Colgan TJ, Siu KW. 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. 2005; 4: 377-386.
11. Ralhan R, DeSouza LV, Matta A, Chandra TS, Ghanny S, Datta GS, Bahadur S, Siu KW. Discovery and verification of head-and-neck cancer biomarkers by differential protein expression analysis using iTRAQ labeling, multidimensional liquid chromatography, and tandem mass spectrometry. Mol Cell Proteomics. 2008; 7: 1162-1173.
12. DeSouza LV, Grigull J, Ghanny S, Dube V, Romaschin AD, Colgan TJ, Siu KW. Endometrial carcinoma biomarker discovery and verification using differentially tagged clinical samples with multidimensional liquid chromatography and tandem mass spectrometry. Mol Cell Proteomics. 2007; 6: 1170-1182.
13. Shilov IV, Seymour SL, Patel AA, Loboda A, Tang WH, Keating SP, Hunter CL, Nuwaysir LM, Schaeffer DA. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics. 2007; 6: 1638-1655.
14. Masui O, White NMA, DeSouza LV, Krakovska O, Matta A, Metias S, Khalil B, Romaschin AD, Honey RJ, Stewart R, Pace K, Bjarnason GA, Siu KW, Yousef GM. Quantitative Proteomic Analysis in Metastatic Renal Cell Carcinoma Reveals a Unique Set of Proteins with Potential Prognostic Significance. Mol Cell Proteomics. 2013; 12: 132-144.
15. Tang WH, Shilov IV, Seymour SL. Nonlinear fitting method for determining local false discovery rates from decoy database searches. J Proteome Res. 2008; 7: 3661-3667.
16. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998; 95: 14863-14868.
17. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011; 39: D561-D568.
18. Romaschin AD, Youssef Y, Chow TF, Siu KW, DeSouza LV, Honey RJ, Stewart R, Pace KT, Yousef GM. Exploring the pathogenesis of renal cell carcinoma: pathway and bioinformatics analysis of dysregulated genes and proteins. Biol Chem. 2009; 390: 125-135.
19. Siu KW, DeSouza LV, Scorilas A, Romaschin AD, Honey RJ, Stewart R, Pace K, Youssef Y, Chow TF, Yousef GM. Differential protein expressions in renal cell carcinoma: new biomarker discovery by mass spectrometry. J Proteome Res. 2009; 8: 3797-3807.
20. Unwin RD, Craven RA, Harnden P, Hanrahan S, Totty N, Knowles M, Eardley I, Selby PJ, Banks RE. Proteomic changes in renal cancer and co-ordinate demonstration of both the glycolytic and mitochondrial aspects of the Warburg effect. Proteomics. 2003; 3: 1620-1632.
21. Sudarshan S, Karam JA, Brugarolas J, Thompson RH, Uzzo R, Rini B, Margulis V, Patard JJ, Escudier B, Linehan WM. Metabolism of Kidney Cancer: From the Lab to Clinical Prac tice. Eur Urol. 2013; 63: 244-251.
22. Perroud B, Lee J, Valkova N, Dhirapong A, Lin PY, Fiehn O, Kultz D, Weiss RH. Pathway analysis of kidney cancer using proteomics and metabolic profiling. Mol Cancer. 2006; 5: 64.
23. Shi T, Dong F, Liou LS, Duan ZH, Novick AC, DiDonato JA. Differential protein profiling in renal-cell carcinoma. Mol Carcinog. 2004; 40: 47-61.
24. Hwa JS, Park HJ, Jung JH, Kam SC, Park HC, Kim CW, Kang KR, Hyun JS, Chung KH. Identification of proteins differentially expressed in the conventional renal cell carcinoma by proteomic analysis. J Korean Med Sci. 2005; 20: 450-455.
25. Craven RA, Stanley AJ, Hanrahan S, Dods J, Unwin R, Totty N, Harnden P, Eardley I, Selby PJ, Banks RE. Proteomic analysis of primary cell lines identifies protein changes present in renal cell carcinoma. Proteomics. 2006; 6: 2853-2864.
26. Perego RA, Bianchi C, Corizzato M, Eroini B, Torsello B, Valsecchi C, Di FA, Cordani N, Favini P, Ferrero S, Pitto M, Sarto C, Magni F, Rocco F, Mocarelli P. Primary cell cultures arising from normal kidney and renal cell carcinoma retain the proteomic profile of corresponding tissues. J Proteome Res. 2005; 4: 1503-1510.
27. Koukourakis MI, Giatromanolaki A, Sivridis E, Gatter KC, Trarbach T, Folprecht G, Shi MM, Lebwohl D, Jalava T, Laurent D, Meinhardt G, Harris AL. Prognostic and predictive role of lactate dehydrogenase 5 expression in colorectal cancer patients treated with PTK787/ZK 222584 (vatalanib) antiangiogenic therapy. Clin Cancer Res. 2011; 17: 4892-4900.
28. Rui Z, Jian-Guo J, Yuan-Peng T, Hai P, Bing-Gen R. Use of serological proteomic methods to find biomarkers associated with breast cancer. Proteomics. 2003; 3: 433-439.
29. Chatterjee M, Mohapatra S, Ionan A, Bawa G, Ali-Fehmi R, Wang X, Nowak J, Ye B, Nahhas FA, Lu K, Witkin SS, Fishman D, Munkarah A, Morris R, Levin NK, Shirley NN, Tromp G, Abrams J, Draghici S, Tainsky MA. Diagnostic markers of ovarian cancer by high-throughput antigen cloning and detection on arrays. Cancer Res. 2006; 66: 1181-1190.
30. Boer JM, Huber WK, Sultmann H, Wilmer F, von Heydebreck A, Haas S, Korn B, Gunawan B, Vente A, Fuzesi L, Vingron M, Poustka A. 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. 2001; 11: 1861-1870.
31. Gieseg MA, Cody T, Man MZ, Madore SJ, Rubin MA, Kaldjian EP. Expression profiling of human renal carcinomas with functional taxonomic analysis. BMC Bioinformatics. 2002; 3: 26.
32. Mazurek S, Boschek CB, Hugo F, Eigenbrodt E. Pyruvate kinase type M2 and its role in tumor growth and spreading. Semin Cancer Biol. 2005; 15: 300-308.
33. Kaelin WG, Jr. The von Hippel-Lindau gene, kidney cancer, and oxygen sensing. J Am Soc Nephrol. 2003; 14: 2703-2711.
34. Turner KJ, Moore JW, Jones A, Taylor CF, Cuthbert-Heavens D, Han C, Leek RD, Gatter KC, Maxwell PH, Ratcliffe PJ, Cranston D, Harris AL. Expression of hypoxiainducible factors in human renal cancer: relationship to angiogenesis and to the von Hippel-Lindau gene mutation. Cancer Res. 2002; 62: 2957-2961.
35. Arsanious A, Bjarnason GA, Yousef GM. From bench to bedside: current and future applications of molecular profiling in renal cell carcinoma. Mol Cancer. 2009; 8: 20.