Stage-related alterations in renal cell carcinoma - comprehensive quantitative analysis by 2D-DIGE and Protein Network Analysis

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

  Junker, Heike ^a   Venz, Simone ^a   Zimmermann, Uwe ^a   Thiele, Andrea ^a   Scharf, Christian ^a   Walther, Reinhard ^a  

^a UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CALGRANULIN B; PEROXIREDOXIN 3; PROHIBITIN; PROTEOME; TUMOR PROTEIN;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CANCER STAGING; COMPUTER PROGRAM; CONTROLLED STUDY; CYTOSKELETON; DISORDERS OF MITOCHONDRIAL FUNCTIONS; HUMAN; HUMAN TISSUE; IMAGE ANALYSIS; IMAGE QUALITY; IMMUNOHISTOCHEMISTRY; KIDNEY CARCINOMA; LIPID METABOLISM; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PATHOLOGY; PREDICTION; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN FUNCTION; QUALITY CONTROL; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS; VALIDATION PROCESS; WESTERN BLOTTING; ADULT; AGED; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; FEMALE; KIDNEY TUMOR; MALE; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; MIDDLE AGED; PRINCIPAL COMPONENT ANALYSIS; PROTEOMICS; REPRODUCIBILITY; SIGNAL TRANSDUCTION;

ADULT; AGED; AGED, 80 AND OVER; BLOTTING, WESTERN; CARCINOMA, RENAL CELL; CLUSTER ANALYSIS; FEMALE; HUMANS; IMMUNOHISTOCHEMISTRY; KIDNEY NEOPLASMS; MALE; MASS SPECTROMETRY; MIDDLE AGED; NEOPLASM PROTEINS; NEOPLASM STAGING; PRINCIPAL COMPONENT ANALYSIS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; TWO-DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS;

EID: 79960048284     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021867     Document Type: Article

References (68)

1. Rini BI, Campbell SC, Escudier B, (2009) Renal cell carcinoma. Lancet 373: 1119-1132.
2. Baak JP, Path FR, Hermsen MA, Meijer G, Schmidt J, et al. (2003) Genomics and proteomics in cancer. Eur J Cancer 39: 1199-1215.
3. Boer JM, Huber WK, Sultmann H, Wilmer F, von Heydebreck A, 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.
4. Moch H, Presti JC Jr, Sauter G, Buchholz N, Jordan P, et al. (1996) Genetic aberrations detected by comparative genomic hybridization are associated with clinical outcome in renal cell carcinoma. Cancer Res 56: 27-30.
5. Wilhelm M, Veltman JA, Olshen AB, Jain AN, Moore DH, et al. (2002) Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res 62: 957-960.
6. Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, et al. (1996) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13: 19-50.
7. Balabanov S, Zimmermann U, Protzel C, Scharf C, Klebingat KJ, et al. (2001) Tumour-related enzyme alterations in the clear cell type of human renal cell carcinoma identified by two-dimensional gel electrophoresis. Eur J Biochem 268: 5977-5980.
8. Dallmann K, Junker H, Balabanov S, Zimmermann U, Giebel J, et al. (2004) Human agmatinase is diminished in the clear cell type of renal cell carcinoma. Int J Cancer 108: 342-347.
9. Sarto C, Marocchi A, Sanchez JC, Giannone D, Frutiger S, et al. (1997) Renal cell carcinoma and normal kidney protein expression. Electrophoresis 18: 599-604.
10. Sarto C, Frutiger S, Cappellano F, Sanchez JC, Doro G, et al. (1999) Modified expression of plasma glutathione peroxidase and manganese superoxide dismutase in human renal cell carcinoma. Electrophoresis 20: 3458-3466.
11. Unwin RD, Craven RA, Harnden P, Hanrahan S, Totty N, et al. (2003) Proteomic changes in renal cancer and co-ordinate demonstration of both the glycolytic and mitochondrial aspects of the Warburg effect. Proteomics 3: 1620-1632.
12. Walther R, Balabanov S, Junker H, Scharf C, Zimmermann U, (2004) Proteome analysis of renal cell carcinoma to develop new strategies in diagnosis and therapy. Int J Clin Pharmacol Ther 42: 635-636.
13. Zimmermann U, Balabanov S, Giebel J, Teller S, Junker H, et al. (2004) Increased expression and altered location of annexin IV in renal clear cell carcinoma: a possible role in tumour dissemination. Cancer Lett 209: 111-118.
14. Bjellqvist B, Ek K, Righetti PG, Gianazza E, Gorg A, et al. (1982) Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods 6: 317-339.
15. O'Farrell PH, (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250: 4007-4021.
16. Alessandro R, Belluco C, Kohn EC, (2005) Proteomic approaches in colon cancer: promising tools for new cancer markers and drug target discovery. Clin Colorectal Cancer 4: 396-402.
17. Marouga R, David S, Hawkins E, (2005) The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 382: 669-678.
18. Sobin LH, Wittekind C, (2002) Tnm classification of malignant tumours. New York Wiley.
19. Fuhrman SA, Lasky LC, Limas C, (1982) Prognostic significance of morphologic parameters in renal cell carcinoma. Am J Surg Pathol 6: 655-663.
20. Bradford MM, (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248-254.
21. Eymann C, Dreisbach A, Albrecht D, Bernhardt J, Becher D, et al. (2004) A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics 4: 2849-2876.
22. Sinz A, Bantscheff M, Mikkat S, Ringel B, Drynda S, et al. (2002) Mass spectrometric proteome analyses of synovial fluids and plasmas from patients suffering from rheumatoid arthritis and comparison to reactive arthritis or osteoarthritis. Electrophoresis 23: 3445-3456.
23. Kim DS, Choi YP, Kang S, Gao MQ, Kim B, et al. (2010) Panel of candidate biomarkers for renal cell carcinoma. J Proteome Res 9: 3710-3719.
24. Johann DJ Jr, Wei BR, Prieto DA, Chan KC, Ye X, et al. (2010) Combined blood/tissue analysis for cancer biomarker discovery: application to renal cell carcinoma. Anal Chem 82: 1584-1588.
25. Lichtenfels R, Dressler SP, Zobawa M, Recktenwald CV, Ackermann A, et al. (2009) Systematic comparative protein expression profiling of clear cell renal cell carcinoma: a pilot study based on the separation of tissue specimens by two-dimensional gel electrophoresis. Mol Cell Proteomics 8: 2827-2842.
26. Seliger B, Dressler SP, Wang E, Kellner R, Recktenwald CV, et al. (2009) Combined analysis of transcriptome and proteome data as a tool for the identification of candidate biomarkers in renal cell carcinoma. Proteomics 9: 1567-1581.
27. Siu KW, DeSouza LV, Scorilas A, Romaschin AD, Honey RJ, et al. (2009) Differential protein expressions in renal cell carcinoma: new biomarker discovery by mass spectrometry. J Proteome Res 8: 3797-3807.
28. Okamura N, Masuda T, Gotoh A, Shirakawa T, Terao S, et al. (2008) Quantitative proteomic analysis to discover potential diagnostic markers and therapeutic targets in human renal cell carcinoma. Proteomics 8: 3194-3203.
29. Seliger B, Dressler SP, Lichtenfels R, Kellner R, (2007) Candidate biomarkers in renal cell carcinoma. Proteomics 7: 4601-4612.
30. Perroud B, Lee J, Valkova N, Dhirapong A, Lin PY, et al. (2006) Pathway analysis of kidney cancer using proteomics and metabolic profiling. Mol Cancer 5: 64.
31. Craven RA, Stanley AJ, Hanrahan S, Dods J, Unwin R, et al. (2006) Proteomic analysis of primary cell lines identifies protein changes present in renal cell carcinoma. Proteomics 6: 2853-2864.
32. Warburg O, (1956) On the origin of cancer cells. Science 123: 309-314.
33. Smallbone K, Gavaghan DJ, Gatenby RA, Maini PK, (2005) The role of acidity in solid tumour growth and invasion. J Theor Biol 235: 476-484.
34. Stern R, Shuster S, Neudecker BA, Formby B, (2002) Lactate stimulates fibroblast expression of hyaluronan and CD44: the Warburg effect revisited. Exp Cell Res 276: 24-31.
35. Seyfried TN, Kiebish M, Mukherjee P, Marsh J, (2008) Targeting energy metabolism in brain cancer with calorically restricted ketogenic diets. Epilepsia 49 (Suppl 8): 114-116.
36. Sun RC, Fadia M, Dahlstrom JE, Parish CR, Board PG, et al. (2010) Reversal of the glycolytic phenotype by dichloroacetate inhibits metastatic breast cancer cell growth in vitro and in vivo. Breast Cancer Res Treat 120: 253-260.
37. Xu RH, Pelicano H, Zhou Y, Carew JS, Feng L, et al. (2005) Inhibition of glycolysis in cancer cells: a novel strategy to overcome drug resistance associated with mitochondrial respiratory defect and hypoxia. Cancer Res 65: 613-621.
38. Choi D, Lee SJ, Hong S, Kim IH, Kang S, (2008) Prohibitin interacts with RNF2 and regulates E2F1 function via dual pathways. Oncogene 27: 1716-1725.
39. Fusaro G, Wang S, Chellappan S, (2002) Differential regulation of Rb family proteins and prohibitin during camptothecin-induced apoptosis. Oncogene 21: 4539-4548.
40. Nijtmans LG, Artal SM, Grivell LA, Coates PJ, (2002) The mitochondrial PHB complex: roles in mitochondrial respiratory complex assembly, ageing and degenerative disease. Cell Mol Life Sci 59: 143-155.
41. McClung JK, Danner DB, Stewart DA, Smith JR, Schneider EL, et al. (1989) Isolation of a cDNA that hybrid selects antiproliferative mRNA from rat liver. Biochem Biophys Res Commun 164: 1316-1322.
42. Manjeshwar S, Branam DE, Lerner MR, Brackett DJ, Jupe ER, (2003) Tumor suppression by the prohibitin gene 3′untranslated region RNA in human breast cancer. Cancer Res 63: 5251-5256.
43. Wang S, Nath N, Adlam M, Chellappan S, (1999) Prohibitin, a potential tumor suppressor, interacts with RB and regulates E2F function. Oncogene 18: 3501-3510.
44. Peng X, Mehta R, Wang S, Chellappan S, Mehta RG, (2006) Prohibitin is a novel target gene of vitamin D involved in its antiproliferative action in breast cancer cells. Cancer Res 66: 7361-7369.
45. Asamoto M, Cohen SM, (1994) Prohibitin gene is overexpressed but not mutated in rat bladder carcinomas and cell lines. Cancer Lett 83: 201-207.
46. Chowdhury I, Xu W, Stiles JK, Zeleznik A, Yao X, et al. (2007) Apoptosis of rat granulosa cells after staurosporine and serum withdrawal is suppressed by adenovirus-directed overexpression of prohibitin. Endocrinology 148: 206-217.
47. Gregory-Bass RC, Olatinwo M, Xu W, Matthews R, Stiles JK, et al. (2008) Prohibitin silencing reverses stabilization of mitochondrial integrity and chemoresistance in ovarian cancer cells by increasing their sensitivity to apoptosis. Int J Cancer 122: 1923-1930.
48. Sanchez-Quiles V, Santamaria E, Segura V, Sesma L, Prieto J, et al. (2010) Prohibitin deficiency blocks proliferation and induces apoptosis in human hepatoma cells: molecular mechanisms and functional implications. Proteomics 10: 1609-1620.
49. Sievers C, Billig G, Gottschalk K, Rudel T, (2010) Prohibitins are required for cancer cell proliferation and adhesion. PLoS One 5: e12735.
50. Ande SR, Gu Y, Nyomba BL, Mishra S, (2009) Insulin induced phosphorylation of prohibitin at tyrosine 114 recruits Shp1. Biochim Biophys Acta 1793: 1372-1378.
51. Ande SR, Moulik S, Mishra S, (2009) Interaction between O-GlcNAc modification and tyrosine phosphorylation of prohibitin: implication for a novel binary switch. PLoS One 4: e4586.
52. Thompson WE, Ramalho-Santos J, Sutovsky P, (2003) Ubiquitination of prohibitin in mammalian sperm mitochondria: possible roles in the regulation of mitochondrial inheritance and sperm quality control. Biol Reprod 69: 254-260.
53. Immenschuh S, Baumgart-Vogt E, (2005) Peroxiredoxins, oxidative stress, and cell proliferation. Antioxid Redox Signal 7: 768-777.
54. Wolf G, Aumann N, Michalska M, Bast A, Sonnemann J, et al. (2010) Peroxiredoxin III protects pancreatic ss cells from apoptosis. J Endocrinol 207: 163-175.
55. Zhang B, Wang Y, Su Y, (2009) Peroxiredoxins, a novel target in cancer radiotherapy. Cancer Lett 286: 154-160.
56. Choi JH, Kim TN, Kim S, Baek SH, Kim JH, et al. (2002) Overexpression of mitochondrial thioredoxin reductase and peroxiredoxin III in hepatocellular carcinomas. Anticancer Res 22: 3331-3335.
57. Karihtala P, Mantyniemi A, Kang SW, Kinnula VL, Soini Y, (2003) Peroxiredoxins in breast carcinoma. Clin Cancer Res 9: 3418-3424.
58. Kinnula VL, Lehtonen S, Sormunen R, Kaarteenaho-Wiik R, Kang SW, et al. (2002) Overexpression of peroxiredoxins I, II, III, V, and VI in malignant mesothelioma. J Pathol 196: 316-323.
59. Park JH, Kim YS, Lee HL, Shim JY, Lee KS, et al. (2006) Expression of peroxiredoxin and thioredoxin in human lung cancer and paired normal lung. Respirology 11: 269-275.
60. Soini Y, Kallio JP, Hirvikoski P, Helin H, Kellokumpu-Lehtinen P, et al. (2006) Oxidative/nitrosative stress and peroxiredoxin 2 are associated with grade and prognosis of human renal carcinoma. APMIS 114: 329-337.
61. Ghavami S, Chitayat S, Hashemi M, Eshraghi M, Chazin WJ, et al. (2009) S100A8/A9: a Janus-faced molecule in cancer therapy and tumorgenesis. Eur J Pharmacol 625: 73-83.
62. Arai K, Takano S, Teratani T, Ito Y, Yamada T, et al. (2008) S100A8 and S100A9 overexpression is associated with poor pathological parameters in invasive ductal carcinoma of the breast. Curr Cancer Drug Targets 8: 243-252.
63. Kim HK, Reyzer ML, Choi IJ, Kim CG, Kim HS, et al. (2010) Gastric cancer-specific protein profile identified using endoscopic biopsy samples via MALDI mass spectrometry. J Proteome Res 9: 4123-4130.
64. Koskimaa HM, Kurvinen K, Costa S, Syrjanen K, Syrjanen S, (2010) Molecular markers implicating early malignant events in cervical carcinogenesis. Cancer Epidemiol Biomarkers Prev 19: 2003-2012.
65. Zhao L, Wang H, Sun X, Ding Y, (2010) Comparative proteomic analysis identifies proteins associated with the development and progression of colorectal carcinoma. FEBS J 277: 4195-4204.
66. Hobbs JA, May R, Tanousis K, McNeill E, Mathies M, et al. (2003) Myeloid cell function in MRP-14 (S100A9) null mice. Mol Cell Biol 23: 2564-2576.
67. Manitz MP, Horst B, Seeliger S, Strey A, Skryabin BV, et al. (2003) Loss of S100A9 (MRP14) results in reduced interleukin-8-induced CD11b surface expression, a polarized microfilament system, and diminished responsiveness to chemoattractants in vitro. Mol Cell Biol 23: 1034-1043.
68. Ichikawa M, Williams R, Wang L, Vogl T, Srikrishna G, (2011) S100A8/A9 activate key genes and signaling pathways in colon tumor progression. Mol Cancer Res 9: 133-148.