Combined proteome and transcriptome analyses for the discovery of urinary biomarkers for urothelial carcinoma

British Journal of Cancer

Volumn 108, Issue 9, 2013, Pages 1854-1861

  Shimwell, N J ^a   Bryan, R T ^a   Wei, W ^a   James, N D ^a   Cheng, K K ^a   Zeegers, M P ^a,b   Johnson, P J ^a   Martin, A ^a   Ward, D G ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^b MAASTRICHT UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Biomarker; Bladder cancer; Midkine; Secretome; Urine

Indexed keywords

MESSENGER RNA; PROTEIN; PROTEOME; TRANSCRIPTOME;

ADULT; AGED; ARTICLE; BLADDER CANCER; BLADDER TUMOR; CANCER CELL; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; FEMALE; HEMATURIA; HUMAN; HUMAN CELL; KIDNEY CONCENTRATING CAPACITY; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; PROTEIN URINE LEVEL; PROTEOMICS; TRANSITIONAL CELL CARCINOMA; URINALYSIS;

CARCINOMA, TRANSITIONAL CELL; CELL LINE, TUMOR; CYTOKINES; GENE EXPRESSION PROFILING; HUMANS; PROTEIN ARRAY ANALYSIS; PROTEINASE INHIBITORY PROTEINS, SECRETORY; PROTEINURIA; PROTEOME; RNA, MESSENGER; TRANSCRIPTOME; TUMOR MARKERS, BIOLOGICAL; URINARY BLADDER NEOPLASMS; UROLOGIC NEOPLASMS; UROTHELIUM;

EID: 84878539640     PISSN: 00070920     EISSN: 15321827     Source Type: Journal    
DOI: 10.1038/bjc.2013.157     Document Type: Article

References (47)

1. Anderson N (2010) The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin Chem 56: 177-185.
2. Babjuk M, Oosterlinck W, Sylvester R, Kaasinen E, Böhle A, Palou-Redorta J, Rouprêt M. European Association of Urology (2011) EAU guidelines on non-muscle-invasive urothelial carcinoma of the bladder, the 2011 update. Eur Urol 59: 997-1008.
3. Bolstad BM, Irizarry R, Astrand M, Speed T (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
4. Bryan R, Wei W, Shimwell N, Collins S, Hussain S, Billingham L, Murray P, Deshmukh N, James N, Wallace D, Johnson P, Zeegers M, Cheng K, Martin A, Ward D (2011) Assessment of high-throughput high-resolution MALDI-TOF-MS of urinary peptides for the detection of muscle-invasive bladder cancer. Proteomics Clin Appl 5: 493-503.
5. Cauberg E, de Bruin D, Faber D, van Leeuwen T, de la Rosette J, de Reijke T (2009) A new generation of optical diagnostics for bladder cancer: technology, diagnostic accuracy, and future applications. Eur Urol 56: 287-296.
6. Chang K, Wu C, Chen H, Chen S, Peng P, Tsang N, Lee L, Liu S, Liang Y, Lee Y, Hao S, Chang Y, Yu J (2010) Identification of candidate nasopharyngeal carcinoma serum biomarkers by cancer cell secretome and tissue transcriptome analysis: potential usage of cystatin A for predicting nodal stage and poor prognosis. Proteomics 10: 2644-2660.
7. Chang Y, Wu C, Shyr Y, Chen T, Hwang T, Yeh T, Chang K, Liu H, Liu Y, Tsai M, Chang Y, Yu J (2011) Secretome-based identification of ULBP2 as a novel serum marker for pancreatic cancer detection. PLoS One 6: e20029.
8. Chen Y, Chen C, Chen H, Chung T, Wu C, Chen C, Hsu C, Chen M, Tsui K, Chang P, Chang Y, Yu J (2010) Discovery of novel bladder cancer biomarkers by comparative urine proteomics using iTRAQ technology. J Proteome Res 9: 5803-5815.
9. Dyrskjøt L, Kruhøffer M, Thykjaer T, Marcussen N, Jensen J, Møller K, Ørntoft T (2004) Gene expression in the urinary bladder: a common carcinoma in situ gene expression signature exists disregarding histopathological classification. Cancer Res 64: 4040-4048.
10. Grønborg M, Kristiansen T, Iwahori A, Chang R, Reddy R, Sato N, Molina H, Jensen O, Hruban R, Goggins M, Maitra A, Pandey A (2006) Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics 5: 157-171.
11. Ikematsu S, Okamoto K, Yoshida Y, Oda M, Sugano-Nagano H, Ashida K, Kumai H, Kadomatsu K, Muramatsu H, Muramatsu T, Sakuma S (2003) High levels of urinary midkine in various cancer patients. Biochem Biophys Res Commun 306: 329-332.
12. Irizarry RA, Bolstad BM, Collin F, Cope L, Hobbs B, Speed TP (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
13. Irmak S, Tilki D, Heukeshoven J, Oliveira-Ferrer L, Friedrich M, Huland H, Ergün S (2005) Stage-dependent increase of orosomucoid and zincalpha2- glycoprotein in urinary bladder cancer. Proteomics 5: 4296-4304.
14. James N, Hussain S, Hall E, Jenkins P, Tremlett J, Rawlings C, Crundwell M, Sizer B, Sreenivasan T, Hendron C, Lewis R, Waters R, Huddart R, Investigators B (2012) Radiotherapy with or without chemotherapy in muscle-invasive bladder cancer. N Engl J Med 366: 1477-1488.
15. Kageyama S, Isono T, Iwaki H, Wakabayashi Y, Okada Y, Kontani K, Yoshimura K, Terai A, Arai Y, Yoshiki T (2004) Identification by proteomic analysis of calreticulin as a marker for bladder cancer and evaluation of the diagnostic accuracy of its detection in urine. Clin Chem 50: 857-866.
16. Kataoka H, Shimomura T, Kawaguchi T, Hamasuna R, Itoh H, Kitamura N, Miyazawa K, Koono M (2000) Hepatocyte growth factor activator inhibitor type 1 is a specific cell surface binding protein of hepatocyte growth factor activator (HGFA) and regulates HGFA activity in the pericellular microenvironment. J Biol Chem 275: 40453-40462.
17. Kaufman D, Shipley W, Feldman A (2009) Bladder cancer. Lancet 374: 239-249.
18. Kawanishi H, Matsui Y, Ito M, Watanabe J, Takahashi T, Nishizawa K, Nishiyama H, Kamoto T, Mikami Y, Tanaka Y, Jung G, Akiyama H, Nobumasa H, Guilford P, Reeve A, Okuno Y, Tsujimoto G, Nakamura E, Ogawa O (2008) Secreted CXCL1 is a potential mediator and marker of the tumor invasion of bladder cancer. Clin Cancer Res 14: 2579-2587.
19. Lindén M, Lind S, Mayrhofer C, Segersten U, Wester K, Lyutvinskiy Y, Zubarev R, Malmström P, Pettersson U (2012) Proteomic analysis of urinary biomarker candidates for nonmuscle invasive bladder cancer. Proteomics 12: 135-144.
20. Lotan Y, Roehrborn C (2003) Sensitivity and specificity of commonly available bladder tumor markers versus cytology: results of a comprehensive literature review and meta-analyses. Urology 61: 109-118.
21. Makridakis M, Roubelakis M, Bitsika V, Dimuccio V, Samiotaki M, Kossida S, Panayotou G, Coleman J, Candiano G, Anagnou N, Vlahou A (2010) Analysis of secreted proteins for the study of bladder cancer cell aggressiveness. J Proteome Res 9: 3243-3259.
22. Mengual L, Burset M, Ars E, Lozano J, Villavicencio H, Ribal M, Alcaraz A (2009) DNA microarray expression profiling of bladder cancer allows identification of noninvasive diagnostic markers. J Urol 182: 741-748.
23. Muramaki M, Miyake H, Hara I, Kamidono S (2003) Introduction of midkine gene into human bladder cancer cells enhances their malignant phenotype but increases their sensitivity to antiangiogenic therapy. Clin Cancer Res 9: 5152-5160.
24. Nagakawa O, Yamagishi T, Akashi T, Nagaike K, Fuse H (2006) Serum hepatocyte growth factor activator inhibitor type I (HAI-I) and type 2 (HAI-2) in prostate cancer. Prostate 66: 447-452.
25. Nagaraj N, Mann M (2011) Quantitative analysis of the intra- and interindividual variability of the normal urinary proteome. J Proteome Res 10: 637-645.
26. Nakamura K, Abarzua F, Hongo A, Kodama J, Nasu Y, Kumon H, Hiramatsu Y (2009) The role of hepatocyte growth factor activator inhibitor-1 (HAI- 1) as a prognostic indicator in cervical cancer. Int J Oncol 35: 239-248.
27. Onda H, Ohkubo S, Shintani Y, Ogi K, Kikuchi K, Tanaka H, Yamamoto K, Tsuji I, Ishibashi Y, Yamada T, Kitada C, Suzuki N, Sawada H, Nishimura O, Fujino M (2001) A Novel Secreted Tumor Antigen with a Glycosylphosphatidylinositol-Anchored Structure Ubiquitously Expressed in Human Cancers. Biochem Biophys Res Commun 285: 235-243.
28. Orenes-Piñero E, Cortón M, González-Peramato P, Algaba F, Casal I, Serrano A, Sánchez-Carbayo M (2007) Searching urinary tumor markers for bladder cancer using a two-dimensional differential gel electrophoresis (2D-DIGE) approach. J Proteome Res 6: 4440-4448.
29. O'Brien T, Cranston D, Fuggle S, Bicknell R, Harris A (1996) The angiogenic factor midkine is expressed in bladder cancer, and overexpression correlates with a poor outcome in patients with invasive cancers. Cancer Res 56: 2515-2518.
30. Parr C, Jiang W (2001) Expression of hepatocyte growth factor/scatter factor, its activator, inhibitors and the c-Met receptor in human cancer cells. Int J Oncol 19: 857-863.
31. Parr C, Jiang W (2006) Hepatocyte growth factor activation inhibitors (HAI-1 and HAI-2) regulate HGF-induced invasion of human breast cancer cells. Int J Cancer 119: 1176-1183.
32. Ray S, Reddy P, Jain R, Gollapalli K, Moiyadi A, Srivastava S (2011) Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead. Proteomics 11: 2139-2162.
33. Salo J, Kivisaari L, Lehtonen T (1985) CT in determining the depth of infiltration of bladder tumors. Urol Radiol 7: 88-93.
34. Sánchez-Carbayo M, Herrero E, Megías J, Mira A, Soria F (1999) Initial evaluation of the new urinary bladder cancer rapid test in the detection of transitional cell carcinoma of the bladder. Urology 54: 656-661.
35. Senga Y, Kimura G, Hattori T, Yoshida K (1996) Clinical evaluation of soluble cytokeratin 19 fragments (CYFRA 21-1) in serum and urine of patients with bladder cancer. Urology 48: 703-710.
36. Shariat S, Matsumoto K, Casella R, Jian W, Lerner S (2005) Urinary levels of soluble e-cadherin in the detection of transitional cell carcinoma of the urinary bladder. Eur Urol 48: 69-76.
37. Smyth G (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3, Article 3.
38. Tilki D, Burger M, Dalbagni G, Grossman H, Hakenberg O, Palou J, Reich O, Rouprêt M, Shariat S, Zlotta A (2011) Urine markers for detection and surveillance of non-muscle-invasive bladder cancer. Eur Urol 60: 484-492.
39. van Rhijn B, Burger M, Lotan Y, Solsona E, Stief C, Sylvester R, Witjes J, Zlotta A (2009) Recurrence and progression of disease in non-muscle-invasive bladder cancer: from epidemiology to treatment strategy. Eur Urol 56.
40. Volmer M, Stühler K, Zapatka M, Schöneck A, Klein-Scory S, Schmiegel W, Meyer H, Schwarte-Waldhoff I (2005) Differential proteome analysis of conditioned media to detect Smad4 regulated secreted biomarkers in colon cancer. Proteomics 5: 2587-2601.
41. Waldhauer I, Steinle A (2006) Proteolytic release of soluble UL16-binding protein 2 from tumor cells. Cancer Res 66: 2520-2526.
42. Wang C, Wang C, Wang C, Chen C, Wu C, Liang Y, Tsai Y, Chang Y, Yu J, Yu C (2011) Importin subunit alpha-2 is identified as a potential biomarker for non-small cell lung cancer by integration of the cancer cell secretome and tissue transcriptome. Int J Cancer 128: 2364-2372.
43. Wiśniewski J, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6: 359-362.
44. Yang M, Chu P, Chen S, Chung T, Chen W, Tan L, Kan W, Wang H, Su S, Tyan Y (2011) Characterization of ADAM28 as a biomarker of bladder transitional cell carcinomas by urinary proteome analysis. Biochem Biophys Res Commun 411: 714-720.
45. Yang N, Feng S, Shedden K, Xie X, Liu Y, Rosser C, Lubman D, Goodison S (2011) Urinary glycoprotein biomarker discovery for bladder cancer detection using LC/MS-MS and label-free quantification. Clin Cancer Res 17: 3349-3359.
46. Yu C, Chang K, Chang Y, Hsu C, Liang Y, Yu J, Chi L, Chang Y, Wu C (2011) Identification of guanylate-binding protein 1 as a potential oral cancer marker involved in cell invasion using omics-based analysis. J Proteome Res 10: 3778-3788.
47. Zeegers MP, Bryan RT, Langford C, Billingham L, Murray P, Deshmukh NS, Hussain S, James N, Wallace DM, Cheng KK (2009) The West Midlands Bladder Cancer Prognosis Programme: rationale and design. BJU Int 105: 784-788.