Identification of potential bladder cancer markers in urine by abundant-protein depletion coupled with quantitative proteomics

Journal of Proteomics

Volumn 85, Issue , 2013, Pages 28-43

  Chen, Chien Lun ^a,b   Lin, Tsung Shih ^b   Tsai, Cheng Han ^b   Wu, Chih Ching ^c   Chung, Ting ^b   Chien, Kun Yi ^b   Wu, Maureen ^b   Chang, Yu Sun ^b   Yu, Jau Song ^b   Chen, Yi Ting ^b  

^a CHANG GUNG MEMORIAL HOSPITAL   (Taiwan)

^b CHANG GUNG UNIVERSITY COLLEGE OF MEDICINE   (Taiwan)

^c CHANG GUNG UNIVERSITY   (Taiwan)

Author keywords

Abundant protein depletion; Biomarkers; Bladder cancer; Urine proteome

Indexed keywords

APOLIPOPROTEIN; APOLIPOPROTEIN A1; APOLIPOPROTEIN A2; APOLIPOPROTEIN B; APOLIPOPROTEIN C2; APOLIPOPROTEIN C3; APOLIPOPROTEIN E; EPIDERMAL GROWTH FACTOR; HEXAPEPTIDE; PRO EPIDERMAL GROWTH FACTOR; SERUM AMYLOID A; SERUM AMYLOID A 4; TRIOSEPHOSPHATE ISOMERASE; TUMOR MARKER; UNCLASSIFIED DRUG;

ARTICLE; BLADDER CANCER; CANCER PATIENT; CONTROLLED STUDY; FEMALE; HERNIA; HUMAN; KIDNEY CANCER; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; PROTEIN DEPLETION; PROTEIN URINE LEVEL; PROTEOMICS; RETROSPECTIVE STUDY; URINALYSIS; URINE;

APOLIPOPROTEINS; EPIDERMAL GROWTH FACTOR; FEMALE; HUMANS; MALE; NEOPLASM PROTEINS; PROTEOME; PROTEOMICS; SERUM AMYLOID A PROTEIN; SOFTWARE; TUMOR MARKERS, BIOLOGICAL; URINARY BLADDER NEOPLASMS;

EID: 84877917326     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.04.024     Document Type: Article

References (47)

1. Siegel R., Ward E., Brawley O., Jemal A. Cancer statistics, 2011: the impact of eliminating socioeconomic and racial disparities on premature cancer deaths. CA Cancer J Clin 2011, 61:212-236.
2. Baris D., Karagas M.R., Verrill C., Johnson A., Andrew A.S., Marsit C.J., et al. A case-control study of smoking and bladder cancer risk: emergent patterns over time. J Natl Cancer Inst 2009, 101:1553-1561.
3. Youssef R.F., Lotan Y. Predictors of outcome of non-muscle-invasive and muscle-invasive bladder cancer. Sci World J 2011, 11:369-381.
4. Jacobs B.L., Lee C.T., Montie J.E. Bladder cancer in 2010: how far have we come?. CA Cancer J Clin 2010, 60:244-272.
5. Carroll M.F., Temte J.L. Proteinuria in adults: a diagnostic approach. Am Fam Physician 2000, 62:1333-1340.
6. Caubet C., Lacroix C., Decramer S., Drube J., Ehrich J.H., Mischak H., et al. Advances in urinary proteome analysis and biomarker discovery in pediatric renal disease. Pediatr Nephrol 2009, 25:27-35.
7. Thongboonkerd V., Malasit P. Renal and urinary proteomics: current applications and challenges. Proteomics 2005, 5:1033-1042.
8. Candiano G., Santucci L., Petretto A., Bruschi M., Dimuccio V., Urbani A., et al. 2D-electrophoresis and the urine proteome map: where do we stand?. J Proteomics 2010, 73:829-844.
9. Chen C.L., Lai Y.F., Tang P., Chien K.Y., Yu J.S., Tsai C.H., et al. Comparative and targeted proteomic analyses of urinary microparticles from bladder cancer and hernia patients. J Proteome Res 2012, 11:5611-5629.
10. Chen Y.T., Chen H.W., Domanski D., Smith D.S., Liang K.H., Wu C.C., et al. Multiplexed quantification of 63 proteins in human urine by multiple reaction monitoring-based mass spectrometry for discovery of potential bladder cancer biomarkers. J Proteomics 2012, 75:3529-3545.
11. Kushnir M.M., Mrozinski P., Rockwood A.L., Crockett D.K. A depletion strategy for improved detection of human proteins from urine. J Biomol Tech 2009, 20:101-108.
12. Shores K.S., Knapp D.R. Assessment approach for evaluating high abundance protein depletion methods for cerebrospinal fluid (CSF) proteomic analysis. J Proteome Res 2007, 6:3739-3751.
13. Tu C., Rudnick P.A., Martinez M.Y., Cheek K.L., Stein S.E., Slebos R.J., et al. Depletion of abundant plasma proteins and limitations of plasma proteomics. J Proteome Res 2010, 9:4982-4991.
14. Tang H.Y., Beer L.A., Speicher D.W. In-depth analysis of a plasma or serum proteome using a 4D protein profiling method. Methods Mol Biol 2011, 728:47-67.
15. Vasudev N.S., Ferguson R.E., Cairns D.A., Stanley A.J., Selby P.J., Banks R.E. Serum biomarker discovery in renal cancer using 2-DE and prefractionation by immunodepletion and isoelectric focusing; increasing coverage or more of the same?. Proteomics 2008, 8:5074-5085.
16. Bandhakavi S., Stone M.D., Onsongo G., Van Riper S.K., Griffin T.J. A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva. J Proteome Res 2009, 8:5590-5600.
17. Dwivedi R.C., Krokhin O.V., Cortens J.P., Wilkins J.A. Assessment of the reproducibility of random hexapeptide peptide library-based protein normalization. J Proteome Res 2009, 9:1144-1149.
18. Candiano G., Santucci L., Bruschi M., Petretto A., D'Ambrosio C., Scaloni A., et al. "Cheek-to-cheek" urinary proteome profiling via combinatorial peptide ligand libraries: a novel, unexpected elution system. J Proteomics 2012, 75:796-805.
19. Millioni R., Tolin S., Puricelli L., Sbrignadello S., Fadini G.P., Tessari P., et al. High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity. PLoS One 2011, 6:e19603.
20. Chen Y.T., Chen C.L., Chen H.W., Chung T., Wu C.C., Chen C.D., et al. Discovery of novel bladder cancer biomarkers by comparative urine proteomics using iTRAQ technology. J Proteome Res 2010, 9:5803-5815.
21. Epstein J.I., Amin M.B., Reuter V.R., Mostofi F.K. The World Health Organization/International Society of Urological Pathology consensus classification of urothelial (transitional cell) neoplasms of the urinary bladder. Bladder Consensus Conference Committee. Am J Surg Pathol 1998, 22:1435-1448.
22. Epstein J.I., Eble J.N., Sesterhenn I., Sauter G. World Health Organization Classification of Tumors, Pathology and Genetics of Tumors of the Urinary System and Male Genital Organs 2004, 93. IARC Press, Lyon, France.
23. Olsen J.V., de Godoy L.M., Li G., Macek B., Mortensen P., Pesch R., et al. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics 2005, 4:2010-2021.
24. Keller A., Nesvizhskii A.I., Kolker E., Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 2002, 74:5383-5392.
25. Nesvizhskii A.I., Keller A., Kolker E., Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 2003, 75:4646-4658.
26. Nolen B.M., Langmead C.J., Choi S., Lomakin A., Marrangoni A., Bigbee W.L., et al. Serum biomarker profiles as diagnostic tools in lung cancer. Cancer Biomark 2011, 10:3-12.
27. Mrouprêt M., Zigeuner R., Palou J., Boehle A., Kaasinen E., Sylvester R., et al. Guidelines on upper urinary tract urothelial cell carcinomas [access date: 041512]. http://www.uroweb.org/gls/pdf/06_UUTUCC.pdf.
28. Banks R.E., Craven R.A., Harnden P., Madaan S., Joyce A., Selby P.J. Key clinical issues in renal cancer: a challenge for proteomics. World J Urol 2007, 25:537-556.
29. Mancini V., Battaglia M., Ditonno P., Palazzo S., Lastilla G., Montironi R., et al. Current insights in renal cell cancer pathology. Urol Oncol 2008, 26:225-238.
30. Chow W.H., Dong L.M., Devesa S.S. Epidemiology and risk factors for kidney cancer. Nat Rev Urol 2010, 7:245-257.
31. Lei T., Zhao X., Jin S., Meng Q., Zhou H., Zhang M. Discovery of potential bladder cancer biomarkers by comparative urine proteomics and analysis. Clin Genitourin Cancer 2013, 11:56-62.
32. Connolly M., Marrelli A., Blades M., McCormick J., Maderna P., Godson C., et al. Acute serum amyloid A induces migration, angiogenesis, and inflammation in synovial cells in vitro and in a human rheumatoid arthritis/SCID mouse chimera model. J Immunol 2012, 184:6427-6437.
33. Yamada T., Miyake N., Itoh K., Igari J. Further characterization of serum amyloid A4 as a minor acute phase reactant and a possible nutritional marker. Clin Chem Lab Med 2001, 39:7-10.
34. Glogowska A., Pyka J., Kehlen A., Los M., Perumal P., Weber E., et al. The cytoplasmic domain of proEGF negatively regulates motility and elastinolytic activity in thyroid carcinoma cells. Neoplasia 2008, 10:1120-1130.
35. Mastellos D., Morikis D., Isaacs S.N., Holland M.C., Strey C.W., Lambris J.D. Complement: structure, functions, evolution, and viral molecular mimicry. Immunol Res 2003, 27:367-386.
36. Peitsch M.C., Tschopp J. Assembly of macromolecular pores by immune defense systems. Curr Opin Cell Biol 1991, 3:710-716.
37. Gasque P. Complement: a unique innate immune sensor for danger signals. Mol Immunol 2004, 41:1089-1098.
38. Kohl J. The role of complement in danger sensing and transmission. Immunol Res 2006, 34:157-176.
39. Weisel J.W. Fibrinogen and fibrin. Adv Protein Chem 2005, 70:247-299.
40. Cesarman-Maus G., Hajjar K.A. Molecular mechanisms of fibrinolysis. Br J Haematol 2005, 129:307-321.
41. Stepanova V.V., Tkachuk V.A. Urokinase as a multidomain protein and polyfunctional cell regulator. Biochemistry 2002, 67:109-118.
42. Endsley M.P., Hu Y., Deng Y., He X., Warejcka D.J., Twining S.S., et al. Maspin, the molecular bridge between the plasminogen activator system and beta1 integrin that facilitates cell adhesion. J Biol Chem 2011, 286:24599-24607.
43. Kenny H.A., Leonhardt P., Ladanyi A., Yamada S.D., Montag A., Im H.K., et al. Targeting the urokinase plasminogen activator receptor inhibits ovarian cancer metastasis. Clin Cancer Res 2011, 17:459-471.
44. Madhyastha R., Madhyastha H., Nakajima Y., Omura S., Maruyama M. Curcumin facilitates fibrinolysis and cellular migration during wound healing by modulating urokinase plasminogen activator expression. Pathophysiol Haemost Thromb 2010, 37:59-66.
45. Hasui Y., Marutsuka K., Suzumiya J., Kitada S., Osada Y., Sumiyoshi A. The content of urokinase-type plasminogen activator antigen as a prognostic factor in urinary bladder cancer. Int J Cancer 1992, 50:871-873.
46. Hasui Y., Marutsuka K., Nishi S., Kitada S., Osada Y., Sumiyoshi A. The content of urokinase-type plasminogen activator and tumor recurrence in superficial bladder cancer. J Urol 1994, 151:16-19. [discussion 19-20].
47. Lin C.Y., Tsui K.H., Yu C.C., Yeh C.W., Chang P.L., Yung B.Y. Searching cell-secreted proteomes for potential urinary bladder tumor markers. Proteomics 2006, 6:4381-4389.