Challenges of using mass spectrometry as a bladder cancer biomarker discovery platform

IntroductionBladder cancer (BCa) is one of the most prevalent malignancies worldwide, mostly due to its high recurrence rates. In consequence, the necessity of repeated screening for reappearance demonstrates the urgent need for novel biomarkers as alternatives to invasive standard procedures.MethodsProteomic technologies have emerged as powerful platforms for unbiased biomarker discovery and revolutionized the classical “target-driven” analysis of single marker candidates. Although proteome profiling is still far from demonstrating its full potential in clinical diagnosis, first studies clearly denote its significant potential.ConclusionsThis review provides a discussion of the challenges related to clinical proteomics using mass spectrometry, emphasizing bladder cancer biomarker discovery. An outline of the technological prerequisites for reliable proteome profiling, data mining and interpretation, as well as, reflections on future trends in the field are provided.

[1]  P. O’Farrell.  High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.

[2]  W. N. Burnette,et al.  "Western blotting": electrophoretic transfer of proteins from sodium dodecyl sulfate--polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A. , 1981, Analytical biochemistry.

[3]  J. Bacus,et al.  Cytology, flow cytometry, image analysis, and interphase cytogenetics by fluorescence in situ hybridization in the diagnosis of transitional cell carcinoma in bladder washes: A comparative study , 1995, Diagnostic cytopathology.

[4]  R. Aebersold,et al.  Mass spectrometric approaches for the identification of gel‐separated proteins , 1995, Electrophoresis.

[5]  J. Celis,et al.  Loss of adipocyte-type fatty acid binding protein and other protein biomarkers is associated with progression of human bladder transitional cell carcinomas. , 1996, Cancer research.

[6]  M. Becich,et al.  Bladder cancer-associated nuclear matrix proteins. , 1996, Cancer research.

[7]  J. Celis,et al.  Towards a comprehensive database of proteins from the urine of patients with bladder cancer. , 1996, The Journal of urology.

[8]  T. Ørntoft,et al.  Proteome profiling of bladder squamous cell carcinomas: identification of markers that define their degree of differentiation. , 1997, Cancer research.

[9]  J. C. BurgesChristopher.  A Tutorial on Support Vector Machines for Pattern Recognition , 1998 .

[10]  J. Ferlay,et al.  Estimates of the worldwide mortality from 25 cancers in 1990 , 1999, International journal of cancer.

[11]  J. Ferlay,et al.  Erratum: Estimates of the worldwide mortality from 25 cancers in 1990. Int. J. Cancer, 83, 18–29 (1999). , 1999, International journal of cancer.

[12]  On-line capillary electrophoresis-mass spectrometry , 1999 .

[13]  L. Kiemeney,et al.  Epidemiology of Bladder Cancer , 1999, European Urology.

[14]  T. Ørntoft,et al.  Proteomics and immunohistochemistry define some of the steps involved in the squamous differentiation of the bladder transitional epithelium: a novel strategy for identifying metaplastic lesions. , 1999, Cancer research.

[15]  G. Brenes,et al.  Clinical usefulness of the novel marker BLCA-4 for the detection of bladder cancer. , 2000, The Journal of urology.

[16]  S. Weinberger,et al.  Recent advancements in surface‐enhanced laser desorption/ionization‐time of flight‐mass spectrometry , 2000, Electrophoresis.

[17]  G. Wright,et al.  Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. , 2001, The American journal of pathology.

[18]  H. Issaq,et al.  The role of separation science in proteomics research , 2001, Electrophoresis.

[19]  Uwe Claussen,et al.  Mass spectrometry meets chip technology: A new proteomic tool in cancer research? , 2001, Electrophoresis.

[20]  V. Dolnik,et al.  Capillary electrophoresis of proteins 1999–2001 , 2001, Electrophoresis.

[21]  R. Aebersold,et al.  Mass spectrometry in proteomics. , 2001, Chemical reviews.

[22]  Mitsuaki Yanagida,et al.  Functional proteomics; current achievements. , 2002, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[23]  Thomas P Conrads,et al.  Methods for fractionation, separation and profiling of proteins and peptides , 2002, Electrophoresis.

[24]  J. Fitch,et al.  A rapid method to capture and screen for transcription factors by SELDI mass spectrometry. , 2002, Biochemical and biophysical research communications.

[25]  Morten Østergaard,et al.  Proteomic Strategies to Reveal Tumor Heterogeneity among Urothelial Papillomas * , 2002, Molecular & Cellular Proteomics.

[26]  S. Weinberger,et al.  Tagless extraction‐retentate chromatography: A new global protein digestion strategy for monitoring differential protein expression , 2002, Electrophoresis.

[27]  Thomas P Conrads,et al.  The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. , 2002, Biochemical and biophysical research communications.

[28]  Mark D Johnson,et al.  Proteomic Analysis in the Neurosciences* , 2002, Molecular & Cellular Proteomics.

[29]  Marcus Macht,et al.  A robust approach for the analysis of peptides in the low femtomole range by capillary electrophoresis‐tandem mass spectrometry , 2002, Electrophoresis.

[30]  T. Yip,et al.  SELDI ProteinChip® Array in Oncoproteomic Research , 2002, Technology in cancer research & treatment.

[31]  Thorsten Kaiser,et al.  Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. , 2003, Journal of chromatography. A.

[32]  Thorsten Kaiser,et al.  Capillary electrophoresis coupled to mass spectrometry to establish polypeptide patterns in dialysis fluids. , 2003, Journal of chromatography. A.

[33]  P. Schmitt‐Kopplin,et al.  Capillary electrophoresis – mass spectrometry: 15 years of developments and applications , 2003, Electrophoresis.

[34]  S. Kassim,et al.  Detection of bladder tumours: role of cytology, morphology-based assays, biochemical and molecular markers , 2003, Current opinion in obstetrics & gynecology.

[35]  M. J. Bailey,et al.  Urinary markers in bladder cancer , 2003, BJU international.

[36]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[37]  Y. Kato,et al.  Rapid discovery and identification of a tissue-specific tumor biomarker from 39 human cancer cell lines using the SELDI ProteinChip platform. , 2003, Biochemical and biophysical research communications.

[38]  T. Annesley.  Ion suppression in mass spectrometry. , 2003, Clinical chemistry.

[39]  V. Kašička,et al.  Recent advances in capillary electrophoresis and capillary electrochromatography of peptides , 2003, Electrophoresis.

[40]  V. Thongboonkerd.  Proteomics in Nephrology: Current Status and Future Directions , 2004, American Journal of Nephrology.

[41]  Jonas Bergquist,et al.  Monomer surface modifications for rapid peptide analysis by capillary electrophoresis and capillary electrochromatography coupled to electrospray ionization‐mass spectrometry , 2004, Electrophoresis.

[42]  H. Mischak,et al.  Proteomic patterns established with capillary electrophoresis and mass spectrometry for diagnostic purposes. , 2004, Kidney international.

[43]  T. Isono,et al.  Diagnostic potential in bladder cancer of a panel of tumor markers (calreticulin, γ‐synuclein, and catechol‐o‐methyltransferase) identified by proteomic analysis , 2004, Cancer science.

[44]  T. Isono,et al.  Identification by proteomic analysis of calreticulin as a marker for bladder cancer and evaluation of the diagnostic accuracy of its detection in urine. , 2004, Clinical chemistry.

[45]  A. Vlahou,et al.  Protein Profiling in Urine for the Diagnosis of Bladder Cancer , 2004 .

[46]  H. Mischak,et al.  Differential polypeptide display: the search for the elusive target. , 2004, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[47]  W. Kolch,et al.  Mass spectrometry for the detection of differentially expressed proteins: a comparison of surface-enhanced laser desorption/ionization and capillary electrophoresis/mass spectrometry. , 2004, Rapid communications in mass spectrometry : RCM.

[48]  A. Ganser,et al.  Proteomics applied to the clinical follow-up of patients after allogeneic hematopoietic stem cell transplantation. , 2004, Blood.

[49]  M. Guan,et al.  Tree analysis of mass spectral urine profiles discriminates transitional cell carcinoma of the bladder from noncancer patient. , 2004, Clinical biochemistry.

[50]  Christopher J. C. Burges,et al.  A Tutorial on Support Vector Machines for Pattern Recognition , 1998, Data Mining and Knowledge Discovery.

[51]  Visith Thongboonkerd,et al.  Renal and urinary proteomics: Current applications and challenges , 2005, Proteomics.

[52]  K. Oofusa,et al.  Proteome analysis of gelatin-bound urinary proteins from patients with bladder cancers. , 2005, European urology.

[53]  A. Semjonow,et al.  Pilot study of capillary electrophoresis coupled to mass spectrometry as a tool to define potential prostate cancer biomarkers in urine , 2005, Electrophoresis.

[54]  M. Mann,et al.  Mass spectrometry–based proteomics turns quantitative , 2005, Nature chemical biology.

[55]  M. Babjuk,et al.  Highly specific urine-based marker of bladder cancer. , 2005, Urology.

[56]  W. Kolch,et al.  Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery. , 2005, Mass spectrometry reviews.

[57]  M. J. Chalmers,et al.  Combined top-down and bottom-up mass spectrometric approach to characterization of biomarkers for renal disease. , 2005, Analytical chemistry.

[58]  G. Sauter,et al.  Loss of Expression of the Adipocyte-type Fatty Acid-binding Protein (A-FABP) Is Associated with Progression of Human Urothelial Carcinomas* , 2005, Molecular & Cellular Proteomics.

[59]  Beatrix Ueberheide,et al.  Protein identification using sequential ion/ion reactions and tandem mass spectrometry. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Andrew Emili,et al.  Multidimensional protein identification technology (MudPIT): Technical overview of a profiling method optimized for the comprehensive proteomic investigation of normal and diseased heart tissue , 2005, Journal of the American Society for Mass Spectrometry.

[61]  Eugene A. Kapp,et al.  Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly‐available database , 2005, Proteomics.

[62]  Richard D. Smith,et al.  Combining capillary electrophoresis with mass spectrometry for applications in proteomics , 2005, Electrophoresis.

[63]  Clement Chung,et al.  Human tissue profiling with multidimensional protein identification technology. , 2005, Journal of proteome research.

[64]  D. Driesch,et al.  ProteinChip technology reveals distinctive protein expression profiles in the urine of bladder cancer patients. , 2005, European urology.

[65]  F. Magni,et al.  Proteome profile of human urine with two‐dimensional liquid phase fractionation , 2005, Proteomics.

[66]  Ming Xu,et al.  Using tree analysis pattern and SELDI-TOF-MS to discriminate transitional cell carcinoma of the bladder cancer from noncancer patients. , 2005, European urology.

[67]  H. Mischak,et al.  Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis , 2006, Nature Medicine.

[68]  A. Vlahou,et al.  Overexpression of α-defensin is associated with bladder cancer invasiveness , 2006 .

[69]  Michael Liebman,et al.  Proteomic profiling of human urine using multi-dimensional protein identification technology. , 2006, Journal of chromatography. A.

[70]  H. Mischak,et al.  Biomarker discovery by CE‐MS enables sequence analysis via MS/MS with platform‐independent separation , 2006, Electrophoresis.

[71]  H. Frierson,et al.  Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. , 2006, The Lancet. Oncology.

[72]  Marta Sanchez-Carbayo,et al.  Antibody arrays: technical considerations and clinical applications in cancer. , 2006, Clinical chemistry.

[73]  V. Kašička,et al.  Recent developments in capillary electrophoresis and capillary electrochromatography of peptides , 2006, Electrophoresis.

[74]  J. Coon,et al.  Advancing proteomics with ion/ion chemistry. , 2006, BioTechniques.

[75]  A. Vlahou,et al.  Overexpression of alpha-defensin is associated with bladder cancer invasiveness. , 2006, Urologic oncology.

[76]  John R Yates,et al.  Large Scale Protein Profiling by Combination of Protein Fractionation and Multidimensional Protein Identification Technology (MudPIT)* , 2006, Molecular & Cellular Proteomics.

[77]  M. Gonzalgo,et al.  Toward critical evaluation of the role(s) of molecular biomarkers in the management of bladder cancer , 2006, World Journal of Urology.

[78]  Mark Girolami,et al.  Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors , 2006, Neural Computation.

[79]  V. Dolnik,et al.  Capillary electrophoresis of proteins 2003–2005 , 2006, Electrophoresis.

[80]  Two-dimensional difference gel electrophoresis. , 2006, Methods in molecular biology.

[81]  Mark Girolami,et al.  Analysis of complex, multidimensional datasets. , 2006, Drug discovery today. Technologies.

[82]  Ian Eardley,et al.  Urinary biomarker profiling in transitional cell carcinoma , 2006, International journal of cancer.

[83]  Halima Bensmail,et al.  Bioinformatics and data mining in proteomics , 2006, Expert review of proteomics.

[84]  J. Hudson,et al.  Array of informatics: Applications in modern research. , 2006, Journal of proteome research.

[85]  V. Gnau,et al.  Differential detection of S100A8 in transitional cell carcinoma of the bladder by pair wise tissue proteomic and immunohistochemical analysis , 2006, Proteomics.

[86]  Alexandros Kalousis,et al.  Sample preparation and bioinformatics in MALDI profiling of urinary proteins. , 2007, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[87]  Visith Thongboonkerd,et al.  Practical points in urinary proteomics. , 2007, Journal of proteome research.

[88]  M. Girolami,et al.  Clinical proteomics: A need to define the field and to begin to set adequate standards , 2007, Proteomics. Clinical applications.

[89]  C. Cordon-Cardo,et al.  Molecular alterations associated with bladder cancer progression. , 2007, Seminars in oncology.

[90]  S. Goodison,et al.  Bladder cancer associated glycoprotein signatures revealed by urinary proteomic profiling. , 2007, Journal of proteome research.

[91]  A. Ganser,et al.  Proteomic patterns predict acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation. , 2007, Blood.

[92]  V. Dolnik.  Capillary electrophoresis of proteins 2005–2007 , 2008, Electrophoresis.

[93]  Carl E. Rasmussen,et al.  Gaussian processes for machine learning , 2005, Adaptive computation and machine learning.