title: Combined proteome and transcriptome analyses for the discovery of urinary biomarkers for urothelial carcinoma.
abstract: BACKGROUND
  Proteomic discovery of cancer biomarkers in body fluids is challenging because of their low abundance in a complex background. Altered gene expression in tumours may not reflect protein levels in body fluids. We have tested combining gene expression profiling of tumours with proteomic analysis of cancer cell line secretomes as a strategy to discover urinary biomarkers for bladder cancer.
  
  
  METHODS
  We used shotgun proteomics to identify proteins secreted by three bladder cancer cell lines. Secreted proteins with high mRNA levels in bladder tumours relative to normal urothelium were assayed by ELISA in urine samples from 642 patients.
  
  
  RESULTS
  Midkine and HAI-1 were significantly increased in bladder cancer patients, with the highest levels in invasive disease (area under the receiver operating characteristic curve 0.89 vs non-cancer). The urinary concentration of both proteins was too high to be explained by bladder cancer associated haematuria and most likely arises by direct tumour secretion.
  
  
  CONCLUSIONS
  This 'dual-omic' strategy identified tumour secreted proteins whose urine concentrations are increased significantly by bladder cancer. Combined secretome-transcriptome analysis may be more useful than direct proteomic analysis of body fluids for biomarker discovery in both bladder cancer and other tumour types.
authors.affiliation: School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
authors.forename: N J
authors.initials: NJ
authors.lastname: Shimwell
authors.forename: R T
authors.initials: RT
authors.lastname: Bryan
authors.forename: W
authors.initials: W
authors.lastname: Wei
authors.forename: N D
authors.initials: ND
authors.lastname: James
authors.forename: K K
authors.initials: KK
authors.lastname: Cheng
authors.forename: M P
authors.initials: MP
authors.lastname: Zeegers
authors.forename: P J
authors.initials: PJ
authors.lastname: Johnson
authors.forename: A
authors.initials: A
authors.lastname: Martin
authors.forename: D G
authors.initials: DG
authors.lastname: Ward
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics / Q000652:urine*; D002295:Carcinoma, Transitional Cell / Q000473:pathology / Q000652:urine; D045744:Cell Line, Tumor; D016207:Cytokines / Q000652:urine*; D020869:Gene Expression Profiling; D006801:Humans; D000078792:Midkine; D040081:Protein Array Analysis; D053491:Proteinase Inhibitory Proteins, Secretory / Q000652:urine*; D011507:Proteinuria; D020543:Proteome / Q000032:analysis; D012333:RNA, Messenger / Q000032:analysis; D059467:Transcriptome; D001749:Urinary Bladder Neoplasms / Q000473:pathology / Q000652:urine; D014571:Urologic Neoplasms / Q000473:pathology / Q000652:urine*; D019459:Urothelium / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor; D016207:Cytokines; D053491:Proteinase Inhibitory Proteins, Secretory; D020543:Proteome; D012333:RNA, Messenger; C109149:SPINT1 protein, human; D000078792:Midkine