title: Cancer stroma proteome expression profile of superficial bladder transitional cell carcinoma and biomarker discovery.
abstract: OBJECTIVE
  To globally characterize the stroma expression profile of superficial bladder transitional cell carcinoma and to discuss the cancer biology as well as biomarker discovery from stromal cells.
  
  
  METHODS
  Laser capture microdissection was used to harvest purified bladder cancer stromal cells and normal stromal cells from 4 paired samples. Next, two-dimensional liquid chromatography-tandem mass spectrometry was used to identify the proteome expression profile. The differential proteins were further analyzed using bioinformatics tools and compared with the published literature.
  
  
  RESULTS
  A total of 606/601 proteins commonly appeared in 4 paired samples. Six hundred and thirty-seven proteins were differentially expressed between cancer and normal stroma. Among them, 321/316 proteins specific expressed in cancer/normal stromal cells. Differential proteins were compared with the entire list of the international protein index (IPI). 36/49 GO terms exhibited as enriched and 25/14 exhibited as depleted in biological process; 39/40 GO terms exhibited as enriched and 9/4 exhibited as depleted in cellular component, respectively. Significantly altered pathways between cancer/normal stroma mainly include focal adhesion, EHEC, oxidative phosphorylation, glycolysis/gluconeogenesis, TCA cycle. Finally, descriptive statistics show the data that PI ≤ 8 have normal distribution and the proteins with extremes of PI and MW have the same probability to be a biomarker.
  
  
  CONCLUSIONS
  The present study identified the proteome expression profile of bladder cancer stromal cells and normal stromal cells. Furthermore, our results confirm proteins origin from stroma play important role in cancer biology and highlight a novel view of cancer and stress the importance of including factors related to the cancer stroma into biomarker discovery.
authors.affiliation: Department of Urology, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, China.
authors.forename: Hai Tao
authors.initials: HT
authors.lastname: Niu
authors.forename: Chuan Min
authors.initials: CM
authors.lastname: Yang
authors.forename: Gang
authors.initials: G
authors.lastname: Jiang
authors.forename: Ting
authors.initials: T
authors.lastname: Xu
authors.forename: Yan Wei
authors.initials: YW
authors.lastname: Cao
authors.forename: Jun
authors.initials: J
authors.lastname: Zhao
authors.forename: Xin Sheng
authors.initials: XS
authors.lastname: Wang
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000032:analysis*; D002295:Carcinoma, Transitional Cell / Q000737:chemistry* / Q000473:pathology; D002448:Cell Adhesion; D002454:Cell Differentiation; D049109:Cell Proliferation; D016009:Chi-Square Distribution; D002853:Chromatography, Liquid / Q000379:methods; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007834:Lasers; D008297:Male; D042282:Microdissection / Q000379:methods; D008875:Middle Aged; D009363:Neoplasm Proteins / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D015398:Signal Transduction; D053719:Tandem Mass Spectrometry; D001749:Urinary Bladder Neoplasms / Q000737:chemistry* / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D020543:Proteome