title: Analysis of prostate cancer by proteomics using tissue specimens.
abstract: OBJECTIVE
  Prostate cancer cells differ from their normal counterpart in gene expression. Therefore, cancer and normal tissue/cells would show differences in their proteomes. From a diagnostic standpoint differences in the composition of secreted protein species are especially relevant. We used ProteinChip Array (Ciphergen Biosystems, Fremont, California) surface enhanced laser desorption/ionization (SELDI) time of flight mass spectrometry to profile prostate tissue samples to generate phenomic fingerprints. We used quantitative proteomics based on glycopeptide capture followed by tandem mass spectrometry to identify differentially expressed proteins.
  
  
  METHODS
  Patient matched cancer and noncancer specimens were digested by collagenase to single cells. After digestion the cells were pelleted and the cell-free supernatant was used for analysis. A reversed phase hydrophobic ProteinChip Array was used to generate SELDI patterns from 43 primary prostate tumors, including 26 with matched noncancer specimens. Quantitative proteomics was applied to 1 specimen and the expression pattern was verified by Western blotting and immunohistochemistry.
  
  
  RESULTS
  SELDI profiles showed that cancers of similar TNM stages were more likely to have similar profiles. On quantitative proteomics tissue metalloproteinase inhibitor-1 was identified to be down-regulated in cancer. Tissue metalloproteinase inhibitor-1 expression was localized to secretory cells.
  
  
  CONCLUSIONS
  Protein profiling by SELDI is relatively easy to perform and it has great potential in prostate cancer diagnosis through pattern recognition. Quantitative proteomics can potentially determine the identity of many biomarkers specific for prostate cancer.
authors.affiliation: Department of Urology, University of Washington, Seattle, Washington 98195, USA. aliu@u.washington.edu
authors.forename: Alvin Y
authors.initials: AY
authors.lastname: Liu
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.forename: Carrie M
authors.initials: CM
authors.lastname: Sorensen
authors.forename: Deborah L
authors.initials: DL
authors.lastname: Diamond
mesh_terms: D014408:Biomarkers, Tumor / Q000097:blood*; D015153:Blotting, Western; D006801:Humans; D007150:Immunohistochemistry; D007834:Lasers; D008297:Male; D013058:Mass Spectrometry; D011237:Predictive Value of Tests; D011467:Prostate / Q000473:pathology; D011471:Prostatic Neoplasms / Q000097:blood / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D040081:Protein Array Analysis; D040901:Proteomics / Q000379:methods*; D019715:Tissue Inhibitor of Metalloproteinase-1 / Q000378:metabolism; D014407:Tumor Cells, Cultured
chemical_list: D014408:Biomarkers, Tumor; D019715:Tissue Inhibitor of Metalloproteinase-1