Proteomic analysis of formalin-fixed prostate cancer tissue

Mol Cell Proteomics. 2005 Nov;4(11):1741-53. doi: 10.1074/mcp.M500102-MCP200. Epub 2005 Aug 9.


Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue would enable retrospective biomarker investigations of this vast archive of pathologically characterized clinical samples that exist worldwide. These FFPE tissues are, however, refractory to proteomic investigations utilizing many state of the art methodologies largely due to the high level of covalently cross-linked proteins arising from formalin fixation. A novel tissue microdissection technique has been developed and combined with a method to extract soluble peptides directly from FFPE tissue for mass spectral analysis of prostate cancer (PCa) and benign prostate hyperplasia (BPH). Hundreds of proteins from PCa and BPH tissue were identified, including several known PCa markers such as prostate-specific antigen, prostatic acid phosphatase, and macrophage inhibitory cytokine-1. Quantitative proteomic profiling utilizing stable isotope labeling confirmed similar expression levels of prostate-specific antigen and prostatic acid phosphatase in BPH and PCa cells, whereas the expression of macrophage inhibitory cytokine-1 was found to be greater in PCa as compared with BPH cells.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Cytokines / analysis
  • Cytokines / chemistry
  • Cytokines / metabolism
  • Formaldehyde*
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • Growth Differentiation Factor 15
  • Humans
  • Immunohistochemistry
  • Male
  • Mass Spectrometry
  • Microdissection
  • Molecular Sequence Data
  • Neoplasm Proteins / analysis*
  • Neoplasm Proteins / chemistry
  • Phosphatidylethanolamine Binding Protein / analysis
  • Phosphatidylethanolamine Binding Protein / chemistry
  • Phosphatidylethanolamine Binding Protein / metabolism
  • Prostate / metabolism
  • Prostate / pathology
  • Prostate-Specific Antigen / analysis
  • Prostate-Specific Antigen / chemistry
  • Prostate-Specific Antigen / metabolism
  • Prostatic Hyperplasia / metabolism
  • Prostatic Hyperplasia / pathology
  • Prostatic Neoplasms / metabolism*
  • Prostatic Neoplasms / pathology*
  • Protein Array Analysis
  • Proteome / analysis
  • Proteome / chemistry
  • Proteome / metabolism
  • Proteomics*
  • Tissue Fixation*


  • Cytokines
  • GDF15 protein, human
  • Growth Differentiation Factor 15
  • Neoplasm Proteins
  • Phosphatidylethanolamine Binding Protein
  • Proteome
  • Formaldehyde
  • Prostate-Specific Antigen