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Originally published In Press as doi:10.1074/mcp.M500102-MCP200 on August 9, 2005.
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Molecular & Cellular Proteomics 4:1741-1753, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Proteomic Analysis of Formalin-fixed Prostate Cancer Tissue*,S

Brian L. Hood{ddagger}, Marlene M. Darfler§, Thomas G. Guiel§, Bungo Furusato, David A. Lucas{ddagger}, Bradley R. Ringeisen||, Isabell A. Sesterhenn, Thomas P. Conrads{ddagger}, Timothy D. Veenstra{ddagger},** and David B. Krizman{ddagger},{ddagger}{ddagger}

From the {ddagger} Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., National Cancer Institute, Frederick, MD 21702; § Expression Pathology Incorporated, Gaithersburg, MD 20877; Armed Forces Institute of Pathology, Department of Genitourinary Pathology, Washington, DC 20306; and || Naval Research Laboratory, Washington, DC 20375

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.

** To whom correspondence may be addressed: Laboratory of Proteomics and Analytical Technologies, National Cancer Institute, SAIC-Frederick, Inc., P.O. Box B, Frederick, MD 21702. Tel.: 301-846-7286; Fax: 301-846-6037; E-mail: veenstra{at}ncifcrf.gov

{ddagger}{ddagger} To whom correspondence may be addressed: Expression Pathology Inc., 9290 Gaither Rd., Gaithersburg, MD 20877. Tel.: 301-977-3654; Fax: 301-926-9283; E-mail: d.krizman{at}expressionpathology.com


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