Abstract
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.
Highlights
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
The IHC analysis revealed that epithelial cells and most regions over the entire tissue section stained positive for prostate-specific antigen (PSA) expression (PSAϩ), including the tumor epithelial regions prostate cancer (PCa) 1 and 2, and both benign prostate hyperplasia (BPH) epithelial components (BPH 1 and 2), while the stromal regions stained negative (PSA–) (Fig. 1B)
A variety of prostate-related proteins were identified in this investigation as expressed in microdissected PCa tissue extract including PSA, prostatic acid phosphatase (PAP), macrophage inhibitory cytokine-1 (MIC-1), and Raf kinase inhibitor protein (RKIP) (Fig. 3, A–D)
Summary
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, 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. Development of the capability to conduct large scale analyses of tissues using proteomics approaches analogous to the scale and throughput of high throughput gene expression analysis could have far reaching implications on protein biomarker investigations of disease through interrogation of the vast archived FFPE tissue collections.
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