Evaluation of ethanol-fixed, paraffin-embedded tissues for proteomic applications

We previously reported that ethanol fixation and paraffin embedding of tissues produce excellent histomorphology and good preservation of macromolecules. Here, we present a detailed evaluation of ethanol‐fixed tissues for proteomic initiatives. When proteins were extracted from ethanol‐fixed, paraffin‐embedded prostate tissue, resolved by two‐dimensional gel electrophoresis (2‐DE), and stained by standard methods, several hundred protein molecules could be detected and successfully analyzed by mass spectrometry. Protein profiles obtained from ethanol‐fixed tissues were highly similar to those observed from frozen tissues, in contrast to the poor protein recovery from formalin‐fixed material. The protein content of specific cells that were microdissected from ethanol‐fixed tissue sections using laser capture microdissection could also be successfully analyzed by 2‐DE. We observed that eosin staining of tissue sections had a detrimental effect on protein separation, whereas hematoxylin staining had minimal consequence. In order to illustrate the applicability of ethanol‐fixed tissues for proteomic discovery studies, we compared the protein profiles of patient‐matched, normal prostatic epithelial cells and invasive adenocarcinoma cells obtained from ethanol‐fixed, paraffin‐embedded tissues. A number of differentially expressed proteins was discovered and identified by mass spectrometry. Immunohistochemical analyses performed on ethanol‐fixed tissue sections were in agreement with the proteomic discovery findings. In light of these results, we conclude that ethanol‐fixed tissues can be successfully utilized for proteomic analyses.