Technical Advance Evaluation of Non-Formalin Tissue Fixation for Molecular Profiling Studies

Using a general strategy for evaluating clinical tissuespecimens, we found that 70% ethanol fixation andparaffin embedding is a useful method for molecularprofiling studies. Human prostate and kidney wereused as test tissues. The protein content of the sam-ples was analyzed by one-dimensional gel electro-phoresis, immunoblot, two-dimensional gel electro-phoresis, and layered expression scanning. In eachcase, the fixed and embedded tissues produced re-sults similar to that obtained from snap-frozen spec-imens, although the protein quantity was somewhatdecreased. Recovery of mRNA was reduced in bothquantity and quality in the ethanol-fixed samples, butwas superior to that obtained from formalin-fixedsamples and sufficient to perform reverse transcrip-tion polymerase chain reactions. Recovery of DNAfrom ethanol-fixed specimens was superior to forma-lin-fixed samples as determined by one-dimensionalgel electrophoresis and polymerase chain reaction. Inconclusion, specimens fixed in 70% ethanol and em-bedded in paraffin produce good histology and per-mit recovery of DNA, mRNA, and proteins sufficientfor several downstream molecular analyses. Com-plete protocols and additional discussion of relevantissues are available on an accompanying website(http://cgap-mf.nih.gov/).