Genome-wide expression analysis of recently processed formalin-fixed paraffin embedded human prostate tissues

Formalin fixation and paraffin embedding (FFPE) is the standard practice to process surgical specimens in preparation for pathological evaluation. The FFPE procedure is known to introduce adverse effects on RNA quality and the ensuing RNA based expression analysis. However, the overall impact of the FFPE procedure alone on the reliability and accuracy of expression data, without influences from additional compromising factors introduced during long-term storage, has not been vigorously assessed.

The quality of RNA extracted from recently processed FFPE prostate tissues was examined. FFPE and frozen blocks were prepared from matched surgical specimens and processed in parallel for RNA extraction, two rounds of linear RNA amplification, and genome-wide expression analysis. Expression ratios of prostate cancer versus benign prostatic hyperplasia (BPH) were compared between data derived from the paired FFPE tissues and frozen tissues.

RNA extracted from recently processed FFPE prostate tissues was of high quality and suitable for RNA expression analysis. An unbiased analysis of expression data revealed nearly 80% concordance between FFPE tissues and frozen tissues, in genome-wide gene expression differences of cancer versus BPH, and across a wide spectrum of fold expression differences.

FFPE procedure itself does not lead to adverse effects on genome-wide expression analysis. Prospective molecular archiving or modified long-term storage conditions should be implemented to expand the utility of FFPE tissues without compromising standard surgical pathology routines.