High throughput evaluation of gene expression from formalin-fixed paraffinembedded tissues

In order to understand disease pathogenesis, the signaling networks governing normal and disease tissues must be delineated. The most abundant source of disease tissue material is in the form of formalin-fixed paraffin embedded (FFPE) samples. Unfortunately, the fixation procedure causes damage to the most important biomolecules (DNA, RNA, proteins) with the exception of microRNAs, thus making their extraction and analysis difficult. However, several methods of isolation of these biomolecules have been developed to allow reasonable extraction of DNA, RNA, and proteins, which can subsequently be used for downstream assays. Traditional low-throughput assays, such as immunohistochemistry and reverse transcription polymerase chain reaction (RT-PCR) have been used extensively to study gene expression in FFPE tissue samples. With the advancements of science, several high-throughput methods of gene expression analysis have also been optimized for FFPE material including reverse phase protein microarrays, DNA methylation assays, microarrays, cDNA-mediated Annealing, Selection, Extension and Ligation assay, quantitative RT-PCR. These developments allow the design of explorative studies to study whole genome gene expression changes in disease tissues, which can be related to patient treatment sensitivity or survival. The latter allows the generation of prediction models that are able to predict a patient’s disease progression and response to treatment based on gene expression data.