Research article

Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells

Jinghuan Li¹ , Paul Smyth¹ , Richard Flavin¹ , Susanne Cahill¹ , Karen Denning¹ , Sinead Aherne¹ , Simone M Guenther² , John J O'Leary¹ and Orla Sheils¹

¹Deptment of Histopathology, University of Dublin, Trinity College, Dublin, Ireland

²Applied Biosystems, Foster City, CA, USA

author email corresponding author email

BMC Biotechnology 2007, 7:36doi:10.1186/1472-6750-7-36

Published:	29 June 2007

Abstract

Background

Archival formalin-fixed paraffin-embedded (FFPE) tissues have limited utility in applications involving analysis of gene expression due to mRNA degradation and modification during fixation and processing. This study analyzed 160 miRNAs in paired snap frozen and FFPE cells to investigate if miRNAs may be successfully detected in archival specimens.

Results

Our results show that miRNA extracted from FFPE blocks was successfully amplified using Q-RT-PCR. The levels of expression of miRNA detected in total RNA extracted from FFPE were higher than that extracted from snap frozen cells when the quantity of total RNA was identical. This phenomenon is most likely explained by the fact that larger numbers of FFPE cells were required to generate equivalent quantities of total RNA than their snap frozen counterparts.

Conclusion

We hypothesise that methylol cross-links between RNA and protein which occur during tissue processing inhibit the yield of total RNA. However, small RNA molecules appear to be less affected by this process and are recovered more easily in the extraction process. In general miRNAs demonstrated reliable expression levels in FFPE compared with snap frozen paired samples, suggesting these molecules might prove to be robust targets amenable to detection in archival material in the molecular pathology setting.