Abstract
MicroRNAs (miRNAs) are small (19–23nt), highly conserved noncoding RNAs that posttranscriptionally regulate target gene expression. Altered expression of miRNAs has been demonstrated in many different human diseases, including cancer. The large archives of formalin-fixed, paraffin-embedded (FFPE) tissue specimens with clinical follow-up information that exist are a highly valuable source of tissue to study human diseases. However, RNA in the FFPE tissue is fragmented and may be chemically modified. In this study, we prepared miRNA preserving total RNA from matched pairs of FFPE and respective fresh-frozen clinical samples, and used that in microarray experiments to compare miRNA expression profiles between FFPE and fresh-frozen tissue from the same tissue samples. We demonstrate that miRNA expression profile from FFPE tissues closely resembles that from fresh tissues. These results underscore the suitability of FFPE tissues as appropriate resources for miRNA expression analyses.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Cronin, M., Pho, M., Dutta, D., Stephans, J.C., Shak, S., Kiefer, M.C., et al. (2004) Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am. J. Pathol. 164, 35–42.
Xi, Y., Nakajima, G., Gavin, E., Morris, C.G., Kudo, K., Hayashi, K., Ju, J. (2007) Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samples. RNA. 13:1668–74. Epub 2007 Aug 13.
Li, J., Smyth, P., Flavin, R., Cahill, S., Denning, K., Aherne, S., et al. (2007) Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells. BMC Biotechnol. 7, 36.
Calin, G.A. and Croce, C.M. (2006) MicroRNA signatures in human cancers. Nat. Rev. Cancer 6, 857–866.
Lu, J., Getz, G., Miska, E.A., Alvarez-Saavedra, E., Lamb, J., Peck, D., et al. (2005) MicroRNA expression profiles classify human cancers. Nature 435, 834–838.
Nelson, P.T., Baldwin, D.A., Scearce, L.M., Oberholtzer, J.C., Tobias, J.W., and Mourelatos, Z. ( 2004) Microarray-based, high-throughput gene expression profiling of microRNAs. Nat. Methods 1, 155–161.
Liu, A., Tetzlaff, M., VanBelle, P., Elder, D., Feldman, M., Tobias, J., et al. (2009) MicroRNA expression profiling outperforms mRNA expression profiling in formalin-fixed paraffin-embedded tissues. Int. J. Clin. Exp. Pathol. 2, 519–527.
Tetzlaff, M.T., Liu, A., Xu, X., Master, S.R., Baldwin, D.A., Tobias, J.W., et al. (2007) Differential expression of miRNAs in papillary thyroid carcinoma compared to multinodular goiter using formalin fixed paraffin embedded tissues. Endocr. Pathol. 18,163–173.
Siebolts, U., Varnholt, H., Drebber, U., Dienes, H-P., Wickenhauser, C., and Odenthal, M. (2009) Tissues from routine pathology archives are suitable for microRNA analyses by quantitative PCR. J. Clin. Pathol. 62, 84–88.
Doleshal, M., Magotra, A.A., Choudhury, B., Cannon, B.D., Labourier, E., and Szafranska, A.E. (2008) Evaluation and validation of total RNA extraction methods for microRNA expression analyses in formalin-fixed, paraffin-embedded tissues. J. Mol. Diagn. 10, 203–211.
Zhang, X., Chen, J., Radcliffe, T., LeBrun, D.P., Tron, V.A., and Feilotter, H. (2008) An array-based analysis of microRNA expression comparing matched frozen and formalin-fixed paraffin-embedded human tissue samples. J. Mol. Diagn. 10, 513–519.
Acknowledgment
This work is supported by Specialized Program of Research Excellence (SPORE) on Skin Cancer (CA-093372).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Liu, A., Xu, X. (2011). MicroRNA Isolation from Formalin-Fixed, Paraffin-Embedded Tissues. In: Al-Mulla, F. (eds) Formalin-Fixed Paraffin-Embedded Tissues. Methods in Molecular Biology, vol 724. Humana Press. https://doi.org/10.1007/978-1-61779-055-3_16
Download citation
DOI: https://doi.org/10.1007/978-1-61779-055-3_16
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-054-6
Online ISBN: 978-1-61779-055-3
eBook Packages: Springer Protocols