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MicroRNAs (miRNAs) are short RNA molecules (∼21 nt) that exert global effects on gene regulation by post-transcriptional silencing of specific mRNAs. Functionally, miRNAs influence the regulation of many biological processes, including early development, cell proliferation, apoptosis, or hematopoietic lineage differentiation. Moreover, miRNAs have been linked to human diseases, including several cancer types, disease states and tumor progression status. Therefore, the technology to extract miRNAs from archived histological samples would enable retrospective studies of miRNA profiles from archived tissues for which a wealth of clinical information is accessible. Research services are now available for analyzing the global miRNA profiles from sections of archived formalin-fixed, paraffin-embedded (FFPE) tissue blocks. In this service, RNA is extracted from fixed tissue sections using methods that allow for the reproducible and quantitative recovery of miRNAs. These miRNAs are then labeled and hybridized to commercial oligonucleotide microarrays containing probes to all known human miRNAs. The analytical methods developed to compare miRNA profiles were vetted using a test system that evaluated the accuracy and sensitivity of 480 different permutations of methods for background removal, scaling and normalization. To demonstrate utility, an experiment was designed to compare the miRNA profiles between colonic adenocarcinoma and normal adjacent tissue (NAT), taken from multiple patients at the time of surgery. The reproducibility of results generated by trained technicians applying the standard operating procedures was evaluated using analysis of variance (ANOVA). Results will be presented that measure the variation associated with technical replication from FFPE blocks in comparison to the variation observed between and within experimental groups. This approach demonstrates the feasibility of using FFPE samples to analyze miRNA profiles to discover clinically relevant information from diseased samples.

[Proc Amer Assoc Cancer Res, Volume 47, 2006]