Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues

Abstract

MicroRNAs play a role in regulating diverse biological processes and have considerable utility as molecular markers for diagnosis and monitoring of human disease. Several technologies are available commercially for measuring microRNA expression. However, cross-platform comparisons do not necessarily correlate well, making it difficult to determine which platform most closely represents the true microRNA expression level in a tissue. To address this issue, we have analyzed RNA derived from cell lines, as well as fresh frozen and formalin-fixed paraffin embedded tissues, using Affymetrix, Agilent, and Illumina microRNA arrays, NanoString counting, and Illumina Next Generation Sequencing. We compared the performance within- and between the different platforms, and then verified these results with those of quantitative PCR data. Our results demonstrate that the within-platform reproducibility for each method is consistently high and although the gene expression profiles from each platform show unique traits, comparison of genes that were commonly detectable showed that detection of microRNA transcripts was similar across multiple platforms.

A Differential MicroRNA Profile Distinguishes Cholangiocarcinoma from Pancreatic Adenocarcinoma

“…While these studies along with ours use different profiling platforms, a recent comparison shows that expression profiles yield similar results across platforms in both fresh and paraffin-embedded tissue. 33 …”

Placental transcriptome in development and pathology: expression, function, and methods of analysis

“…130 The initial formalin fixation of the tissue preserves the RNA, but in a suboptimal manner due to fragmentation that results in noisier sequencing data. Fortunately, special kits are now available for the extraction of RNA from fixed samples, which involves reversal of the fixation agent followed by RNA isolation.…”

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“…The RNA targeted for microRNA analysis was labeled with flash-tag biotin HSR (Affymetrix, CA) and hybridized to GeneChip microRNA 3.0 Arrays (Affymetrix) at the University of Texas Southwestern Medical Center microarray facility in Dallas. Affymetrix microarrays show a high correlation with results obtained from other platforms such as qPCR (Kolbert et al, 2013;Mestdagh et al, 2014). This microarray platform uses annotations from miRBase version 17 and contains 19 724 probes for mature microRNAs from 153 organisms.…”