Comparison of MicroRNA Deep Sequencing of Matched Formalin-Fixed Paraffin-Embedded and Fresh Frozen Cancer Tissues

Abstract

MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (2–9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (Pearson’s r = 0.71–0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified.

A Differential MicroRNA Profile Distinguishes Cholangiocarcinoma from Pancreatic Adenocarcinoma

“…Several studies have specifically addressed this issue and have shown that, although, RNA degradation is common, miRNAs are able to be accurately detected and quantified in FFPE tissue. 24–26 Using the newer nCounter System from nanoString Technologies, we identified a profile of 41 significantly dysregulated miRs in cholangiocarcinoma relative to the adjacent normal bile duct epithelium. To date, an expression profile for microRNAs in cholangiocarcinoma has not been reported.…”

MECHANISMS IN ENDOCRINOLOGY: MicroRNA in diagnostics and therapy of thyroid cancer

“…The second unique feature of miRs is their length, which usually does not exceed 24 nucleotides; this makes them resistant to endonucleolytic cleavage. As such, miRs are relatively stable and can be detected and reliably measured in various biological materials, including archived formalin-fixed and paraffinembedded samples (3) or serum (4).…”

MicroRNA Detection: Current Technology and Research Strategies

“…Given the evidence that miR profiles could potentially become predictive biomarkers for disease states, researchers are endeavoring to develop powerful bioinformatics approaches by analyzing routinely preserved samples such as formalin-fixed paraffin-embedded (FFPE) and laser-capture microdissected samples (50)(51)(52). Although mRNA is not stable in such sample preparations, miR has been demonstrated to be quite resilient.…”