Abstract LB-251: Comparison of MicroRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues.

Abstract

Abstract Purpose/Objective(s): 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. Materials/Methods: Nine paired human malignant tissue samples were received. Remnant surgical tissues were taken after diagnostic samples were secured from patients (five males and four females; median age 58 years, range 39-78 years) with breast invasive ductal carcinoma (2), renal clear cell carcinoma (2), lung squamous cell carcinoma (1) and adenocarcinoma (1), prostate adenocarcinoma (1), metastatic melanoma (1), and sarcoma of thigh (1). RNA from FFPE samples were extracted using Recover All Total Nucleic Acid Isolation Kit (Life Technologies Corporation, Carlsbad, CA). Small RNAs from FFPE and fresh frozen samples were prepared for SOLiD (Version 4) system, and reads data were analyzed by using the SOLiD™ small RNA Analysis pipeline (Life Technologies), then normalized as reads per million (RPM). Results: 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=0.74-0.94). 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. Conclusion: 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. Citation Format: Wei Meng, Joseph McElroy, Stefano Volinia, Jeff Palatini, Sarah Warner, Leona Ayers, Kamalakannan Palanichamy, Arnab Chakravarti, Tim Lautenschlaeger. Comparison of MicroRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-251. doi:10.1158/1538-7445.AM2013-LB-251