Validation of Total RNA Spin-column and Non-column Extraction Methods for microRNA Expression Analyses in Formalin-fixed Paraffin-Embedded Liver Samples

  MicroRNAs are small (19–23nt) noncoding RNAs that adjust gene expression post-transcriptionally. In addition, microRNA (miRNA) profile modification is revealed in various abnormalities including cancer. Formalin-fixed paraffin-embedded (FFPE) material archives are valued for searching human diseases. Therefore, the present study aimed to investigate FFPE samples for miRNA expression, as an alternative analyte for gene expression with the growing therapeutic and diagnostic potential. Further, the validity of RNA isolation kits was evaluated in order to identify a preferred method. The two extracted methods were qualitatively and quantitatively assessed in order to compare the archived specimens between these methods. The total RNA and gene expression were quantified in each method as well. Based on the results, the level of RNA extracted from FFPE tissues and real-time polymerase chain reaction (RT-PCR) of hsa-miR-623, hsa-miR-515-5pin miRNeasy FFPE (P value < 0.047) was significantly higher than that in RNAX Plus (P < 0.084). In general, the spin column method for miRNA expression profile had better expression compared to the non-column method. The results further confirmed the validity of FFPE tissues as an appropriate resource for miRNA analyses.