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Concentration and quality of RNA and microRNA isolated from formalin-fixed paraffin-embedded tissue samples of patients diagnosed with colorectal cancer or colorectal adenoma

Formalin-fixed paraffin-embedded (FFPE) tissue samples provide a wealth of information for cancer research. Isolation of RNAs from those samples is technically challenging due to RNA degradation during the fixation process and tissue storage. MicroRNAs (miRNAs) are smaller and have higher stability than other RNA transcripts and can be easily isolated from FFPE tissue samples. In this study we assessed the quality and integrity of the total RNA and miRNA isolated from FFPE tissue samples to determine whether they are suitable for further molecular biology assays. RNA and miRNA were isolated from FFPE tissue samples of 44 patients diagnosed with colorectal cancer or adenoma using RNeasy FFPE Kit (Qiagen) and miRNeasy FFPE Kit (Qiagen). Concentration of RNA and miRNA was determined using the DS-11 spectrophotometer (DeNovix). Quality of the samples was assessed using the RNA Integrity Number (RIN), percentage of RNA fragments less than 200 nucleotides in size and percentage of miRNA from the total small RNA using Bioanalyzer 2100 (Agilent). Concentration of RNA was 511.90 ng/µL with the range 85.52 - 1882.46 ng/µL, and miRNA 568.30 ng/µL with the range 15.33 - 2221.62 ng/µL. RINs indicate the integrity of the total RNA on a scale from 1 to 10. Mean RIN value was 2.17 ± 0.46 for 43 samples, as one sample had to be excluded due to its poor quality. Median percentage of RNA fragments less than 200 nucleotides was 41.5% with the range 14 - 96%. Median percentage of isolated miRNA from the total small RNAs was 29.5% with the range 10 - 80%. In conclusion, out of 44 analyzed FFPE tissue samples, 39 were suitable for further qPCR assays, while only 5 RNA isolates and 2 miRNA isolates do not satisfy the quantity/quality criteria for further gene expression studies.

RNA, microRNA, colorectal cancer, FFPE tissue samples

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