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Updated: May 24, 2026
Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens
Published on: May 5, 2018
Comparison of microRNA expression using different preservation methods of matched psoriatic skin samples
Abstract:
MicroRNAs are non-coding RNA molecules modulating gene expression post-transcriptionally. Formalin-fixed, paraffin-embedding (FFPE) is a standard preservation method often used in clinical practices, but induces RNA degradation. Extracting high-quality RNA from human skin can be challenging as skin contains high levels of RNases. As microRNAs are 19-23 nucleotides long and lack a poly-A tail, they may be less prone to RNA degradation than mRNAs. We investigated whether microRNAs in psoriatic (FFPE) samples reliably reflect microRNA expression in samples less prone to RNA degradation such as fresh-frozen (FS) and Tissue-Tek-embedding (OCT). We found a strong correlation of the microRNA expression levels between all preservation methods of matched psoriatic skin samples (r(s) ranging from 0.91 to 0.95 (P < 0.001)). These observations were further confirmed with qRT-PCR. Our results demonstrate that microRNA detection in human skin is robust irrespective of preservation method; thus, microRNAs offer an appropriate and flexible approach in clinical practices and for diagnostic purposes in skin disorders.
Insights
MicroRNA expression in formalin-fixed, paraffin-embedded (FFPE) skin samples closely mirrors fresh-frozen (FS) and OCT-embedded tissues. This demonstrates microRNA detection is robust across preservation methods for clinical use.
Area of Science:
- Molecular Biology
- Genetics
- Dermatology
Background:
- MicroRNAs regulate gene expression post-transcriptionally.
- Formalin-fixed, paraffin-embedded (FFPE) processing can degrade RNA.
- Human skin's high RNase content complicates RNA extraction.
Purpose of the Study:
- To assess microRNA stability in FFPE skin samples compared to fresh-frozen (FS) and OCT-embedded samples.
- To determine if FFPE preserves reliable microRNA expression profiles for clinical applications.
Main Methods:
- Comparison of microRNA expression levels in matched psoriatic skin samples preserved via FFPE, FS, and OCT embedding.
- Quantitative reverse transcription polymerase chain reaction (qRT-PCR) for validation.
Main Results:
- Strong correlations (r(s) 0.91–0.95, P < 0.001) were observed in microRNA expression between all tested preservation methods.
- qRT-PCR confirmed the high correlation of microRNA levels across sample types.
Conclusions:
- MicroRNA detection in human skin is robust and reliable regardless of preservation method (FFPE, FS, OCT).
- MicroRNAs are suitable for clinical practice and diagnostic purposes in skin disorders due to their stability.
