MicroRNA expression in melanocytic nevi: the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling.
Author(s): Glud M, Klausen M, Gniadecki R, Rossing M, Hastrup N, Nielsen FC, Drzewiecki KT
Publication: J Invest Dermatol, 2009, Vol. 129, Page 1219-24
PubMed ID: 19005486 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
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Study Purpose
The purpose of this study was to determine the effects of using formalin-fixed paraffin-embedded (FFPE) melanocytic nevi instead of specimens frozen in Trizol for the generation of miRNA expression profiles. miRNA was extracted from specimens frozen in trizol with the PureLink kit and from 20 uM sections of FFPE specimens using a modified PureLink protocol after melting in a special buffer.
Summary of Findings:
The RNA yield was higher from specimens frozen in Trizol than from FFPE specimens, but frozen specimens also contained more starting material. The electropherograms generated from frozen specimens had distinct sharp peaks corresponding to the miRNAs and transfer RNAs, but RNA from the FFPE specimens generated smoother peaks that lacked distinctness. Microarray expression profiles in matched frozen and FFPE specimens showed correlations of 0.71-0.94, but miR-768-5p and miR-494 were increased by more than 2 fold and miR-320 and miR-19b were decreased by more than 2 fold in FFPE specimens compared to frozen specimens. The relative abundance of select miRNAs was confirmed using real-time qRT-PCR.
Biospecimens
Preservative Types
- Formalin
- Frozen
Diagnoses:
- Neoplastic - Benign
Platform:
Analyte Technology Platform RNA Real-time qRT-PCR RNA Spectrophotometry RNA DNA microarray RNA Automated electrophoresis/Bioanalyzer Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
Frozen
Real-time qRT-PCR Specific Targeted nucleic acid let-7a
miR-24
miR-25
miR34a
miR-195
miR-203
RNU6B