Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

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MicroRNA expression profiling outperforms mRNA expression profiling in formalin-fixed paraffin-embedded tissues.

Author(s): Liu A, Tetzlaff MT, Vanbelle P, Elder D, Feldman M, Tobias JW, Sepulveda AR, Xu X

Publication: Int J Clin Exp Pathol, 2009, Vol. 2, Page 519-27

PubMed ID: 19636399 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of using FFPE rather than frozen specimens for the measurement of RNA and miRNA integrity and expression profiles in malignant melanoma specimens. RNA was isolated from three 10 um frozen sections using mirVana and from four 20 um FFPE sections using RecoverAll.

   Summary of Findings:

   An miRNA peak was observed in frozen and FFPE specimens, but the FFPE miRNA peak was slightly obscured, which the authors attributed to degradation of ribosomal (r), transfer (t) and mRNA. Further, the RIN numbers from matched FFPE and frozen specimens were 9.30 and 2.70, respectively. The miRNA expression profiles between matched frozen and FFPE specimens were highly correlated (r2=0.956-0.976). The average fold-change in mRNA expression between matched frozen and FFPE specimens was much greater than that for miRNA. Further, while hierarchical clustering based on mRNA expression profiles clustered specimens based on preservation method and not patient, miRNA expression profiles clustered based on patient.

   Biospecimens

   • Tissue - Skin

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Melanoma

   Platform:

   Analyte	Technology Platform
   RNA	Automated electrophoresis/Bioanalyzer
   RNA	DNA microarray

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Frozen
   DNA microarray Specific	Type of array	U133 (mRNA) miRCURY LNA (microRNA)

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