Accurate molecular characterization of formalin-fixed, paraffin-embedded tissues by microRNA expression profiling.

Author(s): Szafranska AE, Davison TS, Shingara J, Doleshal M, Riggenbach JA, Morrison CD, Jewell S, Labourier E

Publication: J Mol Diagn, 2008, Vol. 10, Page 415-23

PubMed ID: 18687792 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 formalin fixation, fixation duration and storage on miRNA profiles in liver, spleen, myometrium, lymph node, and colon.

   Summary of Findings:

   Myometrial and B-cell lymphoma specimens had a correlation of miRNA expression profiles of greater than 0.97 between frozen and fixed (6 or 24 h) specimens. The correlation between fixed and frozen colon specimen was only 0.89, which the authors attribute to the heterogenicity of colon tissue. An average of 60.3%, 55% and 51.5% of 377 total miRNA sequences on the array were detected in frozen myometrium, B-cell lymphoma, and colon specimens, respectively, but 5-8.6% fewer miRNAs were detected in fixed specimens, irrespective of fixation time. FFPE specimens stored for different amounts of time clustered based on storage duration, but a strong correlation of expression was still observed between specimens stored for 7 or 11 years and specimens stored for 1 year (r=0.89 and r=0.84, respectively). The authors report that the decrease in correlation of expression was mostly due to loss of signal with longer storage. However, miR-494 and miR-513 expression levels increased with fixation duration (3.1 and 1.8 fold, respectively) and after storage for 7 years (147 and 63 fold, respectively) or 11 years (464 and 161 fold, respectively) compared to levels in snap-frozen specimens. miRNAs that were differentially expressed between B-cell lymphoma and myometrium showed a high degree of correlation in frozen and FFPE specimens. Technical replicates within the microarray had a correlation of greater than 0.95, and overall correlation of microarray expression values of a subset of 18 miRNAs to real-time PCR expression data was 0.98.

   Biospecimens

   • Tissue - Liver
   • Tissue - Spleen
   • Tissue - Colorectal
   • Tissue - Lymph Node
   • Tissue - Uterus

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Carcinoma
   • Neoplastic - Normal Adjacent
   • Neoplastic - Lymphoma
   • Normal

   Platform:

   Analyte	Technology Platform
   RNA	Real-time qRT-PCR
   RNA	DNA microarray

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen
   Storage	Storage duration	1 year 7 years 11 years
   Biospecimen Preservation	Time in fixative	6 h 24 h
   DNA microarray Specific	Targeted nucleic acid	miR-494 miR-513
   Biospecimen Acquisition	Biospecimen location	Liver Spleen Myometrium Lymph node Colon
   DNA microarray Specific	Technology platform	Real-time PCR

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