Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

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miRNA Isolation from FFPET Specimen: A Technical Comparison of miRNA and Total RNA Isolation Methods.

Author(s): Nagy ZB, Wichmann B, Kalmár A, Barták BK, Tulassay Z, Molnár B

Publication: Pathol Oncol Res, 2016, Vol. 22, Page 505-13

PubMed ID: 26678076 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   This study investigated the effects of using miRNA-specific or general RNA isolation kits on the yield and quality of miRNA extracted from FFPE colorectal specimens and the effects of extraction kit and reference gene choice on the differential expression of miR-21 and miR-34 in tumor specimens. This study included FFPE blocks stored less than 5 years from three patients that contained >60% tumor content and their matched normal adjacent tissue. For each extraction, three 10µm sections were placed in a tube and deparaffinized in two 10 min changes of xylene, washed in ethanol, and air-dried at 55˚C before extraction with each of the 4 kits. miRNA was quantified using the mercury Universal RT microRNA PCR and the Exiqon Ready-to-use microRNA PCR Human Panels I + II V2.

   Summary of Findings:

   RNA yields were higher using RNA isolation kits than miRNA isolation kits, but miRNA kits resulted in selected isolation of 20-200nt RNA. The High Pure RNA paraffin kit produced the highest yields of the RNA isolation kits and the High Pure miRNA isolation kit produced higher yields than the miRCURY RNA Isolation Kit. As expected, a larger number of miRNA were found and were at higher levels in specimens isolated using the miRNA-specific methods than the total RNA kits, but the two miRNA-specific methods were comparable. Levels of the miRNA were strongly correlated between the two miRNA-specific extraction methods (r2=0.8911) and between the two total RNA extraction kits (r²=0.8571), but were only modestly correlated between the miRCURY RNA kit and the two RNA specific kits (r²=0.5216 for the MagNAPure 96 kit and r²=0.6796 for the High Pure Paraffin kit). Of the three tested reference RNAs, U6 was not found in all specimens but the SNORD38B and SNORD49A were reliably detected in all specimens. Importantly, elevated levels of miR-21 and miR-34 in tumor specimens were detected regardless of RNA (or miRNA) extraction method when data was normalized to miR-490-3p, but the elevated levels in tumor specimens were less obvious when the data was normalized to SNORD38B.

   Biospecimens

   • Tissue - Colorectal

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Normal Adjacent
   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	Fluorometry
   RNA	Real-time qRT-PCR
   RNA	Automated electrophoresis/Bioanalyzer

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Analyte Extraction and Purification	Analyte isolation method	High Pure miRNA Isolation Kit miRCURY RNA Isolation Kit High Pure RNA Paraffin Kit MagNA Pure 96 Cellular RNA LV Kit
   Real-time qRT-PCR Specific	Data handling	Normalized to miR-490-3p Normalized to SNORD38B
   Real-time qRT-PCR Specific	Targeted nucleic acid	742 miRNA panel SNORD38B SNORD49A U6 miR-490-3p

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