Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens

Adam Kotorashvili, Andrew Ramnauth, Christina Liu, Juan Lin, Qian K. Ye, Ryung S. Kim, Rachel Hazan, Thomas E. Rohan, Susan A. Fineberg, Olivier Loudig

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

Background: Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin-embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. The former limits accurate correlation whilst the latter is impractical when utilizing rare or limited archived specimens. Principal Findings: For effective recovery of genomic DNA and total RNA from a single FFPE specimen, without splitting the proteinase-K digested tissue solution, we optimized a co-extraction method by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells. These experiments show that the TRIzol-based co-extraction method provides larger amounts of FFPE-DNA and -RNA than the two other methods, and particularly provides higher quality microRNAs and genomic DNA for subsequent molecular analyses. Significance: We determined that co-extraction of genomic DNA and total RNA from a single FFPE specimen is an effective recovery approach to obtain high-quality material for parallel molecular and high-throughput analyses. Our optimized approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies.

Original languageEnglish (US)
Article numbere34683
JournalPLoS One
Volume7
Issue number4
DOIs
StatePublished - Apr 13 2012

Fingerprint

MicroRNAs
microRNA
formalin
Paraffin
alkanes
Formaldehyde
RNA
genomics
Messenger RNA
DNA
Tissue
Recovery
Endopeptidase K
Methylation
Gene Expression Profiling
methodology
retrospective studies
Gene expression
methylation
Nucleic Acids

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens. / Kotorashvili, Adam; Ramnauth, Andrew; Liu, Christina; Lin, Juan; Ye, Qian K.; Kim, Ryung S.; Hazan, Rachel; Rohan, Thomas E.; Fineberg, Susan A.; Loudig, Olivier.

In: PLoS One, Vol. 7, No. 4, e34683, 13.04.2012.

Research output: Contribution to journalArticle

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AU - Ramnauth, Andrew

AU - Liu, Christina

AU - Lin, Juan

AU - Ye, Qian K.

AU - Kim, Ryung S.

AU - Hazan, Rachel

AU - Rohan, Thomas E.

AU - Fineberg, Susan A.

AU - Loudig, Olivier

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