Preliminary Comparison of Quantity, Quality, and Microarray Performance of RNA Extracted from Formalin-fixed Paraffin- embedded and Unfixed Frozen Tissue Samples

Marshall S. Scicchitano ^1*, Deidre A. Dalmas ¹, Melissa A. Bertiaux ¹, Shawn M. Anderson ¹, Leah R. Turner ¹, Roberta A. Thomas ¹, Rossana Mirable ¹ and Rogely W. Boyce ¹

¹ Department of Safety Assessment (MSS,DAD,RAT,RM,RWB) and Department of Genetics Research and Drug Discovery (MAB,SMA), GlaxoSmithkline, King of Prussia, Pennsylvania, and NuGEN Technologies, Inc, San Carlos, California (LRT)

^* To whom correspondence should be addressed. E-mail: Marshall.2.Scicchitano{at}gsk.com.

Submitted on April 24, 2006
Accepted on 12 July 2006

	Abstract

Microarrays have been used to simultaneously monitor the expression of thousands of genes from biological samples, an approach that can potentially uncover previously unrecognized functions of genes. Microarray analyses can rarely be conducted retrospectively because of the requirement for RNA to be obtained from fresh or unfixed frozen tissues. Archived pathology specimens would need to be used for retrospective analyses and these are typically preserved as formalin-fixed paraffin-embedded (FFPE) tissue. Formalin fixed tissues have been shown to yield compromised RNA compared with that obtained from frozen tissue. To begin to assess the performance of RNA extracted from FFPE samples on a microarray format, we compared RNA from a model system of pelleted LPS-stimulated human bone marrow stromal cells that were either snap-frozen with RNA from cells FFPE. RNA integrity and Affymetrix quality control parameters were assessed and differentially regulated genes were analyzed with Ingenuity Pathway Analysis software. Results demonstrate that both snap-frozen and FFPE samples yielded intact RNA suitable for amplification prior to Affymetrix GeneChip analysis. Although some transcriptional information was lost with RNA extracted from the FFPE samples, Ingenuity Pathway Analysis revealed the major pathways identified as affected by drug treatment were similar. Results show that FFPE samples are amenable to Affymetrix GeneChip analysis opening up the possibility for expression profiling on archived tissue blocks in pathology laboratories.

Key Words: FFPE, Affymetrix, gene expression, RNA, TaqMan

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