Gene expression profiling from formalin-fixed paraffin-embedded tumors of pediatric glioblastoma.

Author(s): Haque T, Faury D, Albrecht S, Lopez-Aguilar E, Hauser P, Garami M, Hanzély Z, Bognár L, Del Maestro RF, Atkinson J, Nantel A, Jabado N

Publication: Clin Cancer Res, 2007, Vol. 13, Page 6284-92

PubMed ID: 17975139 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to access the yield and integrity of RNA extracted from fresh frozen and FFPE pGBM and control specimens. The cell isolation techniques of slide scraping and laser capture microdissection were also investigated.

   Summary of Findings:

   Cell capture method significantly affected the yield of extracted RNA, with slide scraping generating as much as a fold more RNA. However, increasing the abundance of template for RNA amplification only increased the yield of amplified RNA for frozen specimens. Further, the yield of amplified RNA was significantly lower among FFPE specimens (25-40 ug) compared to frozen (60-200 ug) specimens. The integrity of RNA extracted from FFPE specimens was compromised, with 18S but not 28S ribosomal peaks observed via a bioanalyzer; however, RT-PCR analysis for three different genes was successful, correlating well with immunohistochemical results for protein expression. Thus, the authors conclude that despite evidence of degradation, expression analysis of FFPE specimens may be possible.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Pediatric
   • Epilepsy

   Platform:

   Analyte	Technology Platform
   RNA	Spectrophotometry
   RNA	RT-PCR
   RNA	Automated electrophoresis/Bioanalyzer
   Protein	Immunohistochemistry

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen
   Biospecimen Aliquots and Components	Cell capture method	Laser capture microdissection Slide scraping

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2. Study Purpose

   The purpose of this study was to compare microarray results of amplified RNA isolated from fresh frozen and FFPE pGBM and control specimens.

   Summary of Findings:

   The number of differentially expressed transcripts among disease states (pGBM and control specimens) differed as a result of the method of specimen preservation, with 777 and 3,647 differentially expressed transcripts identified in FFPE and fresh frozen specimens, respectively. The magnitude of expression differences among disease states was also lower in FFPE specimens compared to frozen specimens. However, despite these differences, a modest correlation (R^2=0.649) was present among differentially preserved specimens, and similar gene expression profile patterns were observed.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Pediatric
   • Epilepsy

   Platform:

   Analyte	Technology Platform
   RNA	DNA microarray

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen

   View more