Expression profiling with RNA from formalin-fixed, paraffin-embedded material.
BACKGROUND
Molecular characterization of breast and other cancers by gene expression profiling has corroborated existing classifications and revealed novel subtypes. Most profiling studies are based on fresh frozen (FF) tumor material which is available only for a limited number of samples while thousands of tumor samples exist as formalin-fixed, paraffin-embedded (FFPE) blocks. Unfortunately, RNA derived of FFPE material is fragmented and chemically modified impairing expression measurements by standard procedures. Robust protocols for isolation of RNA from FFPE material suitable for stable and reproducible measurement of gene expression (e.g. by quantitative reverse transcriptase PCR, QPCR) remain a major challenge.


RESULTS
We present a simple procedure for RNA isolation from FFPE material of diagnostic samples. The RNA is suitable for expression measurement by QPCR when used in combination with an optimized cDNA synthesis protocol and TaqMan assays specific for short amplicons. The FFPE derived RNA was compared to intact RNA isolated from the same tumors. Preliminary scores were computed from genes related to the ER response, HER2 signaling and proliferation. Correlation coefficients between intact and partially fragmented RNA from FFPE material were 0.83 to 0.97.


CONCLUSIONS
We developed a simple and robust method for isolating RNA from FFPE material. The RNA can be used for gene expression profiling. Expression measurements from several genes can be combined to robust scores representing the hormonal or the proliferation status of the tumor.
Oberli
Andrea
A
Department of Clinical Research, University of Bern, Murtenstrasse 35 CH-3010 Bern, Switzerland. andrea.oberli@dkf.unibe.ch
Popovici
Vlad
V
Delorenzi
Mauro
M
Baltzer
Anna
A
Antonov
Janine
J
Matthey
Sybille
S
Aebi
Stefan
S
Altermatt
Hans Jörg
HJ
Jaggi
Rolf
R