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Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays
- Source :
- Laboratory investigation, 88(4) (2008): 430–440., info:cnr-pdr/source/autori:Ravo M, Mutarelli M, Ferraro L, Grober OM, Paris O, Tarallo R, Vigilante A, Cimino D, De Bortoli M, Nola E, Cicatiello L, Weisz A./titolo:Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays./doi:/rivista:Laboratory investigation (Print)/anno:2008/pagina_da:430/pagina_a:440/intervallo_pagine:430–440/volume:88(4)
- Publication Year :
- 2008
- Publisher :
- Elsevier BV, 2008.
-
Abstract
- Microarray-based gene expression profiling is well suited for parallel quantitative analysis of large numbers of RNAs, but its application to cancer biopsies, formalin-fixed paraffin-embedded (FFPE) archived tissues in particular, is limited by the poor quality of the RNA recovered. This represents a serious drawback, since FFPE tumor tissue banks are available with clinical and prognostic annotations, which could be exploited for molecular profiling studies, provided that reliable analytical technologies are found. We applied and evaluated here a microarray-based cDNA-mediated annealing, selection, extension and ligation (DASL) assay for analysis of 502 mRNAs in highly degraded total RNA extracted from cultured cells or FFPE breast cancer biopsies. The study included quantitative and qualitative comparison of data obtained by analysis of the same RNAs with genome-wide oligonucleotide microarrays vs. DASL arrays and, by DASL, before and after extensive in vitro RNA fragmentation. The DASL-based expression profiling assay applied to RNA extracted from MCF-7 cells before or after 24 hours stimulation with a mitogenic dose of 17β-estradiol consistently allowed to detect hormone-induced gene expression changes also following extensive RNA degradation in vitro. Comparable results where obtained with tumor RNA extracted from FFPE breast cancer biopsies (6 to 19 years old). The method proved itself sensitive, reproducible and accurate, when compared with results obtained by microarray analysis of RNA extracted from snap-frozen tissue of the same tumor.
- Subjects :
- Microarray
breast cancer
formalin-fixed tissues
microarrays
Gene Expression
Biopsy
Breast Neoplasms
Biology
Pathology and Forensic Medicine
Cell Line, Tumor
Formaldehyde
Gene expression
medicine
Humans
RNA, Neoplasm
Molecular Biology
Oligonucleotide Array Sequence Analysis
Paraffin Embedding
medicine.diagnostic_test
Microarray analysis techniques
Gene Expression Profiling
Carcinoma, Ductal, Breast
Reproducibility of Results
RNA
Cell Biology
Molecular biology
In vitro
Gene expression profiling
expression profiling
Female
DNA microarray
microarray
Subjects
Details
- ISSN :
- 00236837
- Volume :
- 88
- Database :
- OpenAIRE
- Journal :
- Laboratory Investigation
- Accession number :
- edsair.doi.dedup.....3a0d9021fd491e8b4e5d233331d48875