Optimization of laser capture microdissection and RNA amplification for gene expression profiling of prostate cancer

Dagmar M. Kube, Cemile D. Savci-Heijink, Anne Françoise Lamblin, Farhad Kosari, George Vasmatzis, John C. Cheville, Donald P. Connelly, George G. Klee

Research output: Contribution to journalArticle

61 Citations (Scopus)

Abstract

Background: To discover prostate cancer biomarkers, we profiled gene expression in benign and malignant cells laser capture microdissected (LCM) from prostate tissues and metastatic prostatic adenocarcinomas. Here we present methods developed, optimized, and validated to obtain high 0quality gene expression data. Results: RNase inhibitor was included in solutions used to stain frozen tissue sections for LCM, which improved RNA quality significantly. Quantitative PCR assays, requiring minimal amounts of LCM RNA, were developed to determine RNA quality and concentration. SuperScript II™ reverse transcriptase was replaced with SuperScript III™, and SpeedVac concentration was eliminated to optimize linear amplification. The GeneChip® IVT labeling kit was used rather than the Enzo BioArray™ HighYield™ RNA transcript labeling kit since side-by-side comparisons indicated high-end signal saturation with the latter. We obtained 72 μg of labeled complementary RNA on average after linear amplification of about 2 ng of total RNA. Conclusion: Unsupervised clustering placed 5/5 normal and 2/2 benign prostatic hyperplasia cases in one group, 5/7 Gleason pattern 3 cases in another group, and the remaining 2/7 pattern 3 cases in a third group with 8/8 Gleason pattern 5 cases and 3/3 metastatic prostatic adenocarcinomas. Differential expression of alpha-methylacyl coenzyme A racemase (AMACR) and hepsin was confirmed using quantitative PCR.

Original languageEnglish (US)
Article number25
JournalBMC Molecular Biology
Volume8
DOIs
StatePublished - Mar 21 2007

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Microdissection
Laser Capture Microdissection
Gene Expression Profiling
Gene expression
Amplification
Prostatic Neoplasms
RNA
Lasers
Labeling
Adenocarcinoma
Racemases and Epimerases
Gene Expression
Polymerase Chain Reaction
Complementary RNA
RNA-Directed DNA Polymerase
Prostatic Hyperplasia
Frozen Sections
Coenzyme A
Tumor Biomarkers
Ribonucleases

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry

Cite this

Optimization of laser capture microdissection and RNA amplification for gene expression profiling of prostate cancer. / Kube, Dagmar M.; Savci-Heijink, Cemile D.; Lamblin, Anne Françoise; Kosari, Farhad; Vasmatzis, George; Cheville, John C.; Connelly, Donald P.; Klee, George G.

In: BMC Molecular Biology, Vol. 8, 25, 21.03.2007.

Research output: Contribution to journalArticle

Kube, Dagmar M. ; Savci-Heijink, Cemile D. ; Lamblin, Anne Françoise ; Kosari, Farhad ; Vasmatzis, George ; Cheville, John C. ; Connelly, Donald P. ; Klee, George G. / Optimization of laser capture microdissection and RNA amplification for gene expression profiling of prostate cancer. In: BMC Molecular Biology. 2007 ; Vol. 8.
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