Review
Gene expression analysis in sections and tissue microarrays of archival tissues by mRNA in situ hybridization
R.T. Henke1, A. Maitra2, S. Paik3 and A. Wellstein1
1Lombardi Cancer Center, Georgetown University, Washington, DC, USA, 2Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA and 3Division of Pathology, National Surgical Adjuvant Breast and Bowel Project (NSABP), Pittsburgh, PA, USA
Offprint requests to: Anton Wellstein, MD/PhD, Georgetown University, Lombardi Cancer Center, Research Building E311, 3970 Reservoir Rd. NW, Washington, DC 20057, USA. Fax: (202) 687-4821. e-mail: wellstea@georgetown.edu
Summary. Altered expression of genes in diseased tissues can prognosticate a distinct natural progression of the disease as well as predict sensitivity or resistance to particular therapies. Archival tissues from patients with a known medical history and treatments are an invaluable resource to validate the utility of candidate genes for prognosis and prediction of therapy outcomes. However, stored tissues with associated long-term follow-up information typically are formalin-fixed, paraffin-embedded specimen and this can severely restrict the methods applicable for gene expression analysis. We report here on the utility of tissue microarrays (TMAs) that use valuable tissues sparingly and provide a platform for simultaneous analysis of gene expression in several hundred samples. In particular, we describe a stable method applicable to mRNA expression screening in such archival tissues. TMAs are constructed from sections of small drill cores, taken from tissue blocks of archival tissues and multiple samples can thus be arranged on a single microscope slide. We used mRNA in situ hybridization (ISH) on >500 full sections and >100 TMAs for >10 different cDNAs that yielded >10,000 data points. We provide detailed experimental protocols that can be implemented without major hurdles in a molecular pathology laboratory and discuss quantitative analysis and the advantages and limitations of ISH. We conclude that gene expression analysis in archival tissues by ISH is reliable and particularly useful when no protein detection methods are available for a candidate gene. Histol Histopathol 20, 225-237 (2005)
Key words: mRNA, In situ ybridization, Tissue microarray, Expression analysis
DOI: 10.14670/HH-20.225