Tissue Arrays

Abstract

The development of high-throughput technologies, including DNA arrays and proteomics approaches, has led to a tremendous increase in data acquisition. Numerous groups have reported differentially expressed genes and proteins in a variety of normal and malignant tissues. In fact, many groups are using high-throughput techniques to define new tumor classifications. As important genes are identified by various high-throughput technologies, it is critical to correlate these studies with tissue expression to define the precise cell of origin of a particular transcript or protein. In many DNA array experiments, for example, nonpurified cells are used as a starting material. The RNA from cells to be analyzed is commonly admixed with that from a variety of other cells. In the case of tumor tissues, contaminating stromal cells, blood vessels (endothelial cells and smooth muscle), and other normal cells are typically present. It is difficult, therefore, to be certain that a differentially expressed gene is derived from the cell of interest rather than a “contaminating” cell. Some studies have validated findings using standard techniques based on archival formalin-fixed paraffin-embedded tissues,-including immunohistochemistry (IHC) and in situ hybridization (ISH). ISH and IHC are techniques that can localize the expression of a gene or protein to specific cells in tissues. These techniques can be performed with fixed tissues, while fresh or frozen tissue is required for DNA microarray studies. The amount of archival paraffin-embedded tissue far exceeds the tissue that is adequately preserved for RNA or protein extraction and, thus, can be used to expand the scope and significance of these studies. In the past, the use of these standard approaches to analyze the in situ expression of genes or proteins in tissues has been a slow and labor-intensive process, requiring the processing of numerous slides at a rate of one gene product per slide. Furthermore, a significant amount of tissue is required to perform many tests on a single specimen. Although automated stainers from various manufacturers can facilitate these techniques, they are not widely used and may not be of particular use to investigators who work with newly characterized reagents. The use of high density arrays composed of many tissue samples provides a highly efficient means to validate and extend molecular studies of human cancers.