Tissue microarrays for high-throughput profiling in molecular oncology

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High-throughput genome screening technologies, such as CGH, cDNA microarrays, SAGE, differential display, and DNA sequencing have made it possible to survey thousands of genes per tumor. The translation of such information to improved diagnostic, prognostic and therapeutic applications in the clinic requires extensive data `mining' as well as validation, prioritization and extension of such results to hundreds or thousands of clinical specimens. This is often extremely tedious with conventional molecular pathology technologies. We have developed a novel technology, tissue microarrays (`tissue chips') for facilitating such `genome-scale' translational cancer research [1]. This technology enables high-throughput molecular analyses of hundreds of tissue specimens or cells in a single experiment. Tissue microarrays are constructed by acquiring cylindrical biopsies from 500-1000 individual tumor tissues into a tissue microarray block, which is then sliced to over 200 sections for probing DNA, RNA or protein targets. A single immunostaining or in situ hybridization reaction now provides information on all of the specimens on the slide, while subsequent sections can be analysed with other probes or antibodies. Construction of multiple replicate blocks may allow up to 100 000 sections to be generated from the same series of tumor specimens. This expands the scope of microarray technologies to the rapid, very large-scale molecular analysis of thousands of tissue specimens with thousands of probes for various DNA, RNA and protein targets. For example, we have utilized the combination of cDNA and tissue microarray technologies to uncover genes involved in breast and prostate cancer progression. In summary, tissue microarrays provide a powerful approach for the in vivo validation of gene discoveries, as well as a means to rapidly assess the clinical significance of molecular alterations.