MicroRNA expression profiling of specific cells in complex archival tissue stained by immunohistochemistry

Global implementation of molecular diagnostics in modern pathology has been limited by the use of formalin-fixed, paraffin-embedded (FFPE) tissues in current routine diagnostic procedures because of modification and degradation of nucleic acids and protein molecules. In particular, molecular analysis of a specific cell type potentially important for biomarker identification is largely prevented in highly complex, solid tissues routinely used in histopathology. Accumulating data report on the substantial contribution of microRNA molecules (miRNA) to tumor development and malignant progression of most human malignancies. Our objective was to establish a sensitive and robust procedure to quantify miRNA expression in specific cells from complex archival tumor tissues identified by immunohistochemistry. Here, we show reliable detection of miRNA expression profiles determined from limited amounts of colorectal cancer FFPE tissues after routine staining procedure. The combination of routinely used FFPE specimens stained by immunohistochemistry with the molecular analysis of laser microdissected complex tumor tissue resulted in robust miRNA expression patterns exclusively obtained from epithelial tumor cells. This approach allows for a detailed molecular analysis of cancer cells and distinct stromal cell types and their in situ interaction in solid tumors. Hence, the methodology can offer new perspectives for basic research and, by comprehensive use of present archival tissue collections linked to clinical databases, facilitate miRNA biomarker identification in defined tissue cells for future diagnostic and therapeutic strategies.