A. Microscopic phenotype of primary tumor tissue and corresponding tumor-derived epithelial and stromal cell cultures. (1–3) – H & E-stained frozen sections showing histology of representative cases processed for RNA isolation and cell culture. Case number 061T – 1; 066T – 2; 068T – 3. Note abundant tumor cells in the samples. (4–6) – Early passage epithelial cultures; brightfield, 100× magnification. Note morphological variation between cultures in the context of an epithelial phenotype. (7–9) – abundant cytokeratin expression in the cytoplasm of cultured primary tumor cells analyzed by indirect immunofluorescence. Magnification – 400×. (10–12) – tumor-derived fibroblast cultures; brightfield, 100× magnification. Note morphological distinction between epithelial and stromal cells isolated from the same tissue sample. B – E. cDNA-based gene expression profiles of tumor tissue and tumor derived epithelial cultures. Rows represent genes, and columns represent samples. B, C – unsupervised two-dimensional hierarchical clustering of 17 samples. B – cluster shows genes under expressed in primary tumor tissue and tumor cultures compared to immortal cell lines. C – cluster shows genes over expressed in primary tumor cultures and tumor tissue compared to immortal cell lines. D, E – Gene expression patterns, which distinguish between group 1, consisting of immortal cell lines, and group 2, consisting of primary tumor tissue and tumor cultures. D – Results of SAM analysis showing a thumbnail of 681 differentially expressed genes. E – SAM-identified genes which are in common with the cluster in panel B are shown by red vertical bar, and with the cluster in panel C are shown by green vertical bars. Color scale indicates expression level.