Identification of gene expression patterns in superficial and invasive human bladder cancer

Multiple transcriptional events take place when normal urothelium is transf ormed into tumor tissue. These can now be monitored simultaneously by the u se of oligonucleotide arrays, and expression patterns of superficial and in vasive tumors can be established. Single-cell suspensions mere prepared fro m bladder biopsies (36 normal, 29 tumor). Pools of cells were made from nor mal urothelium and from pT(a) grade I and II and pT(2) grade III and IV bla dder tumors. From these suspensions, and from 10 single-tumor biopsies, lab eled cRNA was hybridized to oligonucleotide arrays carrying probes for 6500 genes. The obtained expression data were sorted according to a weighting s cheme and were subjected to hierarchical cluster analysis of tissues and ge nes. Northern blotting was used to verify the array data, and immunohistolo gy was used to correlate between RNA and protein levels. Hierarchical clust ering of samples correctly identified the stage using both 4076 genes and a subset of 400 genes covarying with the stages and grades of tumors. Hierar chical clustering of gene expression levels identified several stage-charac teristic, functionally related clusters, encoding proteins that mere relate d to cell proliferation, oncogenes and growth factors, cell adhesion, immun ology, transcription, proteinases, and ribosomes. Northern blotting correla ted well with array data. Immunohistology showed a good concordance between transcript level and protein staining. The study indicates that gene expre ssion patterns may be identified in bladder cancer by combining oligonucleo tide arrays and cluster analysis. These patterns give new biological insigh t and may form a basis for the construction of molecular classifiers and fo r developing new therapy for bladder cancer.