Bladder cancer develops in the urothelial lining from intraurothelial preneoplasia via two pathways, papillary and nonpapillary, which correspond to nonaggressive and aggressive forms of the disease. Because these two forms of cancer may develop via distinct molecular events, we examined the gene expression patterns in the development of bladder cancer from preneoplasia along papillary and nonpapillary pathways. The expression profiles of 19 pairs of RNA samples from adjacent urothelium and tumors were analyzed using cDNA microarrays. For selected genes their expressions were verified on a cohort of 251 bladder cancer patients using tissue microarray and immunohistochemistry and were related to clinicopathological parameters including follow-up data. We identified alterations in seven gene clusters controlling proliferation, differentiation, and programmed cell death that were common for papillary and nonpapillary cancer. In contrast, genes controlling cellular and stromal interactions were altered in the nonpapillary cancer. The expression levels of only two genes from this group could be used to define an aggressive form of the disease. Tumors characterized by the low expression of e-cadherin and the high expression of DNA a-topoisomerase II had a high propensity for distant metastasis and were associated with poor survival. Laboratory Investigation (2005) 85, 532-549. doi:10.1038/labinvest.3700250Keywords: cDNA microarray; bladder cancer; gene expression profile; tissue microarray; preneoplasia Many common human epithelial malignancies develop by progression of microscopically identifiable precursor conditions ranging from mild dysplasia to carcinoma in situ. 1 These conditions progress to clinically aggressive invasive cancer by multiple cumulative molecular events. 2 In fact, the earliest incipient changes occur in normal tissue even before preneoplastic lesions can be microscopically identified. The identification of abnormally expressed genes in such occult preneoplastic lesions may provide important clues as to the molecular pathways involved in the development of human cancer and facilitate early cancer detection and prevention.Carcinoma of the bladder is an exceptionally good candidate for such studies representing a model epithelial malignancy, which develops from microscopically recognizable intraurothelial preneoplastic lesions. [2][3][4] The fifth most frequent human cancer, it primarily affects people over the age of 50 years, and accounts for approximately 3% of all cancerrelated deaths. 5 The common bladder carcinomas arise via two distinct, but sometimes overlapping pathways, papillary and nonpapillary. 6-9 Approximately 80% of bladder tumors are superficially growing lesions that originate from urothelial hyperplasia. They frequently recur after excision but usually do not aggressively invade the bladder wall or metastasize. Most aggressive bladder cancers are of the solid, nonpapillary type and originate from intraurothelial precursor conditions such as dysplasia and carcinoma in situ. They a...