To identify gene expression changes along progression of bladder cancer, we compared the expression profiles of early-stage and advanced bladder tumors using cDNA microarrays containing 17,842 known genes and expressed sequence tags. The application of bootstrapping techniques to hierarchical clustering segregated early-stage and invasive transitional carcinomas into two main clusters. Multidimensional analysis confirmed these clusters and more importantly, it separated carcinoma in situ from papillary superficial lesions and subgroups within early-stage and invasive tumors displaying different overall survival. Additionally, it recognized early-stage tumors showing gene profiles similar to invasive disease. Different techniques including standard t-test, singlegene logistic regression, and support vector machine algorithms were applied to identify relevant genes involved in bladder cancer progression. Cytokeratin 20, neuropilin-2, p21, and p33ING1 were selected among the top ranked molecular targets differentially expressed and validated by immunohistochemistry using tissue microarrays (n ؍ 173). Their expression patterns were significantly associated with pathological stage, tumor grade, and altered retinoblastoma (RB) expression. Moreover, p33ING1 expression levels were significantly associated with overall survival. Analysis of the annotation of the most significant genes revealed the relevance of critical genes and pathways during bladder cancer progression, including the overexpression of oncogenic genes such as Transitional cell carcinomas (TCCs) of the bladder define a group of histologically and genetically diverse cancers that account for ϳ4% of all adult malignancies with an annual incidence of ϳ53,200 cases in the United States. Early-stage TCC has been classified into two groups with distinct clinical behavior and different molecular profiles. Superficial low-grade tumors (Ta) are always papillary and may recur but rarely progress, whereas high-grade tumors can be either papillary or flat lesions (Tis) and often progress to invasive disease.2 Clinically, patients diagnosed with localized stage have a 5-year relative survival rate of 93%. However, patients presenting with regional and distant stage have 5-year relative survival rates of 49% and 6%, respectively.1 Among the molecular events that characterize superficial papillary noninvasive bladder tumors are deletions affecting the long arm of chromosome 9, and activation of certain oncogenes, such as H-RAS, alterations identified only in a subset of invasive bladder neoplasms.2 Deletions of 13q at the RB locus and 17p at the TP53 locus, as well as 18q (DCC locus) and 5q (APC locus) losses have been reported in invasive bladder transitional carcinomas, but are absent in papillary noninvasive tumors.2,3 A remaining challenge in bladder cancer is to define targets characteristic of aggressive early-stage tumors before they recur or progress into invasive disease. The present study was designed to identify critical molecular targets altered along the...