Purpose:The aim of the present study was to define gene expression profiles of noninvasive and invasive bladder cancer, to identify potential therapeutic or screening targets in bladder cancer, and to define genetic changes relevant for tumor progression of recurrent papillary bladder cancer (pTa). Experimental Design: Overall, 67 bladder neoplasms (46 pTa, 3 pTis, 10 pT1, and 8 pT2) and eight normal bladder specimens were investigated by a combination of laser microdissection and gene expression profiling. Eight of 16 patients with recurrent noninvasive papillary bladder tumors developed carcinoma in situ (pTis) or invasive bladder cancer (zpT1G2) in the course of time. RNA expression results of the putative progression marker cathepsin E (CTSE) were confirmed by immunohistochemistry using high-throughput tissue microarray analysis (n = 776). Univariate analysis of factors regarding overall survival, progression-free survival, and recurrence-free survival in patients with urothelial bladder cancer was done. Results: Hierarchical cluster analyses revealed no differences between pTaG1 and pTaG2 tumors. However, distinct groups of invasive cancers with different gene expression profiles in papillary and solid tumors were found. Progression-associated gene profiles could be defined (e.g., FABP4 and CTSE) and were already present in the preceding noninvasive papillary tumors. CTSE expression (P = 0.003) and a high Ki-67 labeling index of at least 5% (P = 0.01) were the only factors that correlated significantly with progression-free survival of pTa tumors in our gene expression approach. Conclusions: Gene expression profiling revealed novel genes with potential clinical utility to select patients that are more likely to develop aggressive disease.At the time of first diagnosis, f70% of bladder tumors are noninvasive papillary low-grade tumors (pTa). However, >60% of these tumors will recur at least once and progress to infiltrating or less differentiated neoplasms in 5% to 10% of cases (1). Despite the fact that the majority of superficial bladder tumors are clinically benign, regular cystoscopic follow-up at intervals is done in all patients with noninvasive bladder cancer after complete transurethral resection to detect recurrence and progression. A plethora of potential clinical and histopathologic factors indicative of tumor progression are currently discussed in the context of papillary bladder cancer: high tumor grade (2), tumor size of >5 cm (3), multifocality (4), adjacent carcinoma in situ (5), and high rate of recurrence. However, none of these markers reliably predicts a higher progression rate in papillary carcinoma of the bladder (pTa). It is important to identify the small subgroup of patients that will most likely benefit from close clinical follow-up and Bacillus Calmette-Guerin instillation therapy. New molecular prognostic markers for the prediction of tumor recurrence and progression are urgently needed.Mutations of the tumor suppressor genes TP53 and RB1 are common and have predictive va...