Bladder Cancer Stage and Outcome by Array-Based Comparative Genomic Hybridization

Abstract

Purpose: Bladder carcinogenesis is believed to follow alternative pathways of disease progression driven by an accumulation of genetic alterations. The purpose of this study was to evaluate associations between measures of genomic instability and bladder cancer clinical phenotype. Experimental Design: Genome-wide copy number profiles were obtained for 98 bladder tumors of diverse stages (29 pT a , 14 pT 1 , 55 pT 2-4 ) and grades (21 low-grade and 8 high-grade superficial tumors) by array-based comparative genomic hybridization (CGH). Each array contained 2,464 bacterial artificial chromosome and P1 clones, providing an average resolution of 1.5 Mb across the genome. A total of 54 muscle-invasive cases had follow-up information available. Overall outcome analysis was done for patients with muscle-invasive tumors having ''good'' (alive >2 years) versus ''bad'' (dead in <2 years) prognosis.Results: Array CGH analysis showed significant increases in copy number alterations and genomic instability with increasing stage and with outcome. The fraction of genome altered (FGA) was significantly different between tumors of different stages (pT a versus pT 1 , P = 0.0003; pT a versus pT 2-4 , P = 0.02; and pT 1 versus pT 2-4 , P = 0.03). Individual clones that differed significantly between different tumor stages were identified after adjustment for multiple comparisons (false discovery rate < 0.05). For muscle-invasive tumors, the FGA was associated with patient outcome (bad versus good prognosis patients, P = 0.002) and was identified as the only independent predictor of overall outcome based on a multivariate Cox proportional hazards method. Unsupervised hierarchical clustering separated ''good'' and ''bad'' prognosis muscle-invasive tumors into clusters that showed significant association with FGA and survival (Kaplan-Meier, P = 0.019). Supervised tumor classification (prediction analysis for microarrays) had a 71% classification success rate based on 102 unique clones. Conclusions: Array-based CGH identified quantitative and qualitative differences in DNA copy number alterations at high resolution according to tumor stage and grade. Fraction genome altered was associated with worse outcome in muscle-invasive tumors, independent of other clinicopathologic parameters. Measures of genomic instability add independent power to outcome prediction of bladder tumors.

Gain of 5p15.33 Is Associated with Progression of Bladder Cancer

“…FISH analysis confirmed that gain of 5p15.33 was not only associated with high histological grade but also advanced pathological stage. These observations are comparable with published data on bladder cancer obtained by conventional and array CGH analyses [3, 5, 9, 23]. In this study, we analyzed copy number gains, but not copy number loss.…”

Molecular pathogenesis of bladder cancer

“…Other events found in more than 20% of cases are losses of 10p, 11p, and Y. [38][39][40] Muscle-invasive tumors Muscle-invasive bladder cancers show a wide range of genomic alterations. Many known genes are affected, but there are also large numbers of genomic alterations, particularly copy number changes in regions of the genome within which the target genes have not yet been identifi ed ( Table 2).…”

“…38,[74][75][76] Where multifocal tumors from the same patient have been analyzed, these are often highly divergent, indicating rapid molecular evolution. 77 A great deal of information has come from CGH and array-CGH studies of large tumor panels 38,76,78,79 (Table 2). Candidate genes have been listed for the regions of copy number alteration, but to date functional validation for the majority of these is absent.…”

“…Specifi c genetic differences reported between Ta and T1 tumors include deletions of 2q, 8p, and 11p and gains of 1q and 8q. 38,39 …”

Molecular biology of bladder cancer

“…The most consistent alterations in advanced-stage UCC are gains of 1q, 8q and 20q and losses of 8p, chromosome 11 and 9. Array CGH analysis has been applied to the study of UCC [37][38][39] . A summary of the most common alterations reported, classified on the basis of their chromosomal location, follows.…”