Genetic analysis of multifocal superficial urothelial cancers by array-based comparative genomic hybridisation

Abstract

The purpose of this study was to investigate the accumulation of genetic alterations during metachronous and/or synchronous development of multifocal low-grade superficial urothelial tumours in the same patient, by using array-based comparative genomic hybridisation (array-CGH) and FGFR mutation analysis. We analysed 24 tumours (pTa-1 G1-2) from five patients. We had previously identified a clonal relationship among the tumours of each patient by microsatellite analysis. This time, unsupervised hierarchical cluster analysis revealed that the tumours from each patient were clustered together independently of the tumours from the other patients. All of the tumours from a single patient showed a set of 2-7 identical regional or whole-arm chromosomal changes. In addition, several individual alterations were also found. Cladistic diagrams revealed that the accumulation of genetic alterations could not be explained by a linear model, and the existence of a hypothetical precursor cell was assumed in four patients. In some cases, FGFR mutation seemed to occur later during multifocal tumour development. Taken together, these findings suggest that low-grade superficial urothelial tumours accumulate minor genetic alterations during multifocal development, although these tumours are genetically stable.

Figure 1

Hierarchical clustering of data for 24 tumours obtained from clones in the MCG Cancer Array-800. The data are presented in a matrix format. Each column corresponds to a single tumour, and each row corresponds to a single clone ordered by mapping position. Gain or loss of a clone is represented by the colour of the cells in the matrix (green indicates gain, black is no change, and red means loss). Colour saturation is proportional to the magnitude of the difference. The sidebars to the left of the matrix format represent a chromosome cluster ordered from chromosome 1 to Y. The horizontal dendrogram shows that the associations between tumours and the length of the branches reflect the extent of similarity between tumours. Note that each tumour from a particular patient is more closely related to other tumours from the same patient than to any tumours from the other patients.

Figure 2

Graphical representation of array-CGH analysis of tumours from Patients 2 and 16 (whole genome). Vertical lines indicate the boundaries of the chromosomes. (A) In Patient 2, a concordant pattern was found in 4q32-35, 6q15-22, 9p21-24, 9q, 11p, 17p (loss) and 20q (gain). A later tumour (T3) had additional genetic alterations (2p, 2q (gain)). (B) In Patient 16, several discordant patterns were found in 11p, 13q22-tel, 17p, 18q, and 20p. Average log 2 ratios were plotted for all clones at the chromosome positions. Thresholds for gain or loss are shown within log 2 ratios of 0.3 and −0.3, respectively. Arrows indicate the differences of the pattern of chromosomal aberrations between tumour pairs. T=tumour; Chr=chromosome.

Figure 3

Evolutionary genetic tree depicting the relationship between the multiple tumours of each patient.