Patterns of gene expression and copy-number alterations in von-hippel lindau disease-associated and sporadic clear cell carcinoma of the kidney

Abstract

Recent insights into the role of the von-Hippel Lindau (VHL) tumor suppressor gene in hereditary and sporadic clear-cell renal cell carcinoma (ccRCC) have led to new treatments for patients with metastatic ccRCC, although virtually all patients eventually succumb to the disease. We performed an integrated, genome-wide analysis of copy-number changes and gene expression profiles in 90 tumors, including both sporadic and VHL disease-associated tumors, in hopes of identifying new therapeutic targets in ccRCC. We identified 14 regions of nonrandom copy-number change, including 7 regions of amplification (1q, 2q, 5q, 7q, 8q, 12p, and 20q) and 7 regions of deletion (1p, 3p, 4q, 6q, 8p, 9p, and 14q). An analysis aimed at identifying the relevant genes revealed VHL as one of three genes in the 3p deletion peak, CDKN2A and CDKN2B as the only genes in the 9p deletion peak, and MYC as the only gene in the 8q amplification peak. An integrated analysis to identify genes in amplification peaks that are consistently overexpressed among amplified samples confirmed MYC as a potential target of 8q amplification and identified candidate oncogenes in the other regions. A comparison of genomic profiles revealed that VHL disease-associated tumors are similar to a subgroup of sporadic tumors and thus more homogeneous overall. Sporadic tumors without evidence of biallelic VHL inactivation fell into two groups: one group with genomic profiles highly dissimilar to the majority of ccRCC and a second group with genomic profiles that are much more similar to tumors with biallelic inactivation of VHL.

Figure 1

Significant copy-number alterations in ccRCC. (a) Amplifications (red) and deletions (blue), determined by segmentation analysis of normalized signal intensities from 250K SNP arrays (see Methods), are displayed across the genome (chromosome positions, indicated along the y axis, are proportional to marker density) for 54 sporadic tumors, 36 metachronous tumors from 12 VHL patients, and 18 renal cancer cell lines. Metachronous tumors from the same patient are designated by the same color across the top. (b) GISTIC analysis of copy-number changes in ccRCC tumors. The G-score represents the frequency × average amplitude of the aberrations identified in (a). The FDR q-values, representing the statistical significance associated with these scores with correction for multiple hypothesis testing(20), are displayed along the bottom of each panel. Regions with q-values < 0.25 (green lines) were considered significantly altered. Chromosome positions are indicated along the y axis with centromere positions indicated by dotted lines. The locations of the peak regions of maximal copy-number change are indicated to the right of each panel.

Figure 2

Graphic representation of level of similarity between (a) copy-number and (b) expression profiles of ccRCC samples. Individual tumors, represented in red (germVHL) and blue (sporadic) have been mapped to a 2-dimensional plane to display the Euclidean distances among them. (see Methods). Tumors with biallelic inactivation of VHL (germVHL and mutVHL) are represented by crosses, while those without biallelic inactivation (wtVHL) are represented by dots. Five of the wtVHL tumors, distributed along the periphery of the copy-number space occupied by the tumor set (a), are marked by green circles. The three of these with expression profiles are similarly marked in (b).

Figure 3

Heat map representing expression levels of HIF-1 targets in ccRCC samples. Tumors (across the top) are divided into germVHL, mutVHL, wtVHLcent, and wtVHLedge groups. Genes (along the right) are ordered from top to bottom according to the degree to which they are differentially expressed between tumors with and without biallelic inactivation of VHL.