Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

Abstract

Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.

Figure 1. Gene expression analysis reveals two main classes of tumours - hypoxic and non-hypoxic

A. Heatmap of hypoxia related gene expression (see methods for source of gene list) in primary ccRCC tumours. Red colour indicates a relative increase in gene expression while blue indicates decreased expression. Samples clustered to the left (highlighted with grey bar) do not show a hypoxic gene expression pattern while those to the right display the hypoxic expression pattern. EGLN3 is the most upregulated gene in the hypoxic group. JARID1C (orange bar) and SETD2 (green bar) mutant tumours are all clustered in the hypoxic group while the NF2 mutant tumour (purple bar) is in the non-hypoxic group. B. A similar pattern is observed in RCC cell lines with EGLN3 again being the most upregulated gene in the hypoxic group. Five NF2 mutant cell lines cluster in the non-hypoxic group. C. Clustering of NF2 mutant samples within low VEGF expression/non-hypoxic subgroup of ccRCC.

Figure 2. Gene deregulation in SETD2 and JARID1C/KDM5C mutant samples

A. Genes (n=298) that are deregulated in tumor samples that contain non-synonymous SETD2 mutations (n=13) versus samples that lack such mutations (n=77) are plotted as a heatmap. Red color indicates increased gene expression compared to the average expression in the tumor samples, blue color indicates decreased gene expression. B. The most significantly deregulated genes in the SETD2 mutant samples. C. Heatmap of genes (n=18) that are deregulated in tumor samples that contain non-synonymous JARD1C/KDM5C mutations (n=10) versus samples that lack such mutations (n=80). The asterisks (*) highlights the sample containing the S1222P mutation. D. Expression of the MT1G gene in the tumor samples. Expression values are shown relative to non-diseased tissue and log₂-transformed such that a log₂-transformed value of −2 is equivalent to a 4-fold decrease in expression relative to non-diseased kidney. E. Metallothionein genes (n=8) were isolated examined for deregulated expression in JARID1C and UTX mutant samples. Significantly deregulated genes are indicated.