NEW GENE MUTATIONS FOR RENALCANCER

January 6, 2010 — Mutations in genes modifying histone structure are associated with many cases of clear cell renal cell carcinoma (ccRCC), according to scientists at Wellcome Trust Sanger Institute and their international collaborators. Although most ccRCC — the most common type of kidney cancer in adults — involves mutations that inactivate VHL, the new findings point to greater genetic heterogeneity in this disease.

The study, by senior author P. Andrew Futreal, MB, PhD, from the Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom, and colleagues, was published online today in Nature.

The majority of ccRCC cases differ from other renal cell carcinomas by the presence of mutations that inactivate VHL, a gene coding for a tumor suppressor protein. Inactivation of VHL is associated with von Hippel-Lindau disease, and VHL mutations predispose people to a variety of tumors, both malignant and benign. Patients with ccRCC typically lack mutations in other genes associated with adult epithelial cancers. This study looked for genes other than VHL that might contribute to ccRCC.

Investigators screened 101 ccRCC samples from 96 primary tumors and 5 ccRCC cell lines. The tumor sources were 56 men and 40 women, with ages ranging from 32 to 85 years (median, 62 years). Tumors at diagnosis were at stage I (n = 44), stage II (n = 14), stage III (n = 34), stage IV (n = 2), or not available (n = 2); grade at diagnosis was 1 (n = 4), 2 (n = 35), 3 (n = 39), 4 (n = 16), or not available (n = 2). Consistent with other studies of ccRCC, 55% of the tumors demonstrated VHL mutations.

Two distinct phenotypes were identified among the tumors with respect to gene expression: 82% of the ccRCCs assessed showed greater activity of genes associated with cellular hypoxia, and 65% of this group had point mutations that inactivated VHL. The second phenotype was represented by the 18% of tumors that did not demonstrate a hypoxic gene expression pattern.

In tumors with increased hypoxia-related gene activity, EGLN3 was the most upregulated gene (a hypoxia response element is located in the region of EGLN3). SETD2 and JARID1C mutations were more common in tumors with hypoxic upregulation. Mutations in NF2 were found only in tumors without hypoxic upregulation.

Both SETD2 and JARID1C code for enzymes that modify histones — the main proteins that constitute chromatin and also influence gene expression. SETD2 encodes a "histone H3 lysine 36 methyltransferase," and JARID1C encodes a "histone H3 lysine 4 demethylase." The involvement of a third histone-modifying gene, UTX, which encodes a histone H3 lysine 27 demethylase, was previously reported by this research group.

Histone-Related Mutations Found

Histone-related mutations found in ccRCC in the initial screen, follow-up screen, and RCC cell-lines in this study include

• a total of 16 mutations in SETD2: 4 nonsense, 3 missense, 9 frameshift;
• a total of 14 mutations in JARID1C: 6 nonsense, 2 missense, 2 splice/deletions, and 4 frameshift; and
• a total of 12 mutations in UTX: 1 nonsense, 5 missense, 1 splice, 1 splice/deletion, 4 frameshift.

Seven NF2 mutations were also found: 1 nonsense, 4 frameshift, 1 splice, and 1 splice/deletion. Although this study identified somatic mutations in tumors and cell lines, NF2 germline mutations are known to predispose patients to neurofibromatosis II. Interestingly, none of the NF2 mutations found in this study occurred in tumors with VHL mutation or a hypoxic gene expression pattern. "These data indicate that somatic NF2 mutations may account for a proportion of this subset of cases," the authors note.

Quite different phenotypes were associated with expression of mutated SETD2 or JARID1C. Mutant SETD2 involved "large-scale transcriptional deregulation...with 298 genes showing significant differences in expression relative to other cancers analyzed," the study reports. In contrast, mutation of JARID1C "showed a much more restricted signature.... Eighteen genes showed significant expression changes in cancers with JARID1C mutations."

The authors conclude, "For ccRCC, the data presented here will provide insights into its pathogenesis and the opportunity to understand the role of genetic subtypes in clinical behavior and response to treatment."

In addition, their study indicates 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."

Nature. Published online January 6, 2010.