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The sum of the parts gives a better picture of the whole: Integrated analysis of clear-cell renal carcinoma

Amy Cullinan, Ph.D.
| Sep 27, 2013
cancer puzzle

Clear-cell renal cell carcinoma (ccRCC) is a common, sporadic form of kidney cancer with a hallmark biallelic inactivation of the von Hippel-Lindau (VHL) tumor suppressor gene. Yet a subset of ccRCC cases exists that have no detectable VHL alterations and whose pathogenesis is poorly characterized.  Although recent sequencing studies1,2 have identified frequent mutations in genes involved in chromatin modification and ubiquitin-mediated proteolysis, the role of these genetic and epigenetic changes in ccRCC remains unclear.  Recently, a group of Japanese researchers combined multiple “omics” approaches to elucidate the molecular pathogenesis of clear-cell renal carcinoma3. In this large and comprehensive study, over 100 ccRCC cases were analyzed by combinations of whole-genome sequencing, whole-exome sequencing, RNA sequencing, gene expression, copy number and methylation analyses, and immunohistochemistry.

Using the HiSeq 2000, the group sequenced the whole genomes of matched tumor-normal samples from 14 ccRCC cases. These samples, with an additional 92 tumor-normal pairs underwent whole-exome and RNA sequencing. Using a variety of technologies, targeted sequencing, methylation, copy number, and gene analysis were performed on an additional 240 tumor-normal samples. This unique experimental approach revealed new information about ccRCC pathogenesis, particularly in regards to VHL inactivation.

The results confirmed that VHL and several other genes associated with chromatin modfication (including SETD2, BAP1, and PBRM1), were frequently mutated in ccRCC. Mutations were also discovered that disrupt P53 and PI3K-AKT-mTOR signaling, as well as the formation of KEAP1-NRF2-CUL3 apparatus.  Notably, in ccRCC cases with intact VHL, mutations in a gene called TCEB1 were identified along with loss of chromosome 8This was one of the most significant findings of the study, demonstrating a new pathogenic mechanism for inactivation of the VHL complex in ccRCC.

Perhaps the most exciting aspect of this comprehensive study was that features within mutation profiles, gene expression and DNA methylation patterns, and changes in copy number cluster together and correlate with the clinical behavior of cases. For example, cases featuring hypermethylation, hyperploidy andloss of heterozygosity (LOH) at 9p, correlate with poor prognosis whereas less frequent methylation, hyperploidy, and 9p LOH correlate with excellent prognosis. Although the genetic and pathophysiological contributions of a hypermethylated state to metastatic disease have not been fully characterized, the hypermethylated/hyperploid cluster might benefit from more surveillance and early detection methods or treatments.

This study nicely demonstrates the dramatic increase in power that comes with an integrated molecular approach to cancer. With the availability of greater numbers of comprehensive datasets in different cancer types, better correlations can be made across experiments, bringing clarity to clinical profiling and management.


1. Guo G, Gui Y, Tang A, Hu X, Huang Y et al. (2011) Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet 44(1):17–9.

2. Peña-Llopis S, Vega-Rubín-de-Celis S, Liao A, Leng N, Pavía-Jiménez A, et al. (2012)  BAP1 loss defines a new class of renal cell carcinoma. Nat Genet 44(7):751–9.

3. Sato Y, Yoshizato T, Shiraishi Y, Maekawa S, Okuno Y, et al. (2013) Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet 45(8):860–867.