by ecancer reporter Clare Sansom

Clear cell renal cell carcinoma (ccRCC) is the most common and aggressive form of renal cancer, which in turn is the most lethal urological carcinoma. The incidence of renal cancer has been rising slowly in recent years, with almost 9,000 cases diagnosed in the UK in 2008. 

The gene VHL is known to be inactivated in many cases of ccRCC; this encodes a protein that is involved in the ubiquitin-mediated proteolysis pathway, which provides an important mechanism for the degradation of both nuclear and cytosolic proteins.

A large group of researchers led by Jun Wang and Huanming Yang at the Shenzhen Key Laboratory of Transomics Biotechnologies and Zhiming Cai of Peking University Shenzhen Hospital, Shenzhen, China has now investigated the genetic basis of ccRCC by sequencing the exomes (the protein-coding parts of the genomes) from tumour and matched normal renal cells from ten patients diagnosed with this condition.

Bio-informatics analysis of the resulting sequence data led to the identification of 237 non-synonymous somatic mutations including 167 missense and 17 nonsense mutations, eight splice site mutations and 45 insertions or deletions.

The coding sequences of 234 of these genes; 413 genes that have previously been implicated in cancer in the Cancer Gene Census; and 367 genes with observed ccRCC-related mutations in the Catalogue of Somatic Mutations in Cancer were sequenced in tumours and matched normal tissue from a further 88 patients with this disease.

Genes with non-synonymous changes in at least three of these tumours were selected for verification by Sanger sequencing.

The researchers identified twenty-three genes that were mutated at a significantly higher frequency than expected background mutation levels in the 98 samples tested. 

These included five genes with well-known associations with ccRCC, including VHL and the almost universal tumour suppressor gene TP53. Interestingly, however, VHL was mutated in a lower proportion of tumours than had been observed in some earlier studies.

A total of 12 genes not previously known to be associated with clear cell renal cell carcinoma were identified as being frequently mutated in these tumours.

Two of these, BAP1 and TSC1, were known tumour suppressor genes. BAP1 encodes a further component of the ubiquitin-mediated proteolysis pathway; most of its mutations were predicted to be inactivating truncations, suggesting that this gene also acts as a tumour suppressor in ccRCC. 

Other frequently mutated genes included LRP1B, a gene in the low-density lipoprotein receptor family that has previously been associated with lung and oesophageal cancers but not kidney cancer.

The researchers performed pathway analysis on all genes with statistically significant associations with ccRCC in order to identify pathways likely to be perturbed in this disease.

The ubiquitin-mediated proteolysis pathway was identified as the pathway that was most often perturbed; 49 (50%) of the complete sample of 98 tumours had non-silent mutations in genes in this pathway. This suggested that the pathway as a whole, not only the previously known gene VHL, is frequently altered in this disease.

Knowing that the hypoxia regulatory factors HIF1α and HIF2α are degraded by ubiquitin-mediated proteolysis, Wang and his co-workers investigated the hypothesis that down-regulation of the pathway might promote tumour development through the accumulation of these factors.

They tested this by immunostaining the tumour and matched normal kidney samples for these factors, and found tumours with mutations in genes in this pathway to over-express both HIF1a and HIF2a (p = 0.01 and 0.04 respectively).

Taken together, these results implicate perturbations in the ubiquitin-mediated proteolysis pathway in ccRCC development and suggest that alterations in hypoxia regulation might be one mechanism through which this arises.

Reference

Guo, G., Gui, Y., Gao, S. and 52 others (2011). Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nature Genetics, published online ahead of print 4 December 2011. doi:10.1038/ng.1014