Renal cell carcinoma (RCC) is a collective term applied to a set of cancers arising in the epithelium of the renal tubules comprised of three main histopathological entities. Clear cell RCC (ccRCC) is the dominant histology, accounting for approximately 65% of reported cases, followed by papillary and chromophobe RCC, accounting for approximately 15–20 and 5%, respectively. Other more rare subtypes make up the remainder of RCC cases including collecting duct, mucinous tubular, spindle cell, renal medullary, and MiTF-TFE translocation carcinomas.
Hereditary RCC, which accounts for around 4% of cases, has been a relatively dominant area of RCC genetics. Causative genes have been identified in several familial cancer syndromes that predispose to RCC including VHL
mutations in von Hippel-Lindau disease that predispose to ccRCC[1
mutations in familial papillary renal cancer[2
(fumarate hydratase) mutations in hereditary leiomyomatosis and renal cell cancer that predispose to papillary RCC[3
] and FLCN
(folliculin) mutations in Birt-Hogg-Dubé syndrome that predispose to primarily chromophobe RCC[4
]. In addition, germline mutations in the TSC1
/2 genes predispose to tuberous sclerosis complex where approximately 3% of cases develop ccRCC[5
] and SDHB
(succinate dehydrogenase type B) germline mutations in patients with paraganglioma syndrome give rise to increased risk of developing multiple types of RCC[6
]. Moving away from rare monogenic disease to population-based RCC susceptibility, genome wide association study results from a recent study of almost 6000 RCC cases has implicated loci on 2p21 and 11q13.3 in RCC susceptibility[7
]. 2p21 contains the EPAS1
gene encoding a transcription factor operative in hypoxia-regulated responses while the other region has no known coding genes.
There has been, however, comparatively less progress in the elaboration of the somatic genetics of sporadic RCC. By far, the most studied somatically mutated gene is VHL
, which follows the classic tumor suppressor gene paradigm of a germline cancer susceptibility gene also manifesting as being somatically mutated in the sporadic form of cancer type[8
is somatically mutated in up to 80% of ccRCC[9
]. The majority of these mutations are protein-terminating mutations with loss of the wild-type allele via large-scale loss of heterozygosity of chromosome 3p. There is a further small proportion (5–10%) of cases with no apparent somatic mutations that apparently methylate the locus and thus are functionally VHL
]. Along a similar theme of congruence of germline and somatic genetics, albeit with a diminished magnitude of effect, there are dominantly activating kinase domain MET
mutation reported in 4–10% of sporadic papillary RCC[2
]. Conversely, somatic mutations in FLCN
in chromophobe RCC are rare[12
] and somatic FH
mutations in sporadic papillary renal cancers were not found [12
]. Similarly, somatic mutations of TSC12
were not identified in sporadic RCC [13
]. Recently however, somatic mutations in TSC1
have been found in sporadic ccRCC [15
mutations occur in 5% of ccRCCs and may predict for extraordinary sensitivity to mTORC1 inhibitors clinically [15
Further investigation of RCC somatic genetics has included evaluation of cancer genes important in other adult epithelial cancers. Taking all histologies combined, the COSMIC database reports somatic point mutations in TP53
in 10% of cases, KRAS/HRAS/NRAS
combined ≤1%, CDKN2A
1% and BRAF
≤1% (http://www.sanger.ac.uk/ genetics/CGP/cosmic/
has been reported to be amplified in papillary RCC [16
] and rare cases of RCC have been reported with EGFR
]. Focusing on the most prevalent histology, ccRCC, the contribution of cancer genes commonly mutated in other tumor types provides limited insight into what additional somatic genetic events are contributing to pathogenesis.
With this as a background, systematic approaches have been undertaken to elaborate the somatic genetics of ccRCC. A screen of 3,544 protein coding genes via PCR-based exon re-sequencing in 101 cases of ccRCC identified several new cancer genes in RCC [18
]. Remarkably, four out of five genes with robust statistical support for being new cancer genes encode proteins involved in histone methylation/demethylation. Truncating mutations were identified in KDM6A/UTX
which encode an histone 3 lysine 27 (H3K27) demethylase, an histone 3 lysine 36 (H3K36) methyltransferase and an histone 3 lysine 4 (H3K4) demethylase, respectively. MLL2
, an H3K4 methyltransferase, was also mutated at a significant rate. These data implicate deregulation of histone H3, known to be a major regulator of euchromatin/transcription, as a new area of RCC biology for exploration. Of note and further confirming the utility of large-scale systematic approaches, NF2
truncating mutations were unexpectedly identified in a significant proportion of the small subset of ccRCC that are VHL
wildtype. Taken together, however, these genes are mutated in less than 15% of ccRCC suggesting the existence of additional cancer genes.
A subsequent study has moved to solution capture and sequencing of the coding exons of 20,000 protein coding genes utilizing next-generation sequencing technologies to more comprehensively investigate ccRCC somatic genetics. This work identified a second major somatically mutated cancer gene in ccRCC and thus substantially reshaped the field of RCC genetics. Truncating mutations in the PBRM1
gene were identified in a remarkable 41% (92/227) of ccRCC [20
encodes the Baf180 protein, a chromatin targeting subunit of the SWI/SNF chromatin remodeling complex implicated in multiple chromatin/transcriptionally mediated processes through interaction with histone H3 [21
], reinforcing the striking theme of deregulated chromatin in ccRCC biology. Of note, VHL, SETD2
are all located on chromosome 3p, thus providing a likely explanation for the near pathognomonic loss of 3p seen in ccRCC. Indeed, half of all cases with a demonstrable VHL
point mutation in this series have a PBRM1
truncating mutation and 9/9 cases with a SETD2
mutation also have concurrent VHL
mutations. This work has framed important new areas for ccRCC basic and clinical research.
Recent work performing deep sequencing on samples from a variety of locations from individual large tumors and metastatic lesions shows that considerable heterogeneity exists within these tumors suggesting a branched pattern of evolution [23
]. Mutational events, such as the VHL mutation among others were ubiquitous to all samples, however, certain mutations were present only in either the primary tumor or the metastatic lesions, and many mutations were private. Of particular interest, different phylogenetic branches demonstrated distinct SETD2 mutations, indicating a convergent pattern of selection for certain genotypic events. More work to understand this process, and the implications for biomarker development is needed.
Given the findings of these recent studies, it is a certainty that other RCC cancer genes and driver mutations remain to be identified. To this end, there are international efforts underway (ICGC www.icgc.org
and TCGA cancergenome.nih.gov
) to sequence large numbers of RCC at the whole genome level, coupled with transcriptomic and epigenomic analyses. This work is proceeding at pace, and thus the comprehensive structure of RCC somatic architecture will be revealed in the coming few years.