Single-cell exome sequencing of a ccRCC sample

Recent advances in DNA sequencing have led to the discovery of genes and mutations which drive tumourigenesis. In this blog, we have previously described papers by Varela et al. (2011), Dalgliesh et al. (2011) and Guo et al. (2011) which all used exome sequencing to identify genes involved in kidney cancer (described here, here and here respectively). It is hoped that by understanding more about the cancer genome, effective targeted therapies can be developed.

A recent study by Xu et al. (2012) performed sequencing analysis on one ccRCC kidney tumour sample, this time by using single-cell exome sequencing. Exome sequencing was first used on a sample of ccRCC tissue to analyse the mutational status of VHL and PBRM1, the main drivers of ccRCC tumourigenesis. Three low frequency mutations in PBRM1 were identified, but no mutations were found in VHL.

Single-cell exome sequencing was then performed on 20 cells from the tumour sample and 5 cells from noncancerous adjacent tissue, which were used as controls. In total, 260 somatic mutations were identified in the cancer cells, compared with 12 somatic mutations in the healthy control cells. Mutations in 94 genes were identified.

The mutation pattern for each individual cell was compared and the results were found to be significantly different from each other. The authors therefore suggest that the tumour does not contain subpopulations of cells. Additionally, more than 70% of the mutations were classed as cell-specific, meaning they only occurred in a small fraction of the cells. Both of these results demonstrate the high complexity and heterogeneity of this tumour sample.

The results from this study were compared to the recent sequencing study by Guo et al. (2011). Four of the 94 genes identified here were also mutated in the cohort of 98 patients studied by Guo et al. One gene of particular interest is AHNAK, which was mutated in 5 of the 99 patients from both studies. AHNAK activates protein kinase C and it is also involved in chromatin remodelling, a process in which related genes appear to be frequently mutated in RCC. Furthermore, protein-protein prediction methods used in this study suggest an interaction between AHNAK and HIF1A.

With regards to BHD syndrome, no FLCN mutations were identified in the RCC cells studied here. However, it would be interesting to perform a similar study using cells from a BHD tumour to identify other mutations which could contribute to tumourigenesis in BHD syndrome. The authors of this study suggest that ccRCC is more genetically complex than previously thought. Perhaps the same is true for BHD-related tumours and that there are other, as yet, unidentified mutations which promote tumourigenesis.


  • Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, Li F, Tsang S, Wu K, Wu H, He W, Zeng L, Xing M, Wu R, Jiang H, Liu X, Cao D, Guo G, Hu X, Gui Y, Li Z, Xie W, Sun X, Shi M, Cai Z, Wang B, Zhong M, Li J, Lu Z, Gu N, Zhang X, Goodman L, Bolund L, Wang J, Yang H, Kristiansen K, Dean M, Li Y, & Wang J (2012). Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell, 148 (5), 886-95 PMID: 22385958
  • Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J, Bignell G, Butler A, Cho J, Dalgliesh GL, Galappaththige D, Greenman C, Hardy C, Jia M, Latimer C, Lau KW, Marshall J, McLaren S, Menzies A, Mudie L, Stebbings L, Largaespada DA, Wessels LF, Richard S, Kahnoski RJ, Anema J, Tuveson DA, Perez-Mancera PA, Mustonen V, Fischer A, Adams DJ, Rust A, Chan-on W, Subimerb C, Dykema K, Furge K, Campbell PJ, Teh BT, Stratton MR, & Futreal PA (2011). Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature, 469 (7331), 539-42 PMID: 21248752
  • Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, Davies H, Edkins S, Hardy C, Latimer C, Teague J, Andrews J, Barthorpe S, Beare D, Buck G, Campbell PJ, Forbes S, Jia M, Jones D, Knott H, Kok CY, Lau KW, Leroy C, Lin ML, McBride DJ, Maddison M, Maguire S, McLay K, Menzies A, Mironenko T, Mulderrig L, Mudie L, O’Meara S, Pleasance E, Rajasingham A, Shepherd R, Smith R, Stebbings L, Stephens P, Tang G, Tarpey PS, Turrell K, Dykema KJ, Khoo SK, Petillo D, Wondergem B, Anema J, Kahnoski RJ, Teh BT, Stratton MR, & Futreal PA (2010). Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature, 463 (7279), 360-3 PMID: 20054297
  • Guo G, Gui Y, Gao S, Tang A, Hu X, Huang Y, Jia W, Li Z, He M, Sun L, Song P, Sun X, Zhao X, Yang S, Liang C, Wan S, Zhou F, Chen C, Zhu J, Li X, Jian M, Zhou L, Ye R, Huang P, Chen J, Jiang T, Liu X, Wang Y, Zou J, Jiang Z, Wu R, Wu S, Fan F, Zhang Z, Liu L, Yang R, Liu X, Wu H, Yin W, Zhao X, Liu Y, Peng H, Jiang B, Feng Q, Li C, Xie J, Lu J, Kristiansen K, Li Y, Zhang X, Li S, Wang J, Yang H, Cai Z, & Wang J (2011). Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nature genetics, 44 (1), 17-9 PMID: 22138691

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