CpG methylation profiling in VHL related and VHL unrelated renal cell carcinoma

• Published in: Molecular cancer Vol. 8; no. 31; p. 31
• Main Authors: McRonald, Fiona E, Morris, Mark R, Gentle, Dean, Winchester, Laura, Baban, Dilair, Ragoussis, Jiannis, Clarke, Noel W, Brown, Michael D, Kishida, Takeshi, Yao, Masahiro, Latif, Farida, Maher, Eamonn R
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 03-06-2009; BioMed Central; BMC
• Subjects: Adult; Aged; Biological markers; Carcinoma, Renal cell; Carcinoma, Renal Cell - genetics; Care and treatment; Cluster Analysis; CpG Islands - genetics; DNA Methylation; Epigenesis, Genetic; Gene Regulatory Networks; Genetic aspects; Health aspects; Humans; Kidney Neoplasms - complications; Kidney Neoplasms - genetics; Methylation; Middle Aged; Poisson Distribution; Reproducibility of Results; Risk factors; Statistics, Nonparametric; Transforming growth factors; von Hippel-Lindau Disease - genetics; United Kingdom
• ISSN: 1476-4598; 1476-4598
• DOI: 10.1186/1476-4598-8-31

Renal cell carcinoma (RCC) is histopathologically heterogeneous with clear cell and papillary the most common subtypes. The most frequent molecular abnormality in clear cell RCC is VHL inactivation but promoter methylation of tumour suppressor genes is common in both subtypes of RCC. To investigate whether RCC CpG methylation status was influenced by histopathology and VHL status we performed high-throughput epigenetic profiling using the Illumina Goldengate Methylation Array in 62 RCC (29 RCC from von Hippel-Lindau (VHL) disease patients, 20 sporadic clear cell RCC with wild type VHL and 13 sporadic papillary RCC).
43 genes were methylated in >20% of primary RCC (range 20-45%) and most (37/43) of these had not been reported previously to be methylated in RCC. The distribution of the number of methylated CpGs in individual tumours differed from the expected Poisson distribution (p < 0.00001; log-likelihood G test) suggesting that a subset of RCC displayed a CpG Island Methylator Phenotype. Comparison of RCC subtypes revealed that, on average, tumour specific CpG methylation was most prevalent in papillary RCC and least in VHL RCC. Many of the genes preferentially methylated in pRCC were linked to TGFbeta or ERK/Akt signalling.
These findings demonstrate differing patterns of tumour-specific CpG methylation in VHL and non VHL clear cell RCC and papillary RCC, and identify multiple novel potential CpG methylation biomarkers for RCC.