PRC target genes are overrepresented in the renal cancer methylome.

<p>Proportion of PRC target genes among genes hypermethylated in renal cancer compared to ∼4% with 3 marks or 9.5% with 1 or more marks in human ES cells from Lee et al 2006 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077309#pone.0077309-Lee1" target="_blank">[48]</a>.</p

Genome-Wide Promoter Methylome of Small Renal Masses

<div><p>The majority of renal cell carcinoma (RCC) is now incidentally detected and presents as small renal masses (SRMs) defined as ≤4 cm in size. SRMs are heterogeneous comprising several histological types of RCC each with different biology and behavior, and benign tumors mainly oncocytoma. The varied prognosis of the different types of renal tumor has implications for management options. A key epigenetic alteration involved in the initiation and progression of cancer is aberrant methylation in the promoter region of a gene. The hypermethylation is associated with transcriptional repression and is an important mechanism of inactivation of tumor suppressor genes in neoplastic cells. We have determined the genome-wide promoter methylation profiles of 47 pT1a and 2 pT1b clear cell, papillary or chromophobe RCC, 25 benign renal oncocytoma ≤4 cm and 4 normal renal parenchyma specimens by Infinium HumanMethylation27 beadchip technology. We identify gene promoter hypermethylation signatures that distinguish clear cell and papillary from each other, from chromophobe and oncocytoma, and from normal renal cells. Pairwise comparisons revealed genes aberrantly hypermethylated in a tumor type but unmethylated in normal, and often unmethylated in the other renal tumor types. About 0.4% to 1.7% of genes comprised the promoter methylome in SRMs. The Infinium methylation score for representative genes was verified by gold standard technologies. The genes identified as differentially methylated implicate pathways involved in metabolism, tissue response to injury, epithelial to mesenchymal transition (EMT), signal transduction and G-protein coupled receptors (GPCRs), cancer, and stem cell regulation in the biology of RCC. Our findings contribute towards an improved understanding of the development of RCC, the different biology and behavior of histological types, and discovery of molecular subtypes. The differential methylation signatures may have utility in early detection and particularly differential diagnosis for prognostic stratification as well as identify novel gene and pathway targets for therapeutic intervention.</p></div

Venn diagram of the number of aberrantly hypermethylated genes in each renal tumor type compared to NRP.

<p>Venn diagram of the number of aberrantly hypermethylated genes in each renal tumor type compared to NRP.</p

Barplots of genes aberrantly hypermethylated in RCC or oncocytoma.

<p>Y axis is Infinium β-value. Tumors above the horizontal blue line (delta β 0.2> mean of NRP) are hypermethylated for the gene compared to the unmethylated (β<0.15) 4 NRP. The gene name and Infinium probe ID are given above each barplot.</p

Unsupervised clustering analysis of the most differentially methylated probes.

<p>74 renal tumors and 4 NRP identified by color top right. Top left is color scale unmethylated yellow (β = 0) - methylated blue (β = 1).</p

Barplots of genes differentially methylated between tumor types.

<p>Y axis is Infinium β-value. For each gene, tumors above the horizontal blue line (delta β 0.2> mean of comparison tumor type) are hypermethylated in the tumor type but unmethylated (β<0.15) in the comparison tumor type.</p

Verification of Infinium methylation score by pyrosequencing.

<p>A) Pyrograms of GRIK1 CpG loci hypermethylated in a ccRCC but unmethylated in an oncocytoma and NRP, B) Correlation between Infinium methylation score and pyrosequencing. The R² is the Pearson coefficient. Circled red, gray, and black points correspond to ccRCC, oncocytoma, and NRP specimens respectively shown in A).</p