Kidney Cancer Is Characterized by Aberrant Methylation of Tissue-Specific Enhancers That Are Prognostic for Overall Survival

Abstract

Purpose Even though recent studies have shown that genetic changes at enhancers can influence carcinogenesis, most methylomic studies have focused on changes at promoters. We used renal cell carcinoma (RCC), an incurable malignancy associated with mutations in epigenetic regulators, as a model to study genome wide patterns of DNA methylation at a high resolution. Experimental Design and Results Analysis of 1.3 million CpGs by the HELP assay in RCC and healthy microdissected renal tubular controls demonstrated that the RCC samples were characterized by widespread hypermethylation that preferentially affected gene bodies. Aberrant methylation was particularly enriched in kidney specific enhancer regions associated with H3K4Me1 marks. Various important underexpressed genes such as SMAD6 were associated with aberrantly methylated, intronic enhancers and these changes were validated in an independent cohort. MOTIF analysis of aberrantly hypermethylated regions revealed enrichment for binding sites of AP2alpha, AHR, HAIRY, ARNT and HIF-1 transcription factors, reflecting contributions of dysregulated hypoxia signaling pathways in RCC. The functional importance of this aberrant hypermethylation was demonstrated by selective sensitivity of RCC cells to low levels of decitabine. Most importantly, methylation of enhancers was predictive of adverse prognosis in 405 cases of RCC in multivariate analysis. Additionally, parallel copy number analysis from MspI representations demonstrated novel cnvs that were validated in independent cohort of patients. Conclusions Our study is the first high resolution methylome analysis of RCC; demonstrates that many kidney specific enhancers are targeted by aberrant hypermethylation and reveals the prognostic importance of these epigenetic changes in an independent cohort.

Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer

“…Our studies showed that widespread DNA methylation changes could be seen in CCRCC and affect enhancer regions of the kidney genome. We also observed both novel and well characterized genomic copy numbers changes in these CCRCC samples (8) that were also seen in a large TCGA cohort of CCRCC samples. Analysis of differentially methylated regions in CCRCC in our study revealed enrichment for binding sites of HAIRY transcription factor.…”

“…We developed an integrated epigenomics platform and used it to study CCRCC samples (8). Our studies showed that widespread DNA methylation changes could be seen in CCRCC and affect enhancer regions of the kidney genome.…”

Human Schlafen 5 (SLFN5) Is a Regulator of Motility and Invasiveness of Renal Cell Carcinoma Cells

“…We analyzed a recently obtained RNA-seq data set of 470 RCC samples and compared the data to 68 nontumor control kidney samples (28,31). Although SLFN5 was significantly overexpressed in RCC samples (t test, P value ϭ 2 ϫ 10 Ϫ6 ) (Fig.…”

“…These included 470 RCC samples and 68 nontumor kidney controls. KaplanMeier curves were used for survival analysis as in previous studies (28).…”

The epigenetic landscape of renal cancer

“…133) showed that distant regulatory enhancers also undergo CpG methylation. Enhancer methylation in RCC has been analysed at the genome scale, and one study in particular identified an enrichment of aberrant enhancer methylation associated with networks involved in the cellular response to hypoxia 134 . This study also found that methylation of enhancers correlated with poor prognosis.…”