Aberrant promoter hypermethylation of PBRM1, BAP1, SETD2, KDM6A and other chromatin-modifying genes is absent or rare in clear cell RCC

Abstract

Recent sequencing studies of clear cell (conventional) renal cell carcinoma (ccRCC) have identified inactivating point mutations in the chromatin-modifying genes PBRM1, KDM6A/UTX, KDM5C/JARID1C, SETD2, MLL2 and BAP1. To investigate whether aberrant hypermethylation is a mechanism of inactivation of these tumor suppressor genes in ccRCC, we sequenced the promoter region within a bona fide CpG island of PBRM1, KDM6A, SETD2 and BAP1 in bisulfite-modified DNA of a representative series of 50 primary ccRCC, 4 normal renal parenchyma specimens and 5 RCC cell lines. We also interrogated the promoter methylation status of KDM5C and ARID1A in the Cancer Genome Atlas (TCGA) ccRCC Infinium data set. PBRM1, KDM6A, SETD2 and BAP1 were unmethylated in all tumor and normal specimens. KDM5C and ARID1A were unmethylated in the TCGA 219 ccRCC and 119 adjacent normal specimens. Aberrant promoter hypermethylation of PBRM1, BAP1 and the other chromatin-modifying genes examined here is therefore absent or rare in ccRCC.

Keywords: :

• PBRM1
• BAP1
• SETD2
• KDM6A
• KDM5C
• MLL2
• ARID1A
• renal cell carcinoma
• clear cell RCC
• promoter methylation

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

We thank Kirill Yudin for writing script to generate the schematic of CpG islands in Figure 1, Emmanuelle Nicolas PhD, Genetic Research Facility at FCCC, for design and optimization of BAP1 pyrosequencing, Suraj Peri PhD, Department of Biostatistics at FCCC for help with TSS data in Ensembl and Andrew Kossenkov PhD, Director of Bioinformatics at the Wistar Institute, Philadelphia for help with the interrogation of TCGA data. This publication was supported in part by grant number P30 CA006927 from the National Cancer Institute. Its contents are solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute or the National Institutes of Health. Additional funds were provided by Fox Chase Cancer Center via institutional support of the Kidney Keystone Program.