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Ibragimova I , Maradeo ME , Dulaimi E , Cairns P
Aberrant promoter hypermethylation of PBRM1, BAP1, SETD2, KDM6A and other chromatin-modifying genes is absent or rare in clear cell RCC
Epigenetics. 2013 May;8(5) :486-93
PMID: 23644518    PMCID: PMC3741218    URL: https://www.ncbi.nlm.nih.gov/pubmed/23644518
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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.
Notes
Ibragimova, Ilsiya Maradeo, Marie E Dulaimi, Essel Cairns, Paul eng Research Support, N.I.H., Extramural Epigenetics. 2013 May;8(5):486-93. doi: 10.4161/epi.24552. Epub 2013 May 1.