NSD1 Inactivation and SETD2 Mutation Drive a Convergence toward Loss of Function of H3K36 Writers in Clear Cell Renal Cell Carcinomas

Abstract

Extensive dysregulation of chromatin-modifying genes in dear cell renal cell carcinoma (ccRCC) has been uncovered through next-generation sequencing. However, a scientific understanding of the cross-talk between epigenetic and genomic aberrations remains limited. Here we identify three ccRCC epigenetic clusters, including a clear cell CpG island methylatorphenotype (C-CIMP) subgroup associated with promoter methylation of VEGF genes (FLT4, FLT1, and KDR). C-CIMP was furthermore characterized by silencing of genes related to vasculature development. Through an integrative analysis, we discovered frequent silencing of the his-tone H3 K36 methyltransferase NSD1 as the sole chromatin-modifying gene silenced by DNA methylation in ccRCC. Notably, tumors harboring NSD1 methylation were of higher grade and stage in different ccRCC datasets. NSD1 promoter methylation correlated with SETD2 somatic mutations across and within spatially distinct regions of primary ccRCC tumors. ccRCC harboring epigenetic silencing of NSD1 displayed a specific genome-wide methylome signature consistent with the NSD1 mutation methylome signature observed in Sotos syndrome. Thus, we concluded that epigenetic silencing of genes involved in angio-genesis is a hallmark of the methylator phenotype in ccRCC, implying a convergence toward loss of function of epigenetic writers of the H3K36 histone mark as a root feature of aggressive ccRCC.

Molecular characterization of sarcomatoid clear cell renal cell carcinoma unveils new candidate oncogenic drivers

“…In addition to recurrent mutations of BAP1, PBRM1 and SETD2 previously described, we found mutations of SWI/SNF members ARID1B in 3 samples and ARID1A in one, as well as mutations of epigenetic regulators KDM6A (4%), MLL (4%), ASXL1 (4%), NSD1 (4%), DNMT3A (2%), MLL2 (2%) and MLL3 (2%). Notably, 2 paired epithelial and mesenchymal samples from one tumour presented with convergent mutations of SETD2 and NSD1, which have been described to be associated with an aggressive phenotype in ccRCC 9 . Other frequent alterations involved the MTOR pathway (25/50, 50%), DNA repair (15/50, 30%) and the Hippo pathway (10/50, 20%).…”

Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition

“…Thus, the regulation of SETD2 levels through intrinsically disordered region-facilitated proteolysis is important to maintain the fidelity of transcription and splicing related processes. gene coding for the SETD2 histone methyltransferase is often deleted or mutated )(Su et al, 2017)(Li et al, 2016.In yeast, the SET domain-containing protein Set2 (ySet2) is the sole H3K36 methyltransferase (Strahl et al, 2002). ySet2 interacts with the large subunit of the RNA polymerase II, Rpb1, through its SRI domain, and co-transcriptionally deposits H3K36me3 (Xiao et al, 2003).…”

“…Thus, the regulation of SETD2 levels through intrinsically disordered region-facilitated proteolysis is important to maintain the fidelity of transcription and splicing related processes. gene coding for the SETD2 histone methyltransferase is often deleted or mutated )(Su et al, 2017)(Li et al, 2016.…”

Integrated Genomic and Proteomic Analyses Reveal Novel Mechanisms of the Methyltransferase SETD2 in Renal Cell Carcinoma Development

“…SETD2 is known to be frequently mutated in ccRCC; however, there were limited analyses about the genetic and proteomic alterations elicited by deficiency in SETD2 (1,3,39,40). Here we embarked on a systematic, multi-pronged approach to elucidate the perturbations in genome-wide occupancies of two relevant histone epigenetic marks (H3K36me3 and H4K16ac), mRNA transcriptome and chromatin-bound proteins evoked by SETD2 depletion.…”