Mutations in SETD2, a
histone H3 lysine trimethyltransferase, have been identified in
clear cell renal cell carcinoma (ccRCC); however it is unclear if loss of SETD2 function alters the genomic distribution of
histone 3
lysine 36 trimethylation (H3K36me3) in ccRCC. Furthermore, published epigenomic profiles are not specific to H3K36me3 or metastatic
tumors. To determine if progressive SETD2 and H3K36me3 dysregulation occurs in metastatic
tumors, H3K36me3, SETD2 copy number (CN) or SETD2
mRNA abundance was assessed in two independent cohorts: metastatic ccRCC (n=71) and the
Cancer Genome Atlas Kidney Renal Clear Cell
Carcinoma data set (n=413). Although SETD2 CN loss occurs with high frequency (>90%), H3K36me3 is not significantly impacted by monoallelic loss of SETD2. H3K36me3-positive nuclei were reduced an average of ~20% in primary ccRCC (90% positive nuclei in uninvolved vs 70% positive nuclei in ccRCC) and reduced by ~60% in
metastases (90% positive in uninvolved kidney vs 30% positive in
metastases) (P<0.001). To define a kidney-specific H3K36me3 profile, we generated genome-wide H3K36me3 profiles from four cytoreductive
nephrectomies and SETD2 isogenic
renal cell carcinoma (RCC) cell lines using
chromatin immunoprecipitation coupled with high-throughput
DNA sequencing and
RNA sequencing. SETD2 loss of
methyltransferase activity leads to regional alterations of H3K36me3 associated with aberrant RNA splicing in a SETD2 mutant RCC and SETD2 knockout cell line. These data suggest that during progression of ccRCC, a decline in H3K36me3 is observed in distant
metastases, and regional H3K36me3 alterations influence alternative splicing in ccRCC.