Defining mechanisms that generate intratumour heterogeneity and branched evolution may inspire novel therapeutic approaches to limit tumour diversity and adaptation. SETD2 (Su(var), Enhancer of zeste, Trithorax-domain containing 2) trimethylates histone-3 lysine-36 (H3K36me3) at sites of active transcription and is mutated in diverse tumour types, including clear cell renal carcinomas (ccRCCs). Distinct SETD2 mutations have been identified in spatially separated regions in ccRCC, indicative of intratumour heterogeneity. In this study, we have addressed the consequences of SETD2 loss-of-function through an integrated bioinformatics and functional genomics approach. We find that bi-allelic SETD2 aberrations are not associated with microsatellite instability in ccRCC. SETD2 depletion in ccRCC cells revealed aberrant and reduced nucleosome compaction and chromatin association of the key replication proteins minichromosome maintenance complex component (MCM7) and DNA polymerase δ hindering replication fork progression, and failure to load lens epithelium-derived growth factor and the Rad51 homologous recombination repair factor at DNA breaks. Consistent with these data, we observe chromosomal breakpoint locations are biased away from H3K36me3 sites in SETD2 wild-type ccRCCs relative to tumours with bi-allelic SETD2 aberrations and that H3K36me3-negative ccRCCs display elevated DNA damage in vivo. These data suggest a role for SETD2 in maintaining genome integrity through nucleosome stabilization, suppression of replication stress and the coordination of DNA repair.

Barts Cancer Institute Experimental Cancer Medicine Centre Queen Mary University of London London UK

Cancer Genome Project Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridgeshire UK

Cancer Research UK London Research Institute London UK

Children's Hospital Boston Informatics Enders 1506 Boston MA USA

Danish Cancer Society Research Center Copenhagen Denmark

Department of Medicine The Royal Marsden Hospital London UK

Department of Systems Biology Center for Biological Sequence Analysis Technical University of Denmark Kongens Lyngby Denmark

Faculty of Medicine and Dentistry Institute of Molecular and Translational Medicine Palacky University Olomouc Czech Republic

UCL Cancer Institute Paul O'Gorman Building London UK

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Nat Rev Urol. 2015 Apr;12(4):183. doi: 10.1038/nrurol.2015.53. PubMed

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