SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair.
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.
UCL Cancer Institute, Paul O'Gorman Building, London, UK.
N
N
Kanu
Cancer Research UK London Research Institute, London, UK.
E
E
Grönroos
Cancer Research UK London Research Institute, London, UK.
P
P
Martinez
Cancer Research UK London Research Institute, London, UK.
R A
RA
Burrell
Cancer Research UK London Research Institute, London, UK.
X
X
Yi Goh
Danish Cancer Society Research Center, Copenhagen, Denmark.
J
J
Bartkova
Danish Cancer Society Research Center, Copenhagen, Denmark.
A
A
Maya-Mendoza
Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic.
M
M
Mistrík
Cancer Research UK London Research Institute, London, UK.
A J
AJ
Rowan
Cancer Research UK London Research Institute, London, UK.
H
H
Patel
Cancer Research UK London Research Institute, London, UK.
A
A
Rabinowitz
Cancer Research UK London Research Institute, London, UK.
P
P
East
Cancer Research UK London Research Institute, London, UK.
G
G
Wilson
Cancer Research UK London Research Institute, London, UK.
C R
CR
Santos
Cancer Research UK London Research Institute, London, UK.
N
N
McGranahan
Cancer Research UK London Research Institute, London, UK.
S
S
Gulati
Cancer Research UK London Research Institute, London, UK.
M
M
Gerlinger
UCL Cancer Institute, Paul O'Gorman Building, London, UK.|Cancer Research UK London Research Institute, London, UK.|Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
N J
NJ
Birkbak
Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
T
http://orcid.org/0000-0002-0939-2982
T
Joshi
Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, UK.
L B
LB
Alexandrov
Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, UK.
M R
MR
Stratton
Barts Cancer Institute, Experimental Cancer Medicine Centre, Queen Mary University of London, London, UK.
T
T
Powles
Cancer Research UK London Research Institute, London, UK.
N
N
Matthews
Cancer Research UK London Research Institute, London, UK.
P A
PA
Bates
Cancer Research UK London Research Institute, London, UK.
A
A
Stewart
Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.|Children's Hospital Boston, Informatics-Enders 1506, Boston, MA, USA.
Z
Z
Szallasi
Department of Medicine, The Royal Marsden Hospital, London, UK.
J
J
Larkin
Danish Cancer Society Research Center, Copenhagen, Denmark.|Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic.
J
J
Bartek
UCL Cancer Institute, Paul O'Gorman Building, London, UK.|Cancer Research UK London Research Institute, London, UK.
C
C
Swanton
D002292:Carcinoma, Renal Cell / Q000235:genetics* / Q000378:metabolism; D045744:Cell Line, Tumor; D004260:DNA Repair; D004261:DNA Replication; D018740:Genetic Heterogeneity; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics* / Q000378:metabolism*; D006657:Histones / Q000378:metabolism; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics* / Q000378:metabolism; D053842:Microsatellite Instability; D009154:Mutation; D009707:Nucleosomes / Q000473:pathology
D006657:Histones; D009707:Nucleosomes; D011495:Histone-Lysine N-Methyltransferase; C521636:SETD2 protein, human