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SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair.

Kanu N, Grönroos E, Martinez P, Burrell RA, Yi Goh X, Bartkova J, Maya-Mendoza A, Mistrík M, Rowan AJ, Patel H, Rabinowitz A, East P, Wilson G, Santos CR, McGranahan N, Gulati S, Gerlinger M, Birkbak NJ, Joshi T, Alexandrov LB, Stratton MR, Powles T, Matthews N, Bates PA, Stewart A, Szallasi Z, Larkin J, Bartek J, Swanton C - Oncogene (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: UCL Cancer Institute, Paul O'Gorman Building, London, UK.

ABSTRACT
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.

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(a) Proportion of samples showing LOH along chromosome 3 using SNP 6.0 array data in 450 RCCs from TCGA. The genomic loci of VHL, SETD2 and PBRM1 are indicated. (b) Schematic of the locations of mutations reported in the SETD2 gene from published studies (2–5). Arrows indicate distinct mutations found within spatially separated regions of the same tumour.4
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fig1: (a) Proportion of samples showing LOH along chromosome 3 using SNP 6.0 array data in 450 RCCs from TCGA. The genomic loci of VHL, SETD2 and PBRM1 are indicated. (b) Schematic of the locations of mutations reported in the SETD2 gene from published studies (2–5). Arrows indicate distinct mutations found within spatially separated regions of the same tumour.4

Mentions: SETD2 is encoded on chromosome 3, and 3p LOH has previously been reported to be an early event in RCC.12, 13 In all, 98.8% (391/396) of TCGA samples with LOH at the VHL locus (3p25.3) also displayed LOH at the SETD2 locus (3p21.31) (Figure 1a and Supplementary Table S1). Non-synonymous SETD2 mutations or homozygous SETD2 deletions were found in 34 samples (Figure 1b), with paired DNA copy number data available for 30 samples. In total, 93.3% of these cases (28/30) showed LOH at the SETD2 locus. Ten of the 28 mutations were missense mutations (five were in the SET domain, one in the SRI domain and four in uncharacterized regions of the protein). One sample harboured homozygous deletion of SETD2. Therefore in total, both SETD2 alleles were mutated or deleted in 29 samples, collectively referred to as SETD2mut. The 210 samples with LOH at the SETD2 locus but no mutation of the gene are referred to as SETD2LOH.


SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair.

Kanu N, Grönroos E, Martinez P, Burrell RA, Yi Goh X, Bartkova J, Maya-Mendoza A, Mistrík M, Rowan AJ, Patel H, Rabinowitz A, East P, Wilson G, Santos CR, McGranahan N, Gulati S, Gerlinger M, Birkbak NJ, Joshi T, Alexandrov LB, Stratton MR, Powles T, Matthews N, Bates PA, Stewart A, Szallasi Z, Larkin J, Bartek J, Swanton C - Oncogene (2015)

(a) Proportion of samples showing LOH along chromosome 3 using SNP 6.0 array data in 450 RCCs from TCGA. The genomic loci of VHL, SETD2 and PBRM1 are indicated. (b) Schematic of the locations of mutations reported in the SETD2 gene from published studies (2–5). Arrows indicate distinct mutations found within spatially separated regions of the same tumour.4
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4660036&req=5

fig1: (a) Proportion of samples showing LOH along chromosome 3 using SNP 6.0 array data in 450 RCCs from TCGA. The genomic loci of VHL, SETD2 and PBRM1 are indicated. (b) Schematic of the locations of mutations reported in the SETD2 gene from published studies (2–5). Arrows indicate distinct mutations found within spatially separated regions of the same tumour.4
Mentions: SETD2 is encoded on chromosome 3, and 3p LOH has previously been reported to be an early event in RCC.12, 13 In all, 98.8% (391/396) of TCGA samples with LOH at the VHL locus (3p25.3) also displayed LOH at the SETD2 locus (3p21.31) (Figure 1a and Supplementary Table S1). Non-synonymous SETD2 mutations or homozygous SETD2 deletions were found in 34 samples (Figure 1b), with paired DNA copy number data available for 30 samples. In total, 93.3% of these cases (28/30) showed LOH at the SETD2 locus. Ten of the 28 mutations were missense mutations (five were in the SET domain, one in the SRI domain and four in uncharacterized regions of the protein). One sample harboured homozygous deletion of SETD2. Therefore in total, both SETD2 alleles were mutated or deleted in 29 samples, collectively referred to as SETD2mut. The 210 samples with LOH at the SETD2 locus but no mutation of the gene are referred to as SETD2LOH.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: UCL Cancer Institute, Paul O'Gorman Building, London, UK.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus