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Replication stress links structural and numerical cancer chromosomal instability

A Corrigendum to this article was published on 03 July 2013

Abstract

Cancer chromosomal instability (CIN) results in an increased rate of change of chromosome number and structure and generates intratumour heterogeneity1,2. CIN is observed in most solid tumours and is associated with both poor prognosis and drug resistance3,4. Understanding a mechanistic basis for CIN is therefore paramount. Here we find evidence for impaired replication fork progression and increased DNA replication stress in CIN+ colorectal cancer (CRC) cells relative to CIN CRC cells, with structural chromosome abnormalities precipitating chromosome missegregation in mitosis. We identify three new CIN-suppressor genes (PIGN (also known as MCD4), MEX3C (RKHD2) and ZNF516 (KIAA0222)) encoded on chromosome 18q that are subject to frequent copy number loss in CIN+CRC. Chromosome 18q loss was temporally associated with aneuploidy onset at the adenoma–carcinoma transition. CIN-suppressor gene silencing leads to DNA replication stress, structural chromosome abnormalities and chromosome missegregation. Supplementing cells with nucleosides, to alleviate replication-associated damage5, reduces the frequency of chromosome segregation errors after CIN-suppressor gene silencing, and attenuates segregation errors and DNA damage in CIN+ cells. These data implicate a central role for replication stress in the generation of structural and numerical CIN, which may inform new therapeutic approaches to limit intratumour heterogeneity.

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Figure 1: Replication stress generates chromosome segregation errors in CIN + cells.
Figure 2: Somatic copy number loss of chromosome 18q in CIN + CRC.
Figure 3: Candidate suppressors of replication stress and CIN encoded on chromosome 18q.
Figure 4: Nucleoside supplementation reduces segregation error frequency and prometaphase DNA damage.

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Acknowledgements

We thank A. Straube for reagents. C.S. is a senior Medical Research Council clinical research fellow and is funded by Cancer Research UK, the Medical Research Council, EU FP7 (projects PREDICT and RESPONSIFY), Prostate Cancer Foundation, and the Breast Cancer Research Foundation. We thank A. Futreal and The Wellcome Trust Sanger Centre and The Cancer Genome Atlas Research Network for providing genomics data. I.P.T. is supported by the Oxford Biomedical Research Centre and Cancer Research UK. J.B. is funded by the Danish Cancer Society, the Lundbeck Foundation, and the European Commission (FP7 projects DDResponse, Biomedreg and Infla-Care). T.H. is funded by the Swedish Cancer Society, the Swedish Research Council and the Torsten and Ragnar Söderberg Foundation.

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Contributions

C.S., R.A.B., S.E.M., J.B. and T.H. devised experiments. R.A.B. and S.E.M. performed most cell biological experiments with help from N.S., S.K.C., E.G., S.M.D., A.J.R. and N.K. D.E., A.S. and M.S. performed bioinformatics analysis supervised by M.K. P.G., M.-C.W. and T.H. performed and analysed the DNA fibre assays. E.D. and I.P.T. provided the adenoma-in-carcinoma cohort and CGH for aneuploid tumours. M.H. and A.B. provided experimental advice. C.S. supervised all aspects of the project. C.S., R.A.B., S.E.M., I.P.T. and J.B. wrote the paper. All authors discussed results and approved the manuscript.

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Correspondence to Charles Swanton.

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This file contains Supplementary Figures 1-14; Supplementary Tables 1, 4, 6 and 7; legends for Supplementary Tables 2, 3 and 5; Supplementary References and a Supplementary Sweave document. (PDF 5025 kb)

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Burrell, R., McClelland, S., Endesfelder, D. et al. Replication stress links structural and numerical cancer chromosomal instability. Nature 494, 492–496 (2013). https://doi.org/10.1038/nature11935

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