Abstract
Improved sequencing technologies offer unprecedented opportunities for investigating the role of rare genetic variation in common disease. However, there are considerable challenges with respect to study design, data analysis and replication1. Using pooled next-generation sequencing of 507 genes implicated in the repair of DNA in 1,150 samples, an analytical strategy focused on protein-truncating variants (PTVs) and a large-scale sequencing case–control replication experiment in 13,642 individuals, here we show that rare PTVs in the p53-inducible protein phosphatase PPM1D are associated with predisposition to breast cancer and ovarian cancer. PPM1D PTV mutations were present in 25 out of 7,781 cases versus 1 out of 5,861 controls (P = 1.12 × 10−5), including 18 mutations in 6,912 individuals with breast cancer (P = 2.42 × 10−4) and 12 mutations in 1,121 individuals with ovarian cancer (P = 3.10 × 10−9). Notably, all of the identified PPM1D PTVs were mosaic in lymphocyte DNA and clustered within a 370-base-pair region in the final exon of the gene, carboxy-terminal to the phosphatase catalytic domain. Functional studies demonstrate that the mutations result in enhanced suppression of p53 in response to ionizing radiation exposure, suggesting that the mutant alleles encode hyperactive PPM1D isoforms. Thus, although the mutations cause premature protein truncation, they do not result in the simple loss-of-function effect typically associated with this class of variant, but instead probably have a gain-of-function effect. Our results have implications for the detection and management of breast and ovarian cancer risk. More generally, these data provide new insights into the role of rare and of mosaic genetic variants in common conditions, and the use of sequencing in their identification.
This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Analysis of clinical and genomic profiles of therapy-related myeloid neoplasm in Korea
Human Genomics Open Access 23 February 2023
-
Wip1 suppresses angiogenesis through the STAT3-VEGF signalling pathway in serous ovarian cancer
Journal of Ovarian Research Open Access 10 May 2022
-
The burden of rare protein-truncating genetic variants on human lifespan
Nature Aging Open Access 03 March 2022
Access options
Subscribe to this journal
Receive 51 print issues and online access
$199.00 per year
only $3.90 per issue
Rent or buy this article
Get just this article for as long as you need it
$39.95
Prices may be subject to local taxes which are calculated during checkout
References
Cirulli, E. T. & Goldstein, D. B. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nature Rev. Genet. 11, 415–425 (2010)
Turnbull, C. & Rahman, N. Genetic predisposition to breast cancer: past, present, and future. Annu. Rev. Genomics Hum. Genet. 9, 321–345 (2008)
Gayther, S. A. & Pharoah, P. D. The inherited genetics of ovarian and endometrial cancer. Curr. Opin. Genet. Dev. 20, 231–238 (2010)
Rahman, N. et al. PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nature Genet. 39, 165–167 (2007)
Renwick, A. et al. ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nature Genet. 38, 873–875 (2006)
Seal, S. et al. Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles. Nature Genet. 38, 1239–1241 (2006)
Meijers-Heijboer, H. et al. Low-penetrance susceptibility to breast cancer due to CHEK2*1100delC in noncarriers of BRCA1 or BRCA2 mutations. Nature Genet. 31, 55–59 (2002)
Meindl, A. et al. Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene. Nature Genet. 42, 410–414 (2010)
Loveday, C. et al. Germline RAD51C mutations confer susceptibility to ovarian cancer. Nature Genet. 44, 475–476 (2012)
Loveday, C. et al. Germline mutations in RAD51D confer susceptibility to ovarian cancer. Nature Genet. 43, 879–882 (2011)
Rivas, M. A. et al. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nature Genet. 43, 1066–1073 (2011)
Snape, K. et al. Predisposition gene identification in common cancers by exome sequencing: insights from familial breast cancer. Breast Cancer Res. Treat. 134, 429–433 (2012)
Caruccio, N. Preparation of next-generation sequencing libraries using Nextera technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition. Methods Mol. Biol. 733, 241–255 (2011)
Schouten, J. P. et al. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 30, e57 (2002)
Fiscella, M. et al. Wip1, a novel human protein phosphatase that is induced in response to ionizing radiation in a p53-dependent manner. Proc. Natl Acad. Sci. USA 94, 6048–6053 (1997)
Lu, X. et al. The type 2C phosphatase Wip1: an oncogenic regulator of tumor suppressor and DNA damage response pathways. Cancer Metastasis Rev. 27, 123–135 (2008)
Lu, X., Nguyen, T. A. & Donehower, L. A. Reversal of the ATM/ATR-mediated DNA damage response by the oncogenic phosphatase PPM1D. Cell Cycle 4, 4060–4064 (2005)
Shreeram, S. et al. Regulation of ATM/p53-dependent suppression of myc-induced lymphomas by Wip1 phosphatase. J. Exp. Med. 203, 2793–2799 (2006)
Fujimoto, H. et al. Regulation of the antioncogenic Chk2 kinase by the oncogenic Wip1 phosphatase. Cell Death Differ. 13, 1170–1180 (2006)
Bulavin, D. V. et al. Amplification of PPM1D in human tumors abrogates p53 tumor-suppressor activity. Nature Genet. 31, 210–215 (2002)
Natrajan, R. et al. Tiling path genomic profiling of grade 3 invasive ductal breast cancers. Clin. Cancer Res. 15, 2711–2722 (2009)
Tan, D. S. et al. PPM1D is a potential therapeutic target in ovarian clear cell carcinomas. Clin. Cancer Res. 15, 2269–2280 (2009)
Rayter, S. et al. A chemical inhibitor of PPM1D that selectively kills cells overexpressing PPM1D. Oncogene 27, 1036–1044 (2008)
Hayashi, R. et al. Optimization of a cyclic peptide inhibitor of Ser/Thr phosphatase PPM1D (Wip1). Biochemistry 50, 4537–4549 (2011)
Chuman, Y. et al. PPM1D430, a novel alternative splicing variant of the human PPM1D, can dephosphorylate p53 and exhibits specific tissue expression. J. Biochem. 145, 1–12 (2009)
Silva, A. L., Ribeiro, P., Inacio, A., Liebhaber, S. A. & Romao, L. Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay. RNA 14, 563–576 (2008)
Jacobs, K. B. et al. Detectable clonal mosaicism and its relationship to aging and cancer. Nature Genet. 44, 651–658 (2012)
Laurie, C. C. et al. Detectable clonal mosaicism from birth to old age and its relationship to cancer. Nature Genet. 44, 642–650 (2012)
Barnes, D. R. et al. Evaluation of assosciation methods for analysing modifiers of disease risk in carriers of high risk mutations. Genet. Epidemiol. 36, 274–291 (2012)
Antoniou, A. C. & Easton, D. F. Polygenic inheritance of breast cancer: implications for design of association studies. Genet. Epidemiol. 25, 190–202 (2003)
Tavassoli, F. A. & Devilee, P. in Pathology and Genetics of Tumours of the Breast and Female Genital Organs (IARC, 2003)
Hernandez, L. et al. Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intra-tumour genetic heterogeneity and clonal selection. J. Pathol. 227, 42–52 (2012)
Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnol. 27, 182–189 (2009)
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009)
Turnbull, C. et al. Genome-wide association study identifies five new breast cancer susceptibility loci. Nature Genet. 42, 504–507 (2010)
Lunter, G. & Goodson, M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 21, 936–939 (2011)
Rimmer, A., Mathieson, I., Lunter, G. & McVean, G. Platypus: An Integrated Variant Caller (http://www.well.ox.ac.uk/platypus) (2012)
Curado, M. P. et al. Cancer incidence in five continents, Volume VIII. IARC Sci. Publ. No 160, 1–781 (2002)
Antoniou, A. C. et al. Evidence for further breast cancer susceptibility genes in addition to BRCA1 and BRCA2 in a population-based study. Genet. Epidemiol. 21, 1–18 (2001)
Lange, K., Weeks, D. & Boehnke, M. Programs for Pedigree Analysis: MENDEL, FISHER, and dGENE. Genet. Epidemiol. 5, 471–472 (1988)
Acknowledgements
We thank all the subjects and families that participated in the research and D. Dudakia, J. Bull and R. Linger for their assistance in recruitment. We are indebted to M. Stratton for discussions of the data and to A. Strydom for editorial assistance. We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford (funded by Wellcome Trust grant reference 090532/Z/09/Z and Medical Research Council (MRC) Hub grant G0900747 91070) for the generation of the phase 1 sequencing data. This work was funded by the Institute of Cancer Research, The Wellcome Trust, Cancer Research UK and Breakthrough Breast Cancer. We acknowledge support by the RMH-ICR National Institute for Health Research (NIHR) Specialist Biomedical Research Centre for Cancer. We acknowledge the use of DNA from the British 1958 Birth Cohort collection funded by the MRC grant G0000934 and the Wellcome Trust grant 068545/Z/02. A.C.A. is a Cancer Research UK Senior Cancer Research Fellow (C12292/A11174). P.Do. is supported by a Wolfson-Royal Society Merit Award. K.S. is supported by the Michael and Betty Kadoorie Cancer Genetics Research Programme.
Author information
Authors and Affiliations
Consortia
Contributions
E.R., K.S., P.H., N.M.W., T.-P.Y., M.A.B., M.J.C., C.T., J.T., M.I.M., P.De., P.Do. and N.R. (chair) are the Wellcome Trust Case Control Consortium (WTCCC) exon-resequencing group who devised and funded phase 1. J.W.A., J.Ba., J.Be., A.F.B., C.B., G.B., C.C., J.C., R.D., A.D., F.D., D.E., D.G.E., L.G., A.H., L.I., A.K., F.L., Z.M., P.J.M., J.P., M.P., M.T.R., S.Sh., L.W. and N.R. are centre leads of the Breast and Ovarian Cancer Susceptibility Collaboration (BOCS), which is coordinated by M.W.-P. and A.Z. A full list of the WTCCC and BOCS consortia is in the Supplementary Information. R.H. and M.G. assembled the unselected ovarian cancer series. L.G. coordinated phase 1 sequencing. P.H., M.R. and P.Do. undertook analysis of the pooled DNA repair panel. J.D., A.M., S.Se., S.H. and E.R. undertook NGS sequencing and analysis. S.Se. E.R., S.D.V.S., N.A.P., A.Re., K.S., C.L. and J.D. undertook Sanger sequencing, MLPA and tumour microsatellite analysis. E.R. undertook sample selection and data analyses with C.T. A.C.A. wrote the risk analysis software and oversaw the penetrance analysis that was performed by E.R. A.Ri. provided and optimized Platypus. D.N.R., A.C.-F. and J.S.R.-F. undertook histopathological analyses and performed microdissections. I.B., R.B., C.J.L. and A.A. undertook functional analyses. E.R., K.S. and N.R. managed and oversaw all aspects of the study and wrote the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Additional information
Lists of participants and their affiliations appear in the Supplementary Information.
Lists of participants and their affiliations appear in the Supplementary Information.
Supplementary information
Supplementary Information
This file contains Supplementary Figures 1-8 and details of the WTCCC and BOCS consortia. (PDF 2900 kb)
Supplementary Tables
This file contains Supplementary Tables 1-8. (XLS 168 kb)
Rights and permissions
About this article
Cite this article
Ruark, E., Snape, K., Humburg, P. et al. Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer. Nature 493, 406–410 (2013). https://doi.org/10.1038/nature11725
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nature11725
This article is cited by
-
Analysis of clinical and genomic profiles of therapy-related myeloid neoplasm in Korea
Human Genomics (2023)
-
Wip1 suppresses angiogenesis through the STAT3-VEGF signalling pathway in serous ovarian cancer
Journal of Ovarian Research (2022)
-
Pharmaco-proteogenomic profiling of pediatric diffuse midline glioma to inform future treatment strategies
Oncogene (2022)
-
The burden of rare protein-truncating genetic variants on human lifespan
Nature Aging (2022)
-
Inhibition of the DNA damage response phosphatase PPM1D reprograms neutrophils to enhance anti-tumor immune responses
Nature Communications (2021)
Comments
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.
