Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer

Abstract

Biallelic inactivation of BRCA1 or BRCA2 is associated with a pattern of genome-wide mutations known as signature 3. By analyzing 1,000 breast cancer samples, we confirmed this association and established that germline nonsense and frameshift variants in PALB2, but not in ATM or CHEK2, can also give rise to the same signature. We were able to accurately classify missense BRCA1 or BRCA2 variants known to impair homologous recombination (HR) on the basis of this signature. Finally, we show that epigenetic silencing of RAD51C and BRCA1 by promoter methylation is strongly associated with signature 3 and, in our data set, was highly enriched in basal-like breast cancers in young individuals of African descent.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Characterization of four distinct mutational signatures in breast cancer.
Figure 2: Overall mutation rates, mutational signature contributions, and clinicopathological features per patient as sorted by descending signature 3 activity.
Figure 3: Signature 3 activity in tumors with somatic, germline, and epigenetic alterations in HR-pathway genes.
Figure 4: The association of RAD51C-promoter methylation with elevated signature 3 activity in basal-like tumors.
Figure 5: Analysis of genetic and epigenetic events in the top quartile of signature 3 activity (n = 248), focused on the largest racial subgroups in our cohort (white and African American).
Figure 6: A framework for enhancing the classification of BRCA1/2 germline missense variants using signature 3 (sig3) and biallelic inactivation.
Figure 7: Prediction accuracy of signature 3 (sig3) relative to established rearrangement-based HRD scores.

References

  1. Prakash, R., Zhang, Y., Feng, W. & Jasin, M. Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins. Cold Spring Harb. Perspect. Biol. 7, a016600 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Antoniou, A. et al. Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: a combined analysis of 22 studies. Am. J. Hum. Genet. 72, 1117–1130 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Ceccaldi, R., Rondinelli, B. & D'Andrea, A.D. Repair pathway choices and consequences at the double-strand break. Trends Cell Biol. 26, 52–64 (2016).

    Article  CAS  PubMed  Google Scholar 

  4. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012).

  5. Burstein, M.D. et al. Comprehensive genomic analysis identifies novel subtypes and targets of triple-negative breast cancer. Clin. Cancer Res. 21, 1688–1698 (2015).

    Article  CAS  PubMed  Google Scholar 

  6. Ellis, M.J. & Perou, C.M. The genomic landscape of breast cancer as a therapeutic roadmap. Cancer Discov. 3, 27–34 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Ciriello, G. et al. Comprehensive molecular portraits of invasive lobular breast cancer. Cell 163, 506–519 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Ceccaldi, R. et al. Homologous-recombination-deficient tumours are dependent on Polθ-mediated repair. Nature 518, 258–262 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Nik-Zainal, S. et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534, 47–54 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Alexandrov, L.B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Lawrence, M.S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kim, J. et al. Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat. Genet. 48, 600–606 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kasar, S. et al. Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution. Nat. Commun. 6, 8866 (2015).

    Article  CAS  PubMed  Google Scholar 

  14. Nielsen, F.C., van Overeem Hansen, T. & Sørensen, C.S. Hereditary breast and ovarian cancer: new genes in confined pathways. Nat. Rev. Cancer 16, 599–612 (2016).

    Article  CAS  PubMed  Google Scholar 

  15. Easton, D.F. et al. Gene-panel sequencing and the prediction of breast-cancer risk. N. Engl. J. Med. 372, 2243–2257 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Lord, C.J. & Ashworth, A. BRCAness revisited. Nat. Rev. Cancer 16, 110–120 (2016).

    Article  CAS  PubMed  Google Scholar 

  17. Eccles, D.M. et al. BRCA1 and BRCA2 genetic testing—pitfalls and recommendations for managing variants of uncertain clinical significance. Ann. Oncol. 26, 2057–2065 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Landrum, M.J. et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 42, D980–D985 (2014).

    Article  CAS  PubMed  Google Scholar 

  20. Meeks, H.D. et al. BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers. J. Natl. Cancer Inst. 108, djv315 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Scully, R. & Livingston, D.M. In search of the tumour-suppressor functions of BRCA1 and BRCA2. Nature 408, 429–432 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Merajver, S.D. et al. Germline BRCA1 mutations and loss of the wild-type allele in tumors from families with early onset breast and ovarian cancer. Clin. Cancer Res. 1, 539–544 (1995).

    CAS  PubMed  Google Scholar 

  23. Cornelis, R.S. et al. High allele loss rates at 17q12-q21 in breast and ovarian tumors from BRCA1-linked families. Genes Chromosom. Cancer 13, 203–210 (1995).

    Article  CAS  PubMed  Google Scholar 

  24. Thompson, E.R. et al. Panel testing for familial breast cancer: calibrating the tension between research and clinical care. J. Clin. Oncol. 34, 1455–1459 (2016).

    Article  CAS  PubMed  Google Scholar 

  25. Southey, M.C. et al. PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS. J. Med. Genet. 53, 800–811 (2016).

    Article  CAS  PubMed  Google Scholar 

  26. Waddell, N. et al. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature 518, 495–501 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Connor, A.A. et al. Association of distinct mutational signatures with correlates of increased immune activity in pancreatic ductal adenocarcinoma. JAMA Oncol. 3, 774–783 (2017).

    Article  PubMed  Google Scholar 

  28. Livingston, D.M. Cancer. Complicated supercomplexes. Science 324, 602–603 (2009).

    Article  CAS  PubMed  Google Scholar 

  29. Loveday, C. et al. Germline RAD51C mutations confer susceptibility to ovarian cancer. Nat. Genet. 44, 475–476 (2012).

    Article  CAS  PubMed  Google Scholar 

  30. Couch, F.J. et al. Inherited mutations in 17 breast cancer susceptibility genes among a large triple-negative breast cancer cohort unselected for family history of breast cancer. J. Clin. Oncol. 33, 304–311 (2015).

    Article  CAS  PubMed  Google Scholar 

  31. Blanco, A. et al. RAD51C germline mutations found in Spanish site-specific breast cancer and breast-ovarian cancer families. Breast Cancer Res. Treat. 147, 133–143 (2014).

    Article  CAS  PubMed  Google Scholar 

  32. Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346–352 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Pereira, B. et al. The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nat. Commun. 7, 11479 2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Foulkes, W.D. et al. Germline BRCA1 mutations and a basal epithelial phenotype in breast cancer. J. Natl. Cancer Inst. 95, 1482–1485 (2003).

    Article  CAS  PubMed  Google Scholar 

  35. Esteller, M. et al. Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors. J. Natl. Cancer Inst. 92, 564–569 (2000).

    Article  CAS  PubMed  Google Scholar 

  36. Foulkes, W.D., Smith, I.E. & Reis-Filho, J.S. Triple-negative breast cancer. N. Engl. J. Med. 363, 1938–1948 (2010).

    Article  CAS  PubMed  Google Scholar 

  37. Dietze, E.C., Sistrunk, C., Miranda-Carboni, G., O'Regan, R. & Seewaldt, V.L. Triple-negative breast cancer in African-American women: disparities versus biology. Nat. Rev. Cancer 15, 248–254 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Rehm, H.L. et al. ClinGen—the Clinical Genome Resource. N. Engl. J. Med. 372, 2235–2242 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Spurdle, A.B. et al. ENIGMA—evidence-based network for the interpretation of germline mutant alleles: an international initiative to evaluate risk and clinical significance associated with sequence variation in BRCA1 and BRCA2 genes. Hum. Mutat. 33, 2–7 (2012).

    Article  CAS  PubMed  Google Scholar 

  40. Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet. Med. 17, 405–424 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Hashizume, R. et al. The RING heterodimer BRCA1-BARD1 is a ubiquitin ligase inactivated by a breast cancer-derived mutation. J. Biol. Chem. 276, 14537–14540 (2001).

    Article  CAS  PubMed  Google Scholar 

  42. Górski, B. et al. Founder mutations in the BRCA1 gene in Polish families with breast-ovarian cancer. Am. J. Hum. Genet. 66, 1963–1968 (2000).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Abkevich, V. et al. Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer. Br. J. Cancer 107, 1776–1782 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Popova, T. et al. Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. Cancer Res. 72, 5454–5462 (2012).

    Article  CAS  PubMed  Google Scholar 

  45. Youden, W.J. Index for rating diagnostic tests. Cancer 3, 32–35 (1950).

    Article  CAS  PubMed  Google Scholar 

  46. Min, A. et al. RAD51C-deficient cancer cells are highly sensitive to the PARP inhibitor olaparib. Mol. Cancer Ther. 12, 865–877 (2013).

    Article  CAS  PubMed  Google Scholar 

  47. Evans, T. & Matulonis, U. PARP inhibitors in ovarian cancer: evidence, experience and clinical potential. Ther. Adv. Med. Oncol. 9, 253–267 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Chan, S.L. & Mok, T. PARP inhibition in BRCA-mutated breast and ovarian cancers. Lancet 376, 211–213 (2010).

    Article  PubMed  Google Scholar 

  49. Fong, P.C. et al. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N. Engl. J. Med. 361, 123–134 (2009).

    Article  CAS  PubMed  Google Scholar 

  50. Kaufman, B. et al. Olaparib monotherapy in patients with advanced cancer and a germline BRCA1/2 mutation. J. Clin. Oncol. 33, 244–250 (2015).

    Article  CAS  PubMed  Google Scholar 

  51. Patch, A.M. et al. Whole-genome characterization of chemoresistant ovarian cancer. Nature 521, 489–494 (2015).

    Article  CAS  PubMed  Google Scholar 

  52. Clamp, A. & Jayson, G. PARP inhibitors in BRCA mutation-associated ovarian cancer. Lancet Oncol. 16, 10–12 (2015).

    Article  CAS  PubMed  Google Scholar 

  53. Pathania, S. et al. BRCA1 haploinsufficiency for replication stress suppression in primary cells. Nat. Commun. 5, 5496 (2014).

    Article  PubMed  Google Scholar 

  54. Yeeles, J.T., Poli, J., Marians, K.J. & Pasero, P. Rescuing stalled or damaged replication forks. Cold Spring Harb. Perspect. Biol. 5, a012815 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Lindor, N.M. et al. A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS). Hum. Mutat. 33, 8–21 (2012).

    Article  CAS  PubMed  Google Scholar 

  56. Hyman, D.M. et al. Precision medicine at Memorial Sloan Kettering Cancer Center: clinical next-generation sequencing enabling next-generation targeted therapy trials. Drug Discov. Today 20, 1422–1428 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol 31, 213–219 (2013).

    CAS  Google Scholar 

  58. Saunders, C. T. et al. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 28, 1811–1817 (2012).

    Article  CAS  PubMed  Google Scholar 

  59. Costello, M. et al. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res. 41, e67– (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Carter, S.L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413–421 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

L.Z.B. was supported by the Louis B. Mayer Foundation. L.W.E. was supported by grants from the Avon Breast Cancer Crusade and the Breast Cancer Research Foundation (BCRF). G.G. and J.K. were partially funded by the NIH TCGA Genome Data Analysis Center (U24CA143845). P.P., N.J.H., Y.E.M., and A.K. were funded by the startup funds of G.G. at Massachusetts General Hospital. A.D.D. was supported by grants from the Ludwig Center at Harvard and the Breast Cancer Research Foundation (BCRF). W.D.F. was supported by Susan G. Komen. G.G. was partly funded by the Paul C. Zamecnick, MD, Chair in Oncology at Massachusetts General Hospital.

Author information

Authors and Affiliations

Authors

Contributions

P.P., J.K., and L.Z.B. conceived the work, performed analyses, and wrote the manuscript. R.K. and N.J.H. performed analyses and wrote the manuscript. G.T., D.R. and D.L. performed analyses. K.K. edited the manuscript. A.K., Y.E.M., and I.L. performed analyses and edited the manuscript. E.S.L. T.R.G., and A.Z. edited the manuscript. K.W.M. and A.O. wrote the manuscript. M.S.L. performed analysis and edited the manuscript. R.N.B. and C.C. provided data. D.A.H., L.W.E., and S.J.C. contributed scientific insight and edited the manuscript. P.W.L. and H.S. performed analysis and wrote the manuscript. A.D.D'A. conceived the work, contributed scientific insight, and edited the manuscript. W.D.F. and G.G. conceived the work, oversaw the analyses, and wrote the manuscript.

Corresponding author

Correspondence to Gad Getz.

Ethics declarations

Competing interests

T.R.G. is a cofounder of Foundation Medicine.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–16 and Supplementary Note 1. (PDF 6139 kb)

Life Sciences Reporting Summary. (PDF 129 kb)

Supplementary Table 1

ClinVar annotations of pathogenicity are reported, along with LOH status. (XLSX 47 kb)

Supplementary Table 2

Association between the functional characterization of BRCA1/2 missense variants with LOH and signature 3. (XLSX 41 kb)

Supplementary Table 3

Signature 3 and putative biallelic inactivation of BRCA1/2 correlate with clinical annotations among rare missense variants. (XLSX 41 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Polak, P., Kim, J., Braunstein, L. et al. A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer. Nat Genet 49, 1476–1486 (2017). https://doi.org/10.1038/ng.3934

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.3934

This article is cited by

Search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer