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Mechanism of tandem duplication formation in BRCA1-mutant cells

Nature volume 551, pages 590595 (30 November 2017) | Download Citation

Abstract

Small, approximately 10-kilobase microhomology-mediated tandem duplications are abundant in the genomes of BRCA1-linked but not BRCA2-linked breast cancer. Here we define the mechanism underlying this rearrangement signature. We show that, in primary mammalian cells, BRCA1, but not BRCA2, suppresses the formation of tandem duplications at a site-specific chromosomal replication fork barrier imposed by the binding of Tus proteins to an array of Ter sites. BRCA1 has no equivalent role at chromosomal double-stranded DNA breaks, indicating that tandem duplications form specifically at stalled forks. Tandem duplications in BRCA1 mutant cells arise by a replication restart-bypass mechanism terminated by end joining or by microhomology-mediated template switching, the latter forming complex tandem duplication breakpoints. Solitary DNA ends form directly at Tus–Ter, implicating misrepair of these lesions in tandem duplication formation. Furthermore, BRCA1 inactivation is strongly associated with ~10 kilobase tandem duplications in ovarian cancer. This tandem duplicator phenotype may be a general signature of BRCA1-deficient cancer.

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Acknowledgements

We thank J. Haber, L. Symington, S. Nik-Zainal and P. J. Campbell for discussions. This work was supported by NCI/DFCI SPORE in Breast Cancer Developmental Research Project Award DF/HCC 5 P50 CA 168504-03 (to N.A.W.), ACS postdoctoral research fellowship PF-12-248-01-DMC (to N.A.W.), R01 ES022054 and R01 CA188032-01 (to E.P.H.), NCI grant P30CA034196 and Andrea Branch and David Elliman Cancer Study Fund (to E.T.L.), grants R01CA095175, R01CA217991, CDMRP OC160440 and HeritX funding (to R.S.), a BIDMC-JAX pilot grant and CDMRP grant BC160172 (to R.S. and E.T.L.). F.W.A. is an investigator of the Howard Hughes Medical Institute.

Author information

Affiliations

  1. Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA.

    • Nicholas A. Willis
    • , Erin E. Duffey
    • , Arvind Panday
    •  & Ralph Scully
  2. Boston Children’s Hospital, Howard Hughes Medical Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

    • Richard L. Frock
    •  & Frederick W. Alt
  3. The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.

    • Francesca Menghi
    •  & Edison T. Liu
  4. Department of Medicine, Flow Cytometry Core, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.

    • Virginia Camacho
  5. The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.

    • E. Paul Hasty
  6. The Jackson Laboratory, Bar Harbor, Maine, USA.

    • Edison T. Liu

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Contributions

N.A.W. and R.S. developed the overall experimental plan. N.A.W. performed or participated in all experiments with the exception of cancer genome analysis. N.A.W. and R.S. planned and designed all the experiments, with additional contributions as follows. HTGTS experiments: plan and design: R.L.F. and F.W.A.; execution: R.L.F. and N.A.W. Cancer genome analysis: plan and design: F.M. and E.T.L.; execution: F.M. Analysis of Brca2 mutant cells: plan and design: E.P.H.; execution: N.A.W. Optimization of FACS analysis and FACS sorting protocols: V.C.; execution: N.A.W. and V.C. Construction and characterization of pHIV lentiviral vectors for expression of Xrcc4: N.A.W., E.E.D., A.P. and R.S. N.A.W. and R.S. wrote the manuscript. Individual figure panels were generated by N.A.W., R.L.F., F.M. and R.S.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Ralph Scully.

Reviewer Information Nature thanks A. Grigoriadis, J. Jonkers, and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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https://doi.org/10.1038/nature24477

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