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Punctuated copy number evolution and clonal stasis in triple-negative breast cancer

Abstract

Aneuploidy is a hallmark of breast cancer; however, knowledge of how these complex genomic rearrangements evolve during tumorigenesis is limited. In this study, we developed a highly multiplexed single-nucleus sequencing method to investigate copy number evolution in patients with triple-negative breast cancer. We sequenced 1,000 single cells from tumors in 12 patients and identified 1–3 major clonal subpopulations in each tumor that shared a common evolutionary lineage. For each tumor, we also identified a minor subpopulation of non-clonal cells that were classified as metastable, pseudodiploid or chromazemic. Phylogenetic analysis and mathematical modeling suggest that these data are unlikely to be explained by the gradual accumulation of copy number events over time. In contrast, our data challenge the paradigm of gradual evolution, showing that the majority of copy number aberrations are acquired at the earliest stages of tumor evolution, in short punctuated bursts, followed by stable clonal expansions that form the tumor mass.

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Figure 1: Highly multiplexed single-nucleus sequencing of patients with TNBC.
Figure 2: Clonal subpopulations identified by clustering aneuploid cells.
Figure 3: Clonal composition and diversity of TNBC tumors.
Figure 4: Divergent subpopulations in polyclonal tumors.
Figure 5: Non-clonal copy number profiles in tumors and normal breast tissues.
Figure 6: Punctuated copy number evolution and phylogenetic trees.
Figure 7: Mathematical modeling of punctuated and gradual tumor evolution.
Figure 8: Intertumoral heterogeneity and focal amplifications in TNBCs.

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Acknowledgements

We thank M. Edgerton, J. Kendall, M. Wigler and J. Hicks for their support and discussions. We are also very grateful to the patients with breast cancer at M.D. Anderson for generously donating their tumor tissues to our research studies. This work was supported by a grant from the Lefkofsky Family Foundation. N.E.N. is a Nadia's Gift Foundation Damon Runyon-Rachleff Innovator (DRR-25-13). This work is also supported by grants to N.E.N. from the NCI (1RO1CA169244-01) and the American Cancer Society (129098-RSG-16-092-01-TBG). N.E.N. is a T.C. Hsu Endowed Scholar, an AAAS Wachtel Scholar and an Andrew Sabin Family Fellow. The study is also supported by the Moonshot Knowledge Gap Award and the Center for Genetics and Genomics. This study was supported by the M.D. Anderson Sequencing Core Facility grant (CA016672) and the Flow Cytometry Facility grant (CA016672) from the NIH. Additional funding support includes the Rosalie B. Hite Fellowship (A.C.); a Center for Genetics and Genomics Postdoctoral Fellowship (R.G.); NIH UL1TR000371 (F.M.-B.); the Nellie B. Connally Breast Cancer Research Endowment (F.M.-B.), Susan Komen SAC10006 (F.M.-B.), CPRIT RP110584 (F.M.-B.) and the M.D. Anderson Cancer Center Support grant (NIH/NCI P30CA016672). F.M. gratefully acknowledges support from the Dana-Farber Cancer Institute Physical Science Oncology Center (U54CA193461-01).

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Authors

Contributions

R.G. analyzed the data and wrote the manuscript. A.D. analyzed the data. T.O.M. and F.M. performed mathematical modeling and wrote the manuscript. E.S., X.S., P.-C.T. and J.W. performed experiments. A.C. and Y.W. analyzed the data. H.Z. and F.M.-B. provided tumor samples and interpreted the data. N.E.N. analyzed the data, led the project and wrote the manuscript.

Corresponding author

Correspondence to Nicholas E Navin.

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The authors declare no competing financial interests.

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Gao, R., Davis, A., McDonald, T. et al. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nat Genet 48, 1119–1130 (2016). https://doi.org/10.1038/ng.3641

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