Abstract

Human cancers, including breast cancers, comprise clones differing in mutation content. Clones evolve dynamically in space and time following principles of Darwinian evolution1,2, underpinning important emergent features such as drug resistance and metastasis3,4,5,6,7. Human breast cancer xenoengraftment is used as a means of capturing and studying tumour biology, and breast tumour xenografts are generally assumed to be reasonable models of the originating tumours8,9,10. However, the consequences and reproducibility of engraftment and propagation on the genomic clonal architecture of tumours have not been systematically examined at single-cell resolution. Here we show, using deep-genome and single-cell sequencing methods, the clonal dynamics of initial engraftment and subsequent serial propagation of primary and metastatic human breast cancers in immunodeficient mice. In all 15 cases examined, clonal selection on engraftment was observed in both primary and metastatic breast tumours, varying in degree from extreme selective engraftment of minor (<5% of starting population) clones to moderate, polyclonal engraftment. Furthermore, ongoing clonal dynamics during serial passaging is a feature of tumours experiencing modest initial selection. Through single-cell sequencing, we show that major mutation clusters estimated from tumour population sequencing relate predictably to the most abundant clonal genotypes, even in clonally complex and rapidly evolving cases. Finally, we show that similar clonal expansion patterns can emerge in independent grafts of the same starting tumour population, indicating that genomic aberrations can be reproducible determinants of evolutionary trajectories. Our results show that measurement of genomically defined clonal population dynamics will be highly informative for functional studies using patient-derived breast cancer xenoengraftment.

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Data deposits

Genome data have been deposited at the European Genome-phenome Archive (http://www.ebi.ac.uk/ega) under accession number EGAS00001000952. Processed data can be viewed at http://www.cbioportal.org.

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Acknowledgements

We are grateful to the staff of the CTAG Molecular Pathology facility, members of the Library Technical Development, Library Construction, Sequencing and Bioinformatics teams at the Michael Smith Genome Sciences Centre for technical assistance with data generation, and S. Kalloger for assistance with sample collection. S.A. and S.P.S. are supported by Canada Research Chairs. P.E. is supported by a Michael Smith Foundation for Health Research (MSFHR) Fellowship. A.S. is supported by an NSERC CREATE scholarship through the graduate program in Genome Science and Technology at UBC. S.P.S. is a MSFHR scholar. We acknowledge long-term funding support provided by the BC Cancer Foundation. The S.A., S.P.S. and C.H. groups receive operating funds from the Canadian Breast Cancer Foundation, Canadian Cancer Society Research Institute, Terry Fox Research Institute, Genome Canada and Canadian Institutes for Health Research (CIHR). We thank S. Mullaly for critical reading of the manuscript.

Author information

Author notes

    • Peter Eirew
    • , Adi Steif
    •  & Jaswinder Khattra

    These authors contributed equally to this work.

Affiliations

  1. Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada

    • Peter Eirew
    • , Adi Steif
    • , Jaswinder Khattra
    • , Gavin Ha
    • , Damian Yap
    • , Hossein Farahani
    • , Adrian Wan
    • , Emma Laks
    • , Justina Biele
    • , Karey Shumansky
    • , Jamie Rosner
    • , Andrew McPherson
    • , Cydney Nielsen
    • , Andrew J. L. Roth
    • , Calvin Lefebvre
    • , Ali Bashashati
    • , Camila de Souza
    • , Celia Siu
    • , Radhouane Aniba
    • , Jazmine Brimhall
    • , Arusha Oloumi
    • , Tomo Osako
    • , Teresa Algara
    • , Sohrab P. Shah
    •  & Samuel Aparicio
  2. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada

    • Peter Eirew
    • , Adi Steif
    • , Jaswinder Khattra
    • , Gavin Ha
    • , Damian Yap
    • , Hossein Farahani
    • , Emma Laks
    • , Justina Biele
    • , Andrew McPherson
    • , Cydney Nielsen
    • , Andrew J. L. Roth
    • , Calvin Lefebvre
    • , Ali Bashashati
    • , Radhouane Aniba
    • , Arusha Oloumi
    • , Tomo Osako
    • , Teresa Algara
    • , David Huntsman
    • , Sohrab P. Shah
    •  & Samuel Aparicio
  3. Department of Medical Oncology, BC Cancer Agency, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada

    • Karen Gelmon
    • , Stephen Chia
    •  & Colin Mar
  4. Department of Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK

    • Alejandra Bruna
    • , Jose L. Sandoval
    • , Wendy Greenwood
    •  & Carlos Caldas
  5. Cancer Research UK Cambridge Research Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK

    • Alejandra Bruna
    • , Jose L. Sandoval
    • , Wendy Greenwood
    •  & Carlos Caldas
  6. Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada

    • Kaston Leung
    •  & Carl Hansen
  7. Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada

    • Kaston Leung
    •  & Carl Hansen
  8. Department of Experimental Therapeutics, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada

    • Hongwei Cheng
    • , Hui Xue
    • , Yuzhuo Wang
    •  & Dong Lin
  9. The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada

    • Hongwei Cheng
    • , Hui Xue
    • , Yuzhuo Wang
    •  & Dong Lin
  10. Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada

    • Andrew J. Mungall
    • , Richard Moore
    • , Yongjun Zhao
    • , Marco A. Marra
    • , Sohrab P. Shah
    •  & Samuel Aparicio
  11. Centre for Translational and Applied Genomics, BC Cancer Agency, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada

    • Julie Lorette
    • , David Huntsman
    •  & Samuel Aparicio
  12. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada

    • Long Nguyen
    •  & Connie J. Eaves
  13. Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada

    • Long Nguyen
    •  & Connie J. Eaves

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Contributions

S.A. and S.P.S. designed the study and supervised the research. S.A., S.P.S., P.E. and A.S. wrote the paper. P.E., A.Br., J.S., T.A., W.G., H.C., H.X., L.N., Y.W. and D.L. performed transplants and passaging. K.G., S.C. and C.M. recruited patients and performed tissue biopsies. A.S., P.E., G.H., C.N., H.F., A.J.L.R., C.L., A.Ba., C.S., K.S., J.R., R.A., A.M., C.d.S., S.P.S. and S.A. carried out bioinformatics analyses. J.K., D.Y., E.L., J.Br., A.W., J.Bi., K.L., A.J.M., A.O., R.M., Y.Z., C.H. and M.A.M. assisted with sequence generations and single-cell experiments. T.O., J.L. and D.H. contributed to histological analysis. C.J.E., C.H., M.A.M., C.C., S.P.S. and S.A. provided intellectual contributions to design or interpretation.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Sohrab P. Shah or Samuel Aparicio.

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About this article

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DOI

https://doi.org/10.1038/nature13952

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