The degree of intrinsic and interpatient phenotypic heterogeneity and its role in tumor evolution is poorly understood. Phenotypic drifts can be transmitted via inheritable transcriptional programs. Cell-type specific transcription is maintained through the activation of epigenetically defined regulatory regions including promoters and enhancers. Here we have annotated the epigenome of 47 primary and metastatic estrogen-receptor (ERα)-positive breast cancer clinical specimens and inferred phenotypic heterogeneity from the regulatory landscape, identifying key regulatory elements commonly shared across patients. Shared regions contain a unique set of regulatory information including the motif for transcription factor YY1. We identify YY1 as a critical determinant of ERα transcriptional activity promoting tumor growth in most luminal patients. YY1 also contributes to the expression of genes mediating resistance to endocrine treatment. Finally, we used H3K27ac levels at active enhancer elements as a surrogate of intra-tumor phenotypic heterogeneity to track the expansion and contraction of phenotypic subpopulations throughout breast cancer progression. By tracking the clonality of SLC9A3R1-positive cells, a bona fide YY1-ERα-regulated gene, we show that endocrine therapies select for phenotypic clones under-represented at diagnosis. Collectively, our data show that epigenetic mechanisms significantly contribute to phenotypic heterogeneity and evolution in systemically treated breast cancer patients.

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The authors acknowledge and thanks all patients and their families for support and for donating research samples. The authors thank the Breast Cancer Now Tissue Bank (project TR0121), Imperial Tissue Bank and the LEGACY study for contributing tissues. The authors acknowledge infrastructure support from the Cancer Research UK Imperial Centre, the Imperial Experimental Cancer Medicine Centre and the National Institute for Health Research Imperial Biomedical Research Centre. L.M. was supported by a CRUK fellowship (C46704/A23110) and an Imperial Junior Fellowship (G53019). D.P. was supported by a Wellcome Trust PhD studentship (103034/Z/13/Z). G.C. was supported by a Marie Skłodowska Curie Training Grant (642691, EpiPredict). G.P. was supported by AIRC IG 2016-18696. The authors thank J.A. Buendia, L. Watson and J. Carrol for constructive comments on the manuscript.

Author information

Author notes

  1. These authors contributed equally: Darren K. Patten, Giacomo Corleone.


  1. Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK

    • Darren K. Patten
    • , Giacomo Corleone
    • , Ylenia Perone
    • , Neil Slaven
    • , Iros Barozzi
    • , Raul C. Coombes
    •  & Luca Magnani
  2. MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary

    • Balázs Győrffy
    •  & Lőrinc Sándor Pongor
  3. Semmelweis University, 2nd Deptartment of Pediatrics, Budapest, Hungary

    • Balázs Győrffy
  4. Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen, Hungary

    • Edina Erdős
  5. Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA

    • Alina Saiakhova
    •  & Peter Scacheri
  6. Department of Breast and General Surgery, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK

    • Kate Goddard
  7. Department of Pathology, European Institute of Oncology, Milan, Italy

    • Andrea Vingiani
  8. Centre for Pathology, Department of Medicine, Imperial College London, London, UK

    • Sami Shousha
    •  & Dimitri J. Hadjiminas
  9. IMED Biotech Unit, AstraZeneca, Cambridge, UK

    • Gaia Schiavon
  10. Department of Breast Surgery, The Royal Marsden NHS Foundation Trust, Sutton, UK

    • Peter Barry
  11. Institute of Translational Medicine University of Liverpool, Clatterbridge Cancer Centre, NHS Foundation Trust, and Royal Liverpool University Hospital, Liverpool, Merseyside, UK

    • Carlo Palmieri
  12. Pathology Department, Fondazione IRCCS Istituto Nazionale Tumori and University of Milan, School of Medicine, Milan, Italy

    • Giancarlo Pruneri


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L.M. conceived the study. D.K.P., E.E., N.S. and Y.P. performed the experiments. L.M., G.C., B.G., A.S., L.S.P., I.B. and P.S. developed and performed bioinformatic analyses. K.G. organized tissue collection. D.J.H., G.S., P.B., C.P. and R.C.C. recruited patients and supplied tissues. S.S. performed pathology assessment of ChIP–seq processed samples. G.P. provided matched material. A.V. and G.P. performed IHC staining and scoring. All authors read and approved the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Luca Magnani.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–19 and Supplementary Methods

  2. Reporting Summary

  3. Supplementary Table 1

    Clinical characteristics of the patient dataset

  4. Supplementary Table 2

    Summary statistics for ChIP-seq in clinical samples

  5. Supplementary Dataset

    Coding mutations at cancer genes

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