TY - JOUR
T1 - Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer
AU - Patten, Darren K.
AU - Corleone, Giacomo
AU - Győrffy, Balázs
AU - Perone, Ylenia
AU - Slaven, Neil
AU - Barozzi, Iros
AU - Erdős, Edina
AU - Saiakhova, Alina
AU - Goddard, Kate
AU - Vingiani, Andrea
AU - Shousha, Sami
AU - Pongor, Lőrinc Sándor
AU - Hadjiminas, Dimitri J.
AU - Schiavon, Gaia
AU - Barry, Peter
AU - Palmieri, Carlo
AU - Coombes, Raul C.
AU - Scacheri, Peter
AU - Pruneri, Giancarlo
AU - Magnani, Luca
PY - 2018/9/1
Y1 - 2018/9/1
N2 - 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.
AB - 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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U2 - 10.1038/s41591-018-0091-x
DO - 10.1038/s41591-018-0091-x
M3 - Article
AN - SCOPUS:85050544773
VL - 24
SP - 1469
EP - 1480
JO - Nature Medicine
JF - Nature Medicine
SN - 1078-8956
IS - 9
ER -