Proteomics

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Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output


ABSTRACT: Estrogen Receptor alpha (ERa) is the main driver of luminal breast cancer development and progression, and represents the main drug target in patient care. ERa chromatin binding has been extensively studied in breast cancer cell lines and a number of human tumors, often focused on differential binding patterns between groups or conditions. However, little is known about the inter-tumor heterogeneity of ERa chromatin action. Here, we use a large set of ERa ChIP-seq data from 70 ERa+ breast cancers (40 women & 30 men) to explore general inter-patient heterogeneity in ERa DNA binding in breast cancers. We found a total universe of 84,565 and 101,653 ERa sites in females and males respectively, with merely 1.2% and 5% of sites shared in at least half of the tumors analyzed, reflecting a high level of inter-patient heterogeneity. This heterogeneity was found to be most variable at putative enhancers as opposed to promoter regions, potentially reflecting a level of functional redundancy in enhancer action. Interestingly, commonly shared ERa sites showed the highest estrogen-driven enhancer activity, as determined using a massive parallel reporter assay, and were most-engaged in long-range chromatin interactions. In addition, the most-commonly shared ERa-occupied enhancers were found enriched for breast cancer risk SNP loci. We experimentally illustrate such SNVs can impact chromatin binding potential for ERa and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we could confirm these variations to associate with differences in expression for the target gene. Cumulatively, our data reveal a natural hierarchy of ERa-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ERa landscape, with the most-common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Mcf-7 Cell, Breast, Breast Cancer Cell

DISEASE(S): Breast Cancer

SUBMITTER: S Stelloo  

LAB HEAD: Prof. Michiel Vermeulen

PROVIDER: PXD045526 | Pride | 2024-05-22

REPOSITORIES: Pride

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Publications

Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions.

Joosten Stacey E P SEP   Gregoricchio Sebastian S   Stelloo Suzan S   Yapıcı Elif E   Huang Chia-Chi Flora CF   Yavuz Kerim K   Donaldson Collier Maria M   Morova Tunç T   Altintaş Umut Berkay UB   Kim Yongsoo Y   Canisius Sander S   Moelans Cathy B CB   van Diest Paul J PJ   Korkmaz Gozde G   Lack Nathan A NA   Vermeulen Michiel M   Linn Sabine C SC   Zwart Wilbert W  

Genome research 20240515 4


Estrogen Receptor 1 (ESR1; also known as ERα, encoded by <i>ESR1</i> gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ESR1 chromatin action, along with its biological implications. Here, we use a large set of ESR1 ChIP-seq data from 70 ESR1<sup>+</sup> breast cancers to e  ...[more]

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