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Two distinct mechanisms underlie estrogen-receptor-negative breast cancer susceptibility at the 2p23.2 locus

European Journal of Human Genetics volume 30, pages 465–473 (2022)Cite this article

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Abstract

Genome wide-association studies (GWAS) have established over 400 breast cancer risk loci defined by common single nucleotide polymorphisms (SNPs), including several associated with estrogen-receptor (ER)-negative disease. Most of these loci have not been studied systematically and the mechanistic underpinnings of risk are largely unknown. Here we explored the landscape of genomic features at an ER-negative breast cancer susceptibility locus at chromosome 2p23.2 and assessed the functionality of 81 SNPs with strong evidence of association from previous fine mapping. Five candidate regulatory regions containing risk-associated SNPs were identified. Regulatory Region 1 in the first intron of WDR43 contains SNP rs4407214, which showed allele-specific interaction with the transcription factor USF1 in in vitro assays. CRISPR-mediated disruption of Regulatory Region 1 led to expression changes in the neighboring PLB1 gene, suggesting that the region acts as a distal enhancer. Regulatory Regions 2, 4, and 5 did not provide sufficient evidence for functionality in in silico and experimental analyses. Two SNPs (rs11680458 and rs1131880) in Regulatory Region 3, mapping to the seed region for miRNA-recognition sites in the 3′ untranslated region of WDR43, showed allele-specific effects of ectopic expression of miR-376 on WDR43 expression levels. Taken together, our data suggest that risk of ER-negative breast cancer associated with the 2p23.2 locus is likely driven by a combinatorial effect on the regulation of WDR43 and PLB1.

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Fig. 1: Chromatin landscape at the 2p23.2 locus.
Fig. 2: Allele-specific transcription factor binding.
Fig. 3: Deletion of regulatory region 1.
Fig. 4: Reporter assays.

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Data availability

All data generated or analyzed during this study are included in this published article and its supplementary information files.

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Funding

This work was funded by the Florida Breast Cancer Foundation, Moffitt Foundation, and by support from the Molecular Genomics Facilities at H. Lee Moffitt Cancer Center & Research Institute, an NCI designated Comprehensive Cancer Center (P30-CA076292).

Author information

Authors and Affiliations

  1. Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA

    Gustavo Mendoza-Fandiño, Carly M. Harro, Xueli Li & Alvaro N. A. Monteiro

  2. Corporación Universitaria Remington, Medellin, Colombia

    Gustavo Mendoza-Fandiño

  3. Faculdade de Ensino e Meio Ambiente, Ariquemes, RO, Brazil

    Paulo Cilas M. Lyra Jr

  4. Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, 20231-050, Brazil

    Thales C. Nepomuceno & Marcelo A. Carvalho

  5. Department of Cell Biology, Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida, Tampa, FL, USA

    Carly M. Harro

  6. Cancer Biology PhD Program, University of South Florida Tampa, Tampa, FL, 33612, USA

    Carly M. Harro

  7. Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, 68198, USA

    Nicholas T. Woods

  8. Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, ES, Brazil

    Leticia B. Rangel

  9. Instituto Federal do Rio de Janeiro - IFRJ, Rio de Janeiro, 20270-021, Brazil

    Marcelo A. Carvalho

  10. Mayo Clinic, Rochester, MN, 55905, USA

    Fergus J. Couch

Authors
  1. Gustavo Mendoza-Fandiño
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  10. Alvaro N. A. Monteiro
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Contributions

G.M.F. and A.M. conceived the project and designed the experiments. G.M.F. and C.H. performed the experiments. G.M.F., P.L., T.N., C.H., and A.M. performed the analysis and interpreted the results. All authors contributed to the overall data interpretation, provided intellectual input, and approved the final paper.

Corresponding author

Correspondence to Alvaro N. A. Monteiro.

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Mendoza-Fandiño, G., Lyra, P.C.M., Nepomuceno, T.C. et al. Two distinct mechanisms underlie estrogen-receptor-negative breast cancer susceptibility at the 2p23.2 locus. Eur J Hum Genet 30, 465–473 (2022). https://doi.org/10.1038/s41431-021-01005-6

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