Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation

Nat Commun. 2014 Sep 23:4:4999. doi: 10.1038/ncomms5999.

Abstract

GWAS have identified a breast cancer susceptibility locus on 2q35. Here we report the fine mapping of this locus using data from 101,943 subjects from 50 case-control studies. We genotype 276 SNPs using the 'iCOGS' genotyping array and impute genotypes for a further 1,284 using 1000 Genomes Project data. All but two, strongly correlated SNPs (rs4442975 G/T and rs6721996 G/A) are excluded as candidate causal variants at odds against >100:1. The best functional candidate, rs4442975, is associated with oestrogen receptor positive (ER+) disease with an odds ratio (OR) in Europeans of 0.85 (95% confidence interval=0.84-0.87; P=1.7 × 10(-43)) per t-allele. This SNP flanks a transcriptional enhancer that physically interacts with the promoter of IGFBP5 (encoding insulin-like growth factor-binding protein 5) and displays allele-specific gene expression, FOXA1 binding and chromatin looping. Evidence suggests that the g-allele confers increased breast cancer susceptibility through relative downregulation of IGFBP5, a gene with known roles in breast cell biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breast Neoplasms / genetics*
  • Breast Neoplasms / metabolism
  • Cell Line, Tumor
  • Chromatin / metabolism
  • Chromosomes, Human, Pair 2 / genetics*
  • Chromosomes, Human, Pair 2 / metabolism
  • Female
  • Genetic Predisposition to Disease
  • Hepatocyte Nuclear Factor 3-alpha / metabolism
  • Humans
  • Insulin-Like Growth Factor Binding Protein 5 / genetics*
  • Insulin-Like Growth Factor Binding Protein 5 / metabolism
  • MCF-7 Cells
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic / genetics*
  • RNA, Messenger / metabolism*

Substances

  • Chromatin
  • FOXA1 protein, human
  • Hepatocyte Nuclear Factor 3-alpha
  • Insulin-Like Growth Factor Binding Protein 5
  • RNA, Messenger

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