The recent whole-genome scan for breast cancer has revealed the FGFR2 (fibroblast growth factor receptor 2) gene as a locus associated with a small, but highly significant, increase in the risk of developing breast cancer. Using fine-scale genetic mapping of the region, it has been possible to narrow the causative locus to a haplotype of eight strongly linked single nucleotide polymorphisms (SNPs) spanning a region of 7.5 kilobases (kb) in the second intron of the FGFR2 gene. Here we describe a functional analysis to define the causative SNP, and we propose a model for a disease mechanism. Using gene expression microarray data, we observed a trend of increased FGFR2 expression in the rare homozygotes. This trend was confirmed using real-time (RT) PCR, with the difference between the rare and the common homozygotes yielding a Wilcox p-value of 0.028. To elucidate which SNPs might be responsible for this difference, we examined protein–DNA interactions for the eight most strongly disease-associated SNPs in different breast cell lines. We identify two cis-regulatory SNPs that alter binding affinity for transcription factors Oct-1/Runx2 and C/EBPβ, and we demonstrate that both sites are occupied in vivo. In transient transfection experiments, the two SNPs can synergize giving rise to increased FGFR2 expression. We propose a model in which the Oct-1/Runx2 and C/EBPβ binding sites in the disease-associated allele are able to lead to an increase in FGFR2 gene expression, thereby increasing the propensity for tumour formation.
Recently, a number of whole-genome association studies have identified genes that predispose individuals to common diseases such as cancer. The challenge now is to understand how the identified risk loci contribute to disease, since the majority of these loci are located within introns (which are discarded after transcription) and intergenic regions, and therefore do not change the coding region of nearby genes. This manuscript describes how two single–base pair changes in intron 2 of the FGFR2 (fibroblast growth factor receptor 2) gene, “the top hit” of the breast cancer susceptibility study, exert their function. We find that the changes alter the binding of two transcription factors and cause an increase in FGFR2 gene expression, thus providing a molecular explanation for the risk phenotype. This is the first functional study, to our knowledge, of the risk loci identified for breast cancer in a whole-genome scan and demonstrates that these studies can be used as valid starting points for studying the underlying biology of cancer.
Recent whole-genome scans have identified novel risk genes for many common diseases, challenging researchers to determine how these genes contribute to disease. A new study provides molecular insights into a breast cancer risk factor.