Genome-wide association studies (GWASs) have identified a locus within the second intron of the FGFR2 gene that is consistently the most strongly associated with estrogen receptor-positive (ER+) breast cancer risk. We have used network-based approaches to better understand the effects of FGFR2 as a risk gene.
Previous work has identified ESR1, GATA3, SPDEF and FOXA1 as master regulators of FGFR2 signalling1. We used the MINDy algorithm2 to identify potential post-translational upstream modulators of SPDEF and FOXA1, and knock-down experiments in SPDEF and FOXA1-dependent cell lines have identified 40 or so candidates, that may play a role in modulating activity of these transcription factors.
We have also studied the effect of risk SNPs on FGFR2 gene expression and how this can explain its role in breast cancer risk. SNPs rs2981578, rs35054928 and rs45631563 have been identified as the top independent breast cancer risk SNPs, and the risk regions overlapping these SNPs interact with the FGFR2 promoter. The effect of the risk SNPs on FGFR2 gene expression was assessed using luciferase reporter assays. Our data show that the three SNPs enhance the silencer activity of two FGFR2 regulatory elements, thereby reducing FGFR2 gene expression in human breast cancer cells. Next, the effect of FGFR2 signalling in ER+ human breast cancer cells was assessed by microarray gene expression. The data was analysed by combining regulatory network information with gene set enrichment analysis (GSEA), and showed that FGFR2 signalling in ER+ breast cancer cells counteracts the effect of estrogen signaling. Our results suggest that increased estrogen responsiveness as a result of reduced FGFR2 expression is associated with risk. Together, our results identify possible mechanisms by which the top risk SNPs associated with ER+ breast cancer risk might promote disease progression, and we have potentially identified candidate modulators which could be targeted in high-risk individuals.