Loss of heterozygosity and DNA methylation affect germline fibroblast growth factor receptor 4 polymorphism to direct allelic selection in breast cancer.

Genome-wide association studies highlight the importance of the fibroblast growth factor (FGF) receptor as a risk factor for breast cancer development. In particular, FGFR4 has been implicated in membrane ruffling, cancer cell invasiveness, and clinical chemoresistance in breast cancer. In this work, we studied FGFR4 in both human breast cancers and cell lines. We examined primary human microdissected breast samples for FGFR4 mutations, polymorphisms, loss of heterozygosity (LOH), and DNA methylation status. We identified no activating somatic mutations of FGFR4; however, we did identify a high proportion of the FGFR4-R388 heterozygous germline polymorphism. Analysis of paired microdissected samples uncovered selective LOH at the FGFR4 locus in 50% of primary tumors. This LOH involved the FGFR4-WT allele as frequently as the cancer progression-associated FGFR4-G388R polymorphic allele. Further, we identified DNA methylation in one-third of cases that targeted the FGFR4-WT allele more often and occurred more frequently either in concert with or exclusively in lymph node metastases. The role of DNA methylation in silencing the FGFR4-WT allele was supported by azacytidine treatment findings and was also confirmed in mouse xenograft studies, demonstrating selective FGFR4-WT allelic methylation with corresponding gene down-regulation. These findings support a growth advantage function for FGFR4-R388 and underscore the complex role of DNA methylation and LOH in determining the penetrance of allelic selection in breast cancer progression. These findings therefore have critical therapeutic importance.