Genetic and epigenetic association studies suggest a role of microRNA biogenesis gene exportin-5 (XPO5) in breast tumorigenesis

Abstract

Given strong evidence implicating an important role of altered microRNA expression in cancer initiation and progression, the genes responsible for microRNA biogenesis may also play a role in tumorigenesis. Exportin-5 (XPO5) is responsible for exporting pre-miRNAs through the nuclear membrane to the cytoplasm, and is thus critical in miRNA biogenesis. In the current study, we performed both genetic and epigenetic association studies of XPO5 in a case control study of breast cancer. We first genotyped two missense SNPs in XPO5, rs34324334 (S241N) and rs11544382 (M1115T), and further analyzed methylation levels in the XPO5 promoter region for blood DNA samples from a breast cancer case-control study. We found the variant genotypes of rs11544382 to be associated with breast cancer risk (OR=1.59, 95% CI: 1.06 -2.39), compared to the homozygous common genotype. When stratified by menopausal status, the variant alleles of both rs11544382 (OR=1.82, 95% CI: 1.09-3.03) and rs34324334 (OR=1.76, 95% CI: 1.10-2.83) were significantly associated with breast cancer risk in post-menopausal women. The methylation analysis showed that the "high" and combined "high/middle" tertiles of methylation index were associated with reduced risk of breast cancer (OR=0.34, 95% CI:0.15-0.81 and OR=0.47, 95% CI:0.24-0.94, respectively; P(trend)=0.015). These results were corroborated by data from a publicly available tissue array, which showed lower levels of XPO5 expression in healthy controls relative to tumor or adjacent tissues from breast cancer patients with tumor tissue exhibiting the highest expression levels. These findings support the hypothesis that variations in components of the miRNA biogenesis pathway, in this case XPO5, may affect an individual's risk of developing breast cancer.

Keywords: XPO5; breast cancer; microRNA biogenesis.

Figure 1

Representation of Exportin-5 and location of nsSNPs. Pfam (pfam.sanger.ac.uk) predicts two functionally conserved domains in XPO5, the Xpo1 domain, which is important for nuclear exchange, and is located from residues 109 to 271 (depicted in red), and an automatically generated PfamB domain from residues 771 to 1203. The multiple species alignment generated by PolyPhen (genetics.bwh.harvard.edu/pph/) is also shown for each SNP. While rs34324334 is not highly conserved, and PolyPhen predicts this mutation to be benign, the amino acid altered by rs11544382 is fairly conserved, and the variant allele (T), is not observed in any species. PolyPhen predicts this SNP to be “probably damaging”.

Figure 2

XPO5 gene expression in breast tissue from breast cancer patients and healthy controls. An array experiment was identified in the publicly available ArrayExpress database (accession #: E-TABM-276) that compared XPO5 expression in breast tissue from patients with breast carcinoma to XPO5 expression levels in breast tissue from healthy controls. Mean normalized expression (±SEM) was 185.3±30.9 for invasive carcinomas (N=23), 71.8±6.2 in tissues adjacent to the tumor (N=28), and 26.0±4.8 for healthy control breast tissue (N=10).