rs604702 confers breast cancer risk by influencing PCAT18/miR-759/SPRR3 axis

Breast cancer is the most common tumor type in women and with apparent genetic predisposition. Recent genome-wide association study suggests that rs527616 is significantly associated with this disease. Analysis on 1000 genomes project data suggests that additional four SNPs, rs604702, rs1667550, rs521667, and rs675150, are in nearly complete linkage disequilibrium with rs527616. However, the causal SNP and the mechanism for this association still remain unclear. Reporter gene assay indicates that the causal SNP might be not rs527616 but rs604702. BARX2 (BARX homeobox 2) is identified to bind the surrounding region of rs604702 and binding affinity difference between alleles is compared. The enhancer containing rs604702 can interact with PCAT18 (prostate cancer associated transcript 18) promoter. Knockdown of PCAT18 can significantly decrease SPRR3 (small proline rich protein 3) expression and breast cell ability of proliferation, migration, wound healing, and colony formation, which verifies that PCAT18 is an oncogene for breast cancer. Transfection of miR-759 inhibitor can rescue abovementioned effect, thus validating that the effect of PCAT18 on breast cancer is through interacting with this miRNA. Knock-out of rs604702 surrounding region by CRISPR/Cas9 can significantly decrease PCAT18 and SPRR3 expression and further breast cell ability of proliferation, migration, wound healing, and colony formation. Our effort identifies a novel mechanism by which the genetic variation in this locus can influence breast cancer susceptibility.