1. The MRPS30 eQTL replicates in a validation cohort 29 discovery eQTL unique to breast cancer were tested in validation MRPS30 eQTL effect was significant only in ER-positive tumors AA allele was associated with higher expression of MRPS30 MRPS30 is estrogen-responsive and correlated with an estrogen signature in ER-positive tumors Estradiol increased MRPS30 expression in MCF7 cells at 6 hours However, estradiol decreased MRPS30 expression at 12 hours The 5p12 breast cancer susceptibility locus is associated with MRPS30 expression in estrogen-receptor positive tumors D.A. Quigley 1,2, E. Fiorito 3, P. Van Loo 4, G.G. Alnæs 1, T. Fleischer 1, D. Zelenieka 5, J. Tost 5, H.K. Vollan 1, A. Hurtado 3, A. Balmain 2, A.L. Børresen-Dale 1, & V. Kristensen 1 1 Department of Genetics, Institute for Cancer Research, University of Oslo 2 Helen Diller Family Comprehensive Cancer Center, UCSF 3 Breast Cancer Research Group, Center for Molecular Medicine, University of Oslo 4 Cancer Genome Project, Wellcome Trust Sanger Institute 5 Laboratory for Epigenetics, Centre National de Génotypage, CEA-Institute de Génomique How do common genetic variants affect breast cancer susceptibility? Many common variants are linked to breast cancer susceptibility, but genome-wide association studies cannot identify causal variations or explain how a locus affects susceptibility Here we show that the susceptibility locus at 5p12 affects MRPS30 gene expression via estrogen-induced epigenetic changes in the MRPS30 promoter region and near the rs7716600 SNP Genome-wide eQTL analysis of breast tumors We performed three expression Quantitative Trait Locus (eQTL) studies: Breast adenocarcinoma, discovery (N=285) Breast adenocarcinoma, validation (N=235) Normal breast (N=99) rs7716600 at 5p12 was linked to MRPS30 expression This locus 1 (specifically the AA allele of rs7716600 2 ) is associated with estrogen receptor positive breast cancer susceptibility 1 Stacey et al. Nature Genetics, 2008 2 Li et al. Breast Cancer Research & Treatment, 2011 rs7716600 is associated with MRPS30 promoter methylation We analyzed 123 samples from the discovery cohort (Illumina 450 chip) AA allele was associated with methylation at MRPS30 promoter ERα and CTCF binding at the MRPS30 promoter and SNP region is affected by estrogen levels A model for estrogen-dependent influence on MRPS30 expression San Antonio Breast Cancer Symposium December 4-8, 2012 This presentation is the intellectual property of the author/presenter. Contact dquigley@cc.ucsf.edu for permission to reprint or distribute. Genome-wide eQTL significance plot showing cis-acting loci affecting gene expression 164 significant loci found (FDR ≤ 5%) 5% FDR cut-off ER-positiveER-negative symbolrhoP P SLC39A60.502x10 -17 0.230.02 TPRG10.482x10 -15 -0.120.28 ESR10.452x10 -14 0.040.70 P4HTM0.445x10 -14 0.100.33 CA120.448x10 -14 -0.060.59 MAGED20.442x10 -13 0.090.41 SIAH20.435x10 -13 0.304x10 -3 ELP20.426x10 -13 0.278x10 -3 HEXIM20.414x10 -12 -0.020.83 C17orf750.414x10 -12 0.295x10 -3 HPN0.416x10 -12 0.090.42 GATA30.404x10 -11 0.040.70 WWP10.401x10 -11 0.020.88 SEMA3B0.402x10 -11 NA POLB0.402x10 -11 0.372x10 -4 COMMD40.394x10 -11 0.220.03 UGCG0.397x10 -11 -0.130.22 C6orf2110.399x10 -11 0.240.02 FOXA10.398x10 -11 -0.070.49 chromosome Strongest correlations with MRPS30 expression in discovery cohort tumors MRPS30 expression in the MCF7 cell line (RT-PCR) P = 0.039 1 hour12 hours FAIRE at promoter 45 minutes ERα binding at region P = 0.08 SNP and SNP region DISCOVERY VALIDATION 3 hours12 hours45 minutes ERα binding at promoter P = 0.10 P = 0.04 ChIP-PCR signal promoterregion CTCF binding at region ChIP-PCR signal P = 0.006 P = 0.005 P = 0.002 Fold-change MRPS30 expression 12 hours6 hours P = 4 x 10 -4 P = 7 x 10 -7