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 tumorsD.A. Quigley1,2, E. Fiorito3, P. Van Loo4, G.G. Alnæs1, T. Fleischer1, D. Zelenieka5, J. Tost5, H.K. Vollan1, A. Hurtado3, A. Balmain2, A.L. Børresen-Dale1, & V. Kristensen1

1Department of Genetics, Institute for Cancer Research, University of Oslo 2Helen Diller Family Comprehensive Cancer Center, UCSF 3 Breast Cancer Research Group, Center for Molecular Medicine, University of Oslo 4Cancer Genome Project, Wellcome Trust Sanger Institute 5Laboratory 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 tumorsWe 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 locus1 (specifically the AA allele of rs77166002) is associated with estrogen receptor positive breast cancer susceptibility

•1 Stacey et al. Nature Genetics, 20082 Li et al. Breast Cancer Research & Treatment, 2011

rs7716600 is associated with MRPS30 promoter methylationWe 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 SymposiumDecember 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-positive ER-negative symbol rho P rho PSLC39A6 0.50 2x10-17 0.23 0.02TPRG1 0.48 2x10-15 -0.12 0.28ESR1 0.45 2x10-14 0.04 0.70P4HTM 0.44 5x10-14 0.10 0.33CA12 0.44 8x10-14 -0.06 0.59MAGED2 0.44 2x10-13 0.09 0.41SIAH2 0.43 5x10-13 0.30 4x10-3

ELP2 0.42 6x10-13 0.27 8x10-3

HEXIM2 0.41 4x10-12 -0.02 0.83C17orf75 0.41 4x10-12 0.29 5x10-3

HPN 0.41 6x10-12 0.09 0.42GATA3 0.40 4x10-11 0.04 0.70WWP1 0.40 1x10-11 0.02 0.88SEMA3B 0.40 2x10-11 NA NAPOLB 0.40 2x10-11 0.37 2x10-4

COMMD4 0.39 4x10-11 0.22 0.03UGCG 0.39 7x10-11 -0.13 0.22C6orf211 0.39 9x10-11 0.24 0.02FOXA1 0.39 8x10-11 -0.07 0.49

chromosome

Strongest correlations with MRPS30expression in discovery cohort tumors

MRPS30 expression in the MCF7 cell line (RT-PCR)

P = 0.039

1 hour 12 hours

FAIRE at promoter

45 minutes

ERα binding at region

P = 0.08

SNP and SNP region

DIS

COVE

RYVA

LID

ATIO

N

3 hours 12 hours45 minutes

ERα binding at promoter

P = 0.10

P = 0.04

ChIP

-PCR

sig

nal

ChIP

-PCR

sig

nal

promoter region

CTCF binding at region

ChIP

-PCR

sig

nal

P = 0.006

P = 0.005

P = 0.002

Fold

-cha

nge

MRP

S30

expr

essi

on

12 hours6 hours

P = 4 x 10-4

P = 7 x 10-7