Analysis of the 10q11 Cancer Risk Locus Implicates MSMB and NCOA4 in Human Prostate Tumorigenesis Mark M. Pomerantz1,2., Yashaswi Shrestha1,3,4., Richard J. Flavin5, Meredith M. Regan 6 , Kathryn L. Penney7, Lorelei A. Mucci7,8, Meir J. Stampfer7,8,9, David J. Hunter7,8,9, Stephen J. Chanock10, Eric J. Schafer1,3,4, Jennifer A. Chan11, Josep Tabernero12, Jose´ Baselga12, Andrea L. Richardson13, Massimo Loda1,3,4,5,13, William K. Oh14, Philip W. Kantoff1,2, William C. Hahn1,2,3,4, Matthew L. Freedman1,3,4* 1 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, 2 Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America, 3 Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, 4 Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 5 Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America, 6 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America, 7 Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America, 8 Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America, 9 Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America, 10 Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America, 11 Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada, 12 Vall d’Hebron Institute of Oncology, Vall d’Hebron University Hospital, Barcelona, Spain, 13 Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America, 14 Tisch Cancer Institute, Mount Sinai School of Medicine, New York, New York, United States of America Abstract Genome-wide association studies (GWAS) have established a variant, rs10993994, on chromosome 10q11 as being associated with prostate cancer risk. Since the variant is located outside of a protein-coding region, the target genes driving tumorigenesis are not readily apparent. Two genes nearest to this variant, MSMB and NCOA4, are strong candidates for mediating the effects of rs109939934. In a cohort of 180 individuals, we demonstrate that the rs10993994 risk allele is associated with decreased expression of two MSMB isoforms in histologically normal and malignant prostate tissue. In addition, the risk allele is associated with increased expression of five NCOA4 isoforms in histologically normal prostate tissue only. No consistent association with either gene is observed in breast or colon tissue. In conjunction with these findings, suppression of MSMB expression or NCOA4 overexpression promotes anchorage-independent growth of prostate epithelial cells, but not growth of breast epithelial cells. These data suggest that germline variation at chromosome 10q11 contributes to prostate cancer risk by influencing expression of at least two genes. More broadly, the findings demonstrate that disease risk alleles may influence multiple genes, and associations between genotype and expression may only be observed in the context of specific tissue and disease states. Citation: Pomerantz MM, Shrestha Y, Flavin RJ, Regan MM, Penney KL, et al. (2010) Analysis of the 10q11 Cancer Risk Locus Implicates MSMB and NCOA4 in Human Prostate Tumorigenesis. PLoS Genet 6(11): e1001204. doi:10.1371/journal.pgen.1001204 Editor: James M. Ford, Stanford University School of Medicine, United States of America Received July 14, 2010; Accepted October 13, 2010; Published November 11, 2010 This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. Funding: MLF is a Howard Hughes Medical Institute Physician-Scientist Early Career Awardee (www.hhmi.org), a recipient of a 2006 Doris Duke Clinical Scientist Development Award (www.ddcf.org), and a recipient of a 2009 Claudia Adams Barr award (www.dana-farber.org). This work was supported by grants from the US National Institutes of Health (R01 CA129435 to MLF), the Mayer Foundation (to MLF), the H.L. Snyder Medical Foundation (to MLF), the Dana-Farber/Harvard Cancer Center Prostate Cancer SPORE (National Cancer Institute Grant No. 5P50CA90381), and the Emerald Foundation, Inc. (to MLF). MMP is supported by the William L. Edwards - Prostate Cancer Foundation Young Investigator Award (www.prostatecancerfoundation.org). WCH receives support from the Prostate Cancer Foundation and the John Snyder Medical Foundation (snydermf.org). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: freedman@broadinstitute.org . These authors contributed equally to this work. Introduction Variation at rs10993994 on chromosome 10q11 is associated with prostate cancer risk [1–5]. The risk polymorphism is located at the telomeric end of a 50 kilobase (kb) linkage disequilibrium block and is within 60 base pairs (bp) of the transcription start site of beta-microseminoprotein (MSMB). MSMB has been character- ized as a tumor suppressor [6], and lower levels of its product, PSP94, are associated with more aggressive forms of prostate cancer [7]. MSMB has therefore been a target of recent investigation into the mechanism of chromosome 10q-associated risk. Reporter assays demonstrate that plasmids carrying the rs10993994 risk allele (T) significantly decrease luciferase activity compared with the wild-type allele (C) [8,9]. In addition, in 19 cancer cell lines of various tissue types expressing MSMB, those carrying the TT genotype have decreased MSMB expression relative to those carrying a C allele [9]. However, no study has definitively linked MSMB expression to risk allele status in human prostate tissue. A second gene, nuclear receptor co-activator 4 (NCOA4, also known as ARA70), is a ligand-dependent androgen PLoS Genetics | www.plosgenetics.org 1 November 2010 | Volume 6 | Issue 11 | e1001204