Abstract
Genome-wide association studies (GWAS) have identified numerous prostate cancer-associated risk loci. Some variants at these loci may be regulatory and influence expression of nearby genes. Such loci are known as cis-expression quantitative trait loci (cis-eQTL). As cis-eQTLs are highly tissue-specific, we asked if GWAS-identified prostate cancer risk loci are cis-eQTLs in human prostate tumor tissues. We investigated 50 prostate cancer samples for their genotype at 59 prostate cancer risk-associated single-nucleotide polymorphisms (SNPs) and performed cis-eQTL analysis of transcripts from paired primary tumors within two megabase windows. We tested 586 transcript–genotype associations, of which 27 were significant (false discovery rate ≤10%). An equivalent eQTL analysis of the same prostate cancer risk loci in lymphoblastoid cell lines did not result in any significant associations. The top-ranked cis-eQTL involved the IRX4 (Iroquois homeobox protein 4) transcript and rs12653946, tagged by rs10866528 in our study (P=4.91 × 10−5). Replication studies, linkage disequilibrium, and imputation analyses highlight population specificity at this locus. We independently validated IRX4 as a potential prostate cancer risk gene through cis-eQTL analysis of prostate cancer risk variants. Cis-eQTL analysis in relevant tissues, even with a small sample size, can be a powerful method to expedite functional follow-up of GWAS.
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References
Murabito JM, Rosenberg CL, Finger D et al: A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study. BMC Med Genet 2007; 8 ((Suppl 1):): S6.
Gudmundsson J, Sulem P, Steinthorsdottir V et al: Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet 2007; 39: 977–983.
Gudmundsson J, Sulem P, Manolescu A et al: Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat Genet 2007; 39: 631–637.
Gudmundsson J, Sulem P, Rafnar T et al: Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat Genet 2008; 40: 281–283.
Takata R, Akamatsu S, Kubo M et al: Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population. Nat Genet 2010; 42: 751–754.
Gudmundsson J, Sulem P, Gudbjartsson DF et al: Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Nat Genet 2009; 41: 1122–1126.
Eeles RA, Kote-Jarai Z, Giles GG et al: Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 2008; 40: 316–321.
Thomas G, Jacobs KB, Yeager M et al: Multiple loci identified in a genome-wide association study of prostate cancer. NatgGenet 2008; 40: 310–315.
Sun J, Zheng SL, Wiklund F et al: Sequence variants at 22q13 are associated with prostate cancer risk. Cancer Res 2009; 69: 10–15.
Eeles RA, Kote-Jarai Z, Al Olama AA et al: Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Nat Genet 2009; 41: 1116–1121.
Maurano MT, Humbert R, Rynes E et al: Systematic localization of common disease-associated variation in regulatory DNA. Science (New York, NY) 2012; 337: 1190–1195.
Morley M, Molony CM, Weber TM et al: Genetic analysis of genome-wide variation in human gene expression. Nature 2004; 430: 743–747.
Cheung VG, Conlin LK, Weber TM et al: Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet 2003; 33: 422–425.
Schadt EE, Monks SA, Drake TA et al: Genetics of gene expression surveyed in maize, mouse and man. Nature 2003; 422: 297–302.
Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ : Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 2010; 6: e1000888.
Dimas AS, Deutsch S, Stranger BE et al: Common regulatory variation impacts gene expression in a cell type-dependent manner. Science (New York, NY) 2009; 325: 1246–1250.
Nica AC, Parts L, Glass D et al: The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study. PLoS Genet 2011; 7: e1002003.
Grisanzio C, Werner L, Takeda D et al: Genetic and functional analyses implicate the NUDT11, HNF1B, and SLC22A3 genes in prostate cancer pathogenesis. Proc Natl Acad Sci USA 2012; 109: 11252–11257.
Pflueger D, Terry S, Sboner A et al: Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res 2011; 21: 56–67.
Habegger L, Sboner A, Gianoulis TA et al: RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics 2011; 27: 281–283.
Barbieri CE, Baca SC, Lawrence MS et al: Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 2012; 44: 685–689.
Setlur SR, Chen CX, Hossain RR et al: Genetic variation of genes involved in dihydrotestosterone metabolism and the risk of prostate cancer. Cancer Epidemiol Biomarkers Prev 2010; 19: 229–239.
Oldridge DA, Banerjee S, Setlur SR, Sboner A, Demichelis F : Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays. Nucleic Acids Res 2010; 38: 3275–3286.
Hindorff LA, Sethupathy P, Junkins HA et al: Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009; 106: 9362–9367.
Chang B-L, Cramer SD, Wiklund F et al: Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk. Hum Mol Genet 2009; 18: 1368–1375.
Xu X, Valtonen-André C, Sävblom C, Halldén C, Lilja H, Klein RJ : Polymorphisms at the Microseminoprotein-beta locus associated with physiologic variation in beta-microseminoprotein and prostate-specific antigen levels. Cancer Epidemiol Biomarkers Prev 2010; 19: 2035–2042.
Gudmundsson J, Besenbacher S, Sulem P et al: Genetic correction of PSA values using sequence variants associated with PSA levels. Sci Transl Med 2010; 2: 62ra92.
Altshuler DM, Gibbs RA, Peltonen L et alInternational HapMap 3 Consortium: Integrating common and rare genetic variation in diverse human populations. Nature 2010; 467: 52–58.
Banerjee S, Oldridge D, Poptsova M, Hussain WM, Chakravarty D, Demichelis F : A computational framework discovers new copy number variants with functional importance. PLoS One 2011; 6: e17539.
Benjamini Y, Hochberg Y : Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995; 57: 289–300.
Stranger BE, Nica AC, Forrest MS et al: Population genomics of human gene expression. Nat Genet 2007; 39: 1217–1224.
Frazer KA, Ballinger DG, Cox DR et alInternational HapMap Consortium: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851–861.
Yeager M, Orr N, Hayes RB et al: Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007; 39: 645–649.
Haiman CA, Patterson N, Freedman ML et al: Multiple regions within 8q24 independently affect risk for prostate cancer. Nat Genet 2007; 39: 638–644.
Howie BN, Donnelly P, Marchini J : A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009; 5: e1000529.
1000 Genomes Project Consortium: A map of human genome variation from population-scale sequencing. Nature 2010; 467: 1061–1073.
Marchini J, Howie B : Genotype imputation for genome-wide association studies. Nat Rev Genet 2010; 11: 499–511.
Vijai J, Kirchhoff T, Gallagher D et al: Genetic architecture of prostate cancer in the Ashkenazi Jewish population. Br J Cancer 2011; 105: 864–869.
Purcell S, Neale B, Todd-Brown K et al: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559–575.
Demichelis F, Setlur SR, Banerjee S et al: Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk. Proc Natl Acad Sci USA 2012; 109: 6686–6691.
Long Q-Z, Du Y-F, Ding X-Y et al: Replication and fine mapping for association of the C2orf43, FOXP4, GPRC6A and RFX6 genes with prostate cancer in the Chinese population. PLoS One 2012; 7: e37866.
Wang M, Liu F, Hsing AW et al: Replication and cumulative effects of GWAS-identified genetic variations for prostate cancer in Asians: a case–control study in the ChinaPCa consortium. Carcinogenesis 2012; 33: 356–360.
Batra J, Lose F, Chambers S et al: A replication study examining novel common single nucleotide polymorphisms identified through a prostate cancer genome-wide association study in a Japanese population. Am J Epidemiol 2011; 174: 1391–1395.
Schumacher FR, Berndt SI, Siddiq A et al: Genome-wide association study identifies new prostate cancer susceptibility loci. Hum Mol Genet 2011; 20: 3867–3875.
Lindstrom S, Schumacher FR, Campa D et al: Replication of five prostate cancer loci identified in an Asian population – results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3). Cancer Epidemiol Biomarkers Prev 2012; 21: 212–216.
Haiman CA, Chen GK, Blot WJ et al: Characterizing genetic risk at known prostate cancer susceptibility loci in African Americans. PLoS Genet 2011; 7: e1001387.
Bao ZZ, Bruneau BG, Seidman JG, Seidman CE, Cepko CL : Regulation of chamber-specific gene expression in the developing heart by Irx4. Science (New York, NY) 1999; 283: 1161–1164.
Bruneau BG, Bao ZZ, Fatkin D et al: Cardiomyopathy in Irx4-deficient mice is preceded by abnormal ventricular gene expression. Mol Cell Biol 2001; 21: 1730–1736.
Nguyen HH, Takata R, Akamatsu S et al: IRX4 at 5p15 suppresses prostate cancer growth through the interaction with vitamin D receptor, conferring prostate cancer susceptibility. HumMol Genet 2012; 21: 2076–2085.
Pomerantz MM, Shrestha Y, Flavin RJ et al: Analysis of the 10q11 cancer risk locus implicates MSMB and NCOA4 in human prostate tumorigenesis. PLoS Genet 2010; 6: e1001204.
Zeller T, Wild P, Szymczak S et al: Genetics and beyond – the transcriptome of human monocytes and disease susceptibility. PLoS One 2010; 5: e10693.
Grisanzio C, Freedman ML : Chromosome 8q24-associated cancers and MYC. Genes Cancer 2010; 1: 555–559.
Pruim RJ, Welch RP, Sanna S et al: LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics (Oxford, UK) 2010; 26: 2336–2337.
Acknowledgements
This research was supported by a grant from the Geoffrey Beene Cancer Research Center (RJK). JV was supported by the Niehaus Clinical Genetics Initiative and the Sharon Levine Corzine Fund at MSKCC. FD was supported by Associazione Italiana Ricerca Cancro (AIRC). We are grateful to the study investigators and funding agencies that supported the work deposited in dbGaP used in this study. Funding support for the CGEMS study of prostate cancer, and the epidemiological studies that provided the samples for the GWAS, was provided by NIH Grants CA CA55075, 5U01CA098233-04 U01 CA098710 and NIH Contracts N01-CN-45165, N01-RC-45035 and N01-RC-37004. Funding support for the GENEVA Prostate Cancer study was provided through the National Cancer Institute (R37CA54281, R01CA63464, P01CA33619, U01CA136792, U01CA98758 and RC2 CA148085) and the National Human Genome Research Institute (U01HG004726). Assistance with phenotype harmonization, SNP selection, data cleaning, meta-analyses, data management and dissemination, and general study coordination was provided by the GENEVA Coordinating Center (U01HG004789-01). We also thank Naoki Kitabayashi for technical support.
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Xu, X., Hussain, W., Vijai, J. et al. Variants at IRX4 as prostate cancer expression quantitative trait loci. Eur J Hum Genet 22, 558–563 (2014). https://doi.org/10.1038/ejhg.2013.195
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DOI: https://doi.org/10.1038/ejhg.2013.195
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