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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci
PLoS Genetics, Volume 10, No. 1, Article e1004102, Year 2014
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Description
Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations- we identified 727 such potentially functional SNPs. We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at r2≥0.5. 88% of the 727 SNPs fall within putative enhancers, and many alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancers, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium ((r2=0.91) with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process. © 2014 Hazelett et al.
Authors & Co-Authors
Hazelett, Dennis J.
United States, Los Angeles
Keck School of Medicine of Usc
Rhie, Suhnkyong
United States, Los Angeles
Keck School of Medicine of Usc
Coetzee, Simon G.
Brazil, Sao Paulo
Universidade de São Paulo
Henderson, Brian E.
United States, Los Angeles
Keck School of Medicine of Usc
Noushmehr, Houtan
Brazil, Sao Paulo
Universidade de São Paulo
Cozen, Wendy
United States, Los Angeles
University of Southern California
Kóte-Jarai, Zsofia S.
United Kingdom, London
The Institute of Cancer Research
Eeles, Rosalind A.
United Kingdom, London
The Institute of Cancer Research
United Kingdom, London
The Royal Marsden Nhs Foundation Trust
d'Adamo, Adamo P.
United Kingdom, Cambridge
University of Cambridge
Haiman, Christopher A.
United States, Los Angeles
Keck School of Medicine of Usc
Coetzee, Gerhard A.
United States, Los Angeles
Keck School of Medicine of Usc
Statistics
Citations: 141
Authors: 11
Affiliations: 6
Identifiers
Doi:
10.1371/journal.pgen.1004102
ISSN:
15537404
Research Areas
Cancer
Genetics And Genomics