Comprehensive functional annotation of 77 prostate cancer risk loci.
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Authors
Hazelett, Dennis J
Rhie, Suhn Kyong
Gaddis, Malaina
Yan, Chunli
Lakeland, Daniel L
Coetzee, Simon G
Ellipse/GAME-ON consortium
Practical consortium
Henderson, Brian E
Noushmehr, Houtan
Cozen, Wendy
Kote-Jarai, Zsofia
Eeles, Rosalind A
Easton, Douglas F
Haiman, Christopher A
Lu, Wange
Farnham, Peggy J
Coetzee, Gerhard A
Publication Date
2014-01Journal Title
PLoS Genet
ISSN
1553-7390
Publisher
Public Library of Science (PLoS)
Volume
10
Issue
1
Pages
e1004102
Language
eng
Type
Article
Physical Medium
Electronic-eCollection
Metadata
Show full item recordCitation
Hazelett, D. J., Rhie, S. K., Gaddis, M., Yan, C., Lakeland, D. L., Coetzee, S. G., Ellipse/GAME-ON consortium, et al. (2014). Comprehensive functional annotation of 77 prostate cancer risk loci.. PLoS Genet, 10 (1), e1004102. https://doi.org/10.1371/journal.pgen.1004102
Abstract
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 r(2) ≥ 0.88%. 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 (r(2) = 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.
Keywords
Alleles, Chromatin, Enhancer Elements, Genetic, Gene Expression Regulation, Neoplastic, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Male, Molecular Sequence Annotation, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Prostatic Neoplasms, Response Elements, Risk Factors, Transcription Factors
Sponsorship
National Cancer Institute (U19CA148537)
Identifiers
External DOI: https://doi.org/10.1371/journal.pgen.1004102
This record's URL: https://www.repository.cam.ac.uk/handle/1810/279915
Rights
Attribution 4.0 International (CC BY 4.0)
Licence URL: https://creativecommons.org/licenses/by/4.0/
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