Fine-mapping of the HNF1B multicancer locus identifies candidate variants that mediate endometrial cancer risk.

Painter JN, O'Mara TA, Batra J, Cheng T, Lose FA, Dennis J, Michailidou K, Tyrer JP, Ahmed S, Ferguson K, Healey CS, Kaufmann S, Hillman KM, Walpole C, Moya L, Pollock P, Jones A, Howarth K, Martin L, Gorman M, Hodgson S, National Study of Endometrial Cancer Genetics Group (NSECG), CHIBCHA Consortium, De Polanco MM, Sans M, Carracedo A, Castellvi-Bel S, Rojas-Martinez A, Santos E, Teixeira MR, Carvajal-Carmona L, Shu XO, Long J, Zheng W, Xiang YB, Australian National Endometrial Cancer Study Group (ANECS), Montgomery GW, Webb PM, Scott RJ, McEvoy M, Attia J, Holliday E, Martin NG, Nyholt DR, Henders AK, Fasching PA, Hein A, Beckmann MW, Renner SP, Dörk T, Hillemanns P, Dürst M, Runnebaum I, Lambrechts D, Coenegrachts L, Schrauwen S, Amant F, Winterhoff B, Dowdy SC, Goode EL, Teoman A, Salvesen HB, Trovik J, Njolstad TS, Werner HM, Ashton K, Proietto T, Otton G, Tzortzatos G, Mints M, Tham E, RENDOCAS, Hall P, Czene K, Liu J, Li J, Hopper JL, Southey MC, Australian Ovarian Cancer Study (AOCS), Ekici AB, Ruebner M, Johnson N, Peto J, Burwinkel B, Marme F, Brenner H, Dieffenbach AK, Meindl A, Brauch H, GENICA Network, Lindblom A, Depreeuw J, Moisse M, Chang-Claude J, Rudolph A, Couch FJ, Olson JE, Giles GG, Bruinsma F, Cunningham JM, Fridley BL, Børresen-Dale AL, Kristensen VN, Cox A, Swerdlow AJ, Orr N, Bolla MK, Wang Q, Weber RP, Chen Z, Shah M, French JD, Pharoah PD, Dunning AM, Tomlinson I, Easton DF, Edwards SL, Thompson DJ, Spurdle AB
Hum Mol Genet. 2015 24 (5): 1478-92

PMID: 25378557 · PMCID: PMC4321445 · DOI:10.1093/hmg/ddu552

Common variants in the hepatocyte nuclear factor 1 homeobox B (HNF1B) gene are associated with the risk of Type II diabetes and multiple cancers. Evidence to date indicates that cancer risk may be mediated via genetic or epigenetic effects on HNF1B gene expression. We previously found single-nucleotide polymorphisms (SNPs) at the HNF1B locus to be associated with endometrial cancer, and now report extensive fine-mapping and in silico and laboratory analyses of this locus. Analysis of 1184 genotyped and imputed SNPs in 6608 Caucasian cases and 37 925 controls, and 895 Asian cases and 1968 controls, revealed the best signal of association for SNP rs11263763 (P = 8.4 × 10(-14), odds ratio = 0.86, 95% confidence interval = 0.82-0.89), located within HNF1B intron 1. Haplotype analysis and conditional analyses provide no evidence of further independent endometrial cancer risk variants at this locus. SNP rs11263763 genotype was associated with HNF1B mRNA expression but not with HNF1B methylation in endometrial tumor samples from The Cancer Genome Atlas. Genetic analyses prioritized rs11263763 and four other SNPs in high-to-moderate linkage disequilibrium as the most likely causal SNPs. Three of these SNPs map to the extended HNF1B promoter based on chromatin marks extending from the minimal promoter region. Reporter assays demonstrated that this extended region reduces activity in combination with the minimal HNF1B promoter, and that the minor alleles of rs11263763 or rs8064454 are associated with decreased HNF1B promoter activity. Our findings provide evidence for a single signal associated with endometrial cancer risk at the HNF1B locus, and that risk is likely mediated via altered HNF1B gene expression.

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MeSH Terms (22)

Alleles Case-Control Studies Cell Line, Tumor Chromosome Mapping Computational Biology Databases, Genetic Endometrial Neoplasms Epigenesis, Genetic European Continental Ancestry Group Female Genetic Loci Genetic Variation Genome-Wide Association Study Genotype Haplotypes Hepatocyte Nuclear Factor 1-beta Humans Linkage Disequilibrium Polymorphism, Single Nucleotide Promoter Regions, Genetic Risk Factors RNA, Messenger

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