CYP19A1 fine-mapping and Mendelian randomization: estradiol is causal for endometrial cancer

Abstract

Candidate gene studies have reported CYP19A1 variants to be associated with endometrial cancer and with estradiol (E2) concentrations. We analyzed 2937 single nucleotide polymorphisms (SNPs) in 6608 endometrial cancer cases and 37 925 controls and report the first genome wide-significant association between endometrial cancer and a CYP19A1 SNP (rs727479 in intron 2, P=4.8×10(-11)). SNP rs727479 was also among those most strongly associated with circulating E2 concentrations in 2767 post-menopausal controls (P=7.4×10(-8)). The observed endometrial cancer odds ratio per rs727479 A-allele (1.15, CI=1.11-1.21) is compatible with that predicted by the observed effect on E2 concentrations (1.09, CI=1.03-1.21), consistent with the hypothesis that endometrial cancer risk is driven by E2. From 28 candidate-causal SNPs, 12 co-located with three putative gene-regulatory elements and their risk alleles associated with higher CYP19A1 expression in bioinformatical analyses. For both phenotypes, the associations with rs727479 were stronger among women with a higher BMI (Pinteraction=0.034 and 0.066 respectively), suggesting a biologically plausible gene-environment interaction.

Keywords: CYP19A1; endometrial cancer; estradiol.

Figure 1

Factors potentially involved in the reported association between circulating post-menopausal E₂ and endometrial cancer risk. Question marks highlight the issues to be addressed in this study.

Figure 2

Association of SNPs in the CYP19A1 region with (A) endometrial cancer and (B) E₂:T, highlighting rs727479. Each point indicates the statistical significance of the association between a SNP and endometrial cancer (Fig. 2A) or between a SNP and the E₂:T ratio (Fig. 2B). Squares denote SNPs directly genotyped by the iCOGS array; circles are SNPs for which genotypes were imputed. The larger purple square is rs727479, the SNP with the strongest evidence of association with endometrial cancer. Other colours show the strength of linkage disequilibrium between each SNP with rs7277479.

Figure 3

Association of SNP rs727479 with (A) endometrial cancer and (B) E₂ levels, by quartile of BMI distribution. In Fig. 3A the log(OR) of endometrial cancer associated with each A allele of SNP rs727479 is shown for each quartile of the BMI distribution, adjusting for age. There is a borderline significant interaction between genotype and BMI quartile (P=0.047). Figure 3B shows the regression coefficient (β) for the association between each A allele of rs727479 and log-transformed E₂ levels (adjusted for laboratory batch, study, age at blood draw, BMI, HRT use and menopausal status), (P_interaction=0.066). For both plots, the error bars are 95% CI, and the quartiles are based on the BMI distribution in endometrial cancer cases, to allow for comparability between plots, and to ensure sufficient cases in each quartile.

Figure 4

The observed and predicted risks of endometrial cancer associated with each rs727479 A allele. The Observed per-A allele OR is that observed in this study of 6608 and 37 925 endometrial cancer cases and controls. The predicted per-A allele OR is estimated based on the observed association between rs727479 and E₂ levels in 2767 healthy post-menopausal women, and on the endometrial cancer OR associated with a doubling of post-menopausal E₂ levels reported by Lukanova et al. (2004).

Figure 5

Candidate endometrial risk variants coincide with three PREs. The 28 best candidate causal SNPs map towards the 3′ end of the CYP19A1 gene. The functional elements displayed were accessed through the UCSC Genome Browser and include: H3K4Me1 and H3K27Ac histone modifications measured by the Encyclopedia of DNA Elements (ENCODE) project in seven cell lines; open chromatin as delineated by DNaseI hypersensitivity sites (HS) in Ishikawa endometrial cancer cells (previously incorrectly named ECC-1)) and 125 other cell types; TF binding in Ishikawa cells and 91 cell lines within ENCODE: 21/28 candidates are predicted to overlap TF binding sites. Roadmap Epigenomics Project chromatin state segmentation of adipose-derived mesenchymal stem cells and adipocytes: orange bars represent enhancers and red bars represent regions flanking active transcription start sites. Twelve SNPs, marked by dbSNP rsIDs, are located in PREs: highlighted in blue. PREs were defined by the presence of histone modifications, DHS, TF binding and Roadmap enhancers.