DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility

Abstract

Aim of the study: A vast majority of human malignancies are associated with ageing, and age is a strong predictor of cancer risk. Recently, DNA methylation-based marker of ageing, known as 'epigenetic clock', has been linked with cancer risk factors. This study aimed to evaluate whether the epigenetic clock is associated with breast cancer risk susceptibility and to identify potential epigenetics-based biomarkers for risk stratification.

Methods: Here, we profiled DNA methylation changes in a nested case-control study embedded in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort (n = 960) using the Illumina HumanMethylation 450K BeadChip arrays and used the Horvath age estimation method to calculate epigenetic age for these samples. Intrinsic epigenetic age acceleration (IEAA) was estimated as the residuals by regressing epigenetic age on chronological age.

Results: We observed an association between IEAA and breast cancer risk (OR, 1.04; 95% CI, 1.007-1.076, P = 0.016). One unit increase in IEAA was associated with a 4% increased odds of developing breast cancer (OR, 1.04; 95% CI, 1.007-1.076). Stratified analysis based on menopausal status revealed that IEAA was associated with development of postmenopausal breast cancers (OR, 1.07; 95% CI, 1.020-1.11, P = 0.003). In addition, methylome-wide analyses revealed that a higher mean DNA methylation at cytosine-phosphate-guanine (CpG) islands was associated with increased risk of breast cancer development (OR per 1 SD = 1.20; 95 %CI: 1.03-1.40, P = 0.02) whereas mean methylation levels at non-island CpGs were indistinguishable between cancer cases and controls.

Conclusion: Epigenetic age acceleration and CpG island methylation have a weak, but statistically significant, association with breast cancer susceptibility.

Keywords: Age acceleration; Biomarkers; Breast cancer; DNA methylation; Epigenomics; Prospective studies.

Fig. 1

Epigenetic clock analysis. a) DNA methylation age (y-axis) versus chronological age (x-axis). Points correspond to female subjects. Red indicates breast cancer case, black control. The dashed line indicates a regression line, b) epigenetic age acceleration versus breast cancer status. Each bar plot depicts the mean value, standard deviation and reports a non-parametric group comparison test p-value (Wilcoxon test), c) epigenetic age acceleration versus breast cancer status (developed within 10 years post blood draw). Each bar plot depicts the mean value, standard deviation and reports a non-parametric group comparison test p-value (Wilcoxon test). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Epigenetic clock analysis for postmenopausal samples. a) DNA methylation age (y-axis) versus chronological age (x-axis). Points correspond to female subjects. Red indicates breast cancer case, black control. The dashed line indicates a regression line; b) epigenetic age acceleration versus breast cancer status. Each bar plot depicts the mean value, standard deviation and reports a non-parametric group comparison test p-value (Wilcoxon test); c) epigenetic age acceleration versus breast cancer status (developed within 10 years post blood draw). Each bar plot depicts the mean value, standard deviation, and reports a non-parametric group comparison test p-value (Wilcoxon test). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)