Abstract 3458: DNA methylation-predicted blood protein levels and breast cancer risk
Authors: Kresovich Jacob K. , Reid Brett , Byrd Doratha A. , O'Brien Katie M. , Xu Zongli , Weinberg Clarice R. , Sandler Dale P. , Taylor Jack A. 
Published: March 2024

Background: Blood DNA methylation (DNAm) profiles can be used to predict a variety of human physiologic traits that are associated with breast cancer incidence and plasma concentrations of over 100 proteins, including those involved in inflammation, coagulation, metabolism, and growth. DNAm predictions of circulating proteins, here referred to as “DNAm proteins,” may be useful in providing molecular insights into breast cancer etiology and could be a valuable resource for personalizing breast cancer risk prediction.

Methods: The Sister Study is a nationwide, prospective cohort of 50,884 women with a family history of breast cancer designed to identify novel environmental and biological risk factors for breast cancer. Epigenome-wide DNAm data were previously generated using the HumanMethylation450 or MethylationEPIC arrays on baseline blood samples collected from two case-cohort samples, for a combined sample of 4,479 women. This sample included 2,151 (48%) women who were selected because they were diagnosed with breast cancer (1,673 invasive cancer and 478 ductal carcinomas in situ) in the 15 years (mean: 7.9 years) following blood draw. Blood levels of 109 DNAm proteins were estimated from DNAm profiles using the method developed by Gadd et al. (eLife, 2022). Weighted Cox regression models were used to estimate associations between these DNAm proteins and incident breast cancer; associations were considered statistically significant at a False Discovery Rate (q) ≤ 0.10.

Results: In age and platform adjusted models, higher breast cancer rates were associated with higher DNAm-predicted blood concentrations of RARRES2, IGFBP4, and CCL21 and lower predicted concentrations of F7, SELL, CXCL9, CD48, and IL19. The strongest associations were observed for RARRES2 (per 1-SD increase, HR: 1.24, 95% CI: 1.10, 1.40, P= 6 × 10−4, q= 0.03) and F7 (per 1-SD increase, HR: 0.82, 95% CI: 0.74, 0.91, P= 3 × 10−4, q= 0.03). Estimates were similar after adjustment for known breast cancer risk factors and excluding those diagnosed within two years of their blood draw. Associations appeared stronger for invasive breast cancer.

Conclusions: Using novel DNAm-based estimates of blood proteins, we identified associations between circulating proteins and breast cancer incidence. IGFBP4 and RARRES2 have previously been reported to be higher in newly-diagnosed breast cancer patients. We also identify new potential protein biomarkers related to immune response (CCL21, SELL, CXCL9, CD48, and IL19).

Citation Format: Jacob K. Kresovich, Brett Reid, Doratha A. Byrd, Katie M. O'Brien, Zongli Xu, Clarice R. Weinberg, Dale P. Sandler, Jack A. Taylor. DNA methylation-predicted blood protein levels and breast cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3458.