Abstract C084: Breast tumor methylation landscape by estrogen receptor status and race using an NGS Methylation Detection System

Abstract Background: While the racial disparities in triple-negative breast cancer (TNBC) are well documented, the etiologic basis and biology of these disparities are not entirely understood. Factors such as ancestry and lifestyle have been implicated in the etiology of TNBC, but do not fully explain the higher incidence among Black women. Compared with White women, Black women are more likely to experience social and economic disadvantages, contributing to an increase in psychosocial stress. Modifications to the DNA methylome are thought to mediate the biological effects of environmental and social exposures. Previous studies have employed array-based methods to investigate DNA methylation in breast cancer, focusing on pre-selected methylation sites. Using novel next-generation sequencing (NGS) DNA methylation techniques can help to further elucidate the epigenomic landscape, identify relevant pathways, help explain disparate rates of TNBC, and inform etiology. Methods: We included 85 Black and White women diagnosed and treated for a first primary breast cancer at Emory University Hospitals (2001–2019). Genome-wide DNA methylation was measured using the Twist NGS Methylation Detection System, examining 3.2 million methylation loci in breast tumor tissue. We conducted differential methylated region (DMR) analyses by Estrogen receptor (ER) status and race, adjusting for age, smoking, obesity, stage, and race or ER status. In addition, we conducted pathway enrichment analyses for gene-containing DMRs. Results: We identified 22,543 differentially methylated regions with 10,191 unique gene-tagged DMRs by ER status in our differential DNA methylation analysis. Of these unique regions, there were 7036 protein-coding, 2989 non-coding RNAs, and 157 pseudogenes. Pathway enrichment analyses identified a 2-fold enrichment of the Hippo signaling pathway, the Axon guidance and glutamatergic synapse pathways, and the Cushing's syndrome pathway—a disorder of the endocrine system due to chronic cortisol elevation. In contrast, for our analysis by race, there were 387 DMRs, with 322 unique gene-tagged DMRs. Of these unique regions, there were 222 protein-coding, 89 non-coding RNAs, and 11 pseudogenes. The pathway enrichment analysis identified one pathway, the Longevity regulating pathway, with a 7-fold enrichment. Conclusions: The application of a comprehensive NGS DNA methylation detection system identified over 20,000 DMRs by ER status and nearly 400 DMRs by race in the breast tumors. These preliminary results dramatically expand the breast cancer epigenetic landscape, providing a broader and richer representation of the breast tumor DNA methylome. Future studies should be conducted to determine the association between social exposures and changes to the breast DNA methylome, and the potential identification of targetable pathways. Citation Format: Jasmine M. Miller-Kleinhenz, Lindsay J. Collin, Bayan M. Toloubadei, Tasmiah T. Aziz, Lauren E. McCullough. Breast tumor methylation landscape by estrogen receptor status and race using an NGS Methylation Detection System abstract. In: Proceedings of the 18th AACR Conference on the Science of Cancer Health Disparities; 2025 Sep 18-21; Baltimore, MD. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2025;34(9 Suppl):Abstract nr C084.