Abstract 222: Unraveling tumor progression in breast cancer: The impact of differential DNA methylation

Abstract Breast cancer affects over 300, 000 Americans annually, with 42, 780 deaths projected in 2024. DNA methylation, an epigenetic modification, has been associated with breast cancer progression (e.g., BRCA1 gene promoter hypermethylation). We hypothesize that we can identify differentially methylated CpG sites linked to cancer progression, thereby revealing the biological functions and pathways involved in tumor progression.We used DNA methylation data characterizing over 487, 000 CpG sites from 1, 032 female breast cancer patients in the Cancer Genome Atlas. CpG methylation was quantified using M values for more accurate homoscedastic statistical analysis. To focus on CpG sites with high methylation variability, sites were filtered by removing those whose variance in the tumor samples were lower than the normal tissue sample. Differential methylation across cancer stages was determined using an analysis of variance (ANOVA; p ≤ 1×10-4). Statistically significant differentially methylated CpG sites were annotated to genes, and these genes were used to perform functional enrichment analysis in DAVID.We identified 473 CpG sites with significant differential methylation across cancer stages that were annotated to 556 genes. Functional enrichment analysis revealed seven significantly enriched pathways, including non-small cell lung cancer (NSCLC; hsa05223, adj. p = 0.0027), gastric acid secretion (hsa04971, adj. p = 0.0032), insulin signaling (hsa04910, adj. p = 0.0066), aldosterone synthesis and secretion (hsa04925, adj. p = 0.0070), viral myocarditis (hsa05416, adj. p = 0.0090), long-term potentiation (hsa04720, adj. p = 0.0090), and propanoate metabolism (hsa00640, adj. p = 0.0091). In the NSCLC pathway, five genes were identified: KRAS, a well-known oncogene promoting cell proliferation; ERBB2 (HER2), driving aggressive HER2-positive breast cancer growth; FHIT, a tumor suppressor gene regulating apoptosis and cell cycle; CASP9, a pro-apoptotic tumor suppressor; and RARB, a tumor suppressor regulating cell growth and differentiation. Methylation differences related to tumor progression have been documented in the literature for several of these genes. Our study identified significant CpG sites and corresponding genes associated with breast cancer progression via differential methylation analysis. These results provide valuable insights into the biological mechanisms driving cancer progression and highlight the potential of DNA methylation as predictive biomarkers. Further research is needed to validate and expand these findings, and to explore their clinical implications in breast cancer surveillance and therapeutic interventions. Citation Format: Navin Jayaswal, Allison N. Tegge. Unraveling tumor progression in breast cancer: The impact of differential DNA methylation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 222.