Abstract 4112: The epigenetic landscape identified through ATACseq reveals the NCAM1/FYN pathway as a potential therapeutic target in p53-/PTEN- transformed breast cancer stem cells
Authors: Abigail G. Weatherford, Margaret V. Leonard, Maria Ouzounova, Hasan Korkaya, Austin Y. Shull
Journal: Cancer Research (2025)

Abstract Metastatic potential in basal-like breast cancers typically correspond with increased enrichment of aggressive progenitor-like populations called cancer stem cells (CSCs), typically identified by the loss of epithelial markers EpCAM and CD49f. In our MCF10A breast cell line model, deletion of p53 and PTEN lead to tumorigenic transformation and cancer stem cell expansion. With these observations that reflect cell dedifferentiation as a mechanism of oncogenic transformation, it was important to better detail the epigenetic events that correspond with breast CSC progression. With this in mind, we performed Assay for Transposase-Accessible Chromatin sequencing (ATACseq) on our isogenic panel of MCF10A breast cell lines where tumor suppressor genes TP53 and PTEN were silenced to drive breast CSC expansion. Furthermore, we performed gene expression analysis of isolated EpCAM-/CD49f- CSCs from MCF10A p53-/PTEN- cells to determine which genes differentially upregulated in CSCs corresponded with open chromatin in our ATACseq analysis. Based on this analysis, we identified 96 genes with open chromatin that were also significantly overexpressed within our isolated CSC populations. Several transcripts identified were potential metastatic drivers, including genes involved in signal transduction (PDE4B, PDE3B), cellular adhesion (MDGA2), transcriptional regulation (NPAS2), and oxidative stress responses (SMOX). Furthermore, many of these genes were also significantly upregulated clinically in basal-like breast cancers from The Cancer Genome Atlas (TCGA) breast cancer dataset. One key pathway of interest identified was the NCAM1/FYN pathway, which showed increased chromatin opening in the promoter regions of these two genes that are a part of the same signal transduction pathway and are of clinical relevance. Comparative analysis demonstrated that NCAM1/FYN pathway components were overexpressed in breast cancer samples, with statistically significant increased protein phosphorylation of MAP2K1 and RAF1 in the CPTAC proteogenomic TCGA samples. Collectively, this work provides an overview of open chromatin sites that contribute to oncogene overexpression in breast cancer and provide rationale for targeting these transcripts via chromatin targeting-based therapies (ex: BET bromodomain inhibition) to prime these CSC populations toward specific drug sensitivities. Citation Format: Abigail G. Weatherford, Margaret V. Leonard, Maria Ouzounova, Hasan Korkaya, Austin Y. Shull. The epigenetic landscape identified through ATACseq reveals the NCAM1/FYN pathway as a potential therapeutic target in p53-/PTEN- transformed breast cancer stem cells [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 4112.