Abstract 4753: ACSS2 inhibition alters epigenetic landscape to improve endocrine therapy outcome in ER+ metastatic breast cancer cells

Endocrine therapies target the hormone dependencies of the cancer cells in various ways. One primary target is estrogen receptor alpha (ERα), which is expressed in approximately 70% of human breast cancers (ER-positive or ER+). Despite treatment, recurrence and metastasis are still observed in 30-40% of ER+ patients, and the 5-year relative overall survival rate for these patients is only 24%. Local Acetyl-CoA availability plays a crucial role in regulating histone acetylation and gene expression, thereby supporting tumor progression. Our previous research demonstrated that ERα antagonist Fulvestrant (Fulv) treatment increased ACSS2 (acetyl-CoA synthetase 2) levels in vivo in metastatic breast tumors. Combining the Fulv with a highly specific ACSS2 inhibitor (ACSI) synergistically reduced cell viability in ER+ metastatic breast cancer (MBC) cells in vitro. In the present study, we employed multiple analytical approaches—including isotope tracing assay with labeled acetate, CUT&RUN sequencing, immunofluorescence, western blot, and RNA sequencing—to characterize the epigenetic and metabolic alterations induced by Fulv treatment and ACSS2 enzyme and how they contribute to endocrine resistance. To investigate how ACSS2 drives endocrine resistance, we examined ACSS2 expression and acetate utilization in response to Fulv. We showed that the ACSS2 expression and acetate utilization by ACSS2 to synthesize Acetyl-CoA increase with Fulv treatment. Isotope tracing assay with labeled acetate indicated that Fulv treatment decreased the acetate flux to the TCA cycle and drove it toward fatty acid synthesis. However, inhibition of fatty acid synthesis did not impact Fulv-induced cell viability, suggesting an additional role for ACSS2-mediated acetyl-CoA production in metastatic breast cancer cells. Immunofluorescence assays showed that ACSS2 was almost exclusively located in the nucleus, supporting a role in epigenetic regulation. We then examined chromatin enrichment of ACSS2, ER⍺, and H3K27ac using the CUT&RUN sequencing method in ER+ MBC cells. Fulv treatment resulted in an increased number of global ACSS2 binding sites as well as overlapping binding sites of ER⍺, ACSS2, and H3K27ac. These sites were lost with the ACSI and Fulv combination. Global gene expression profiling using RNA sequencing assay showed that the gene expression is increased for genes involved in cell proliferation with Fulv treatment. In conclusion, our findings suggest a nuclear role for ACSS2 in endocrine therapy resistance by providing a substrate for epigenetic alterations. Targeting these alterations caused by cancer cell adaptations is a novel approach that could potentially lead to new therapies. This strategy may help reduce metastasis-related mortality in breast cancer patients, offering additional opportunities for improved treatment outcomes in the future. Citation Format: Ayca N. Mogol, Jin Young Yoo, David J. Dutton, Zeynep Madak-Erdogan. ACSS2 inhibition alters epigenetic landscape to improve endocrine therapy outcome in ER+ metastatic breast cancer 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 4753.