Metabolic Mechanisms Underlying Late Recurrence in Hormone Receptor Positive Breast Cancer

Hormone receptor positive (HR+) breast tumors are anomalous in their tendency for late recurrence. In the clinic, an mRNA ratio of HOXB13 to IL17RB (H/I) from the primary tumor is used to determine a patient’s risk for late recurrence and benefit of extended adjuvant hormonal therapy. Little is known about the tie between the H/I ratio and the biology leading to late recurrence. Herein we present data from primary breast tumors, in silico analyses and cell-based models that support our hypothesis that dysregulation of one-carbon metabolism and the SAM cycle is linked to the H/I signature and contributes to epithelial-mesenchymal plasticity (EMP), which has been shown to mediate the late recurring phenotype. We conducted proteomics analysis of 86 HR+ breast tumors and identified Choline Dehydrogenase (CHDH) as the most significant differentially expressed protein between HOXB13 high and low groups; with CHDH being associated with HOXB13 low tumors. Notably, RNA expression of CHDH is highly correlated with expression of IL17RB due to a shared promoter region. These links with both HOXB13 and IL17RB led us to hypothesize that CHDH contributes to the phenotype of late recurrence. To determine if signatures of differences in CHDH function could be seen in H/I low and high cell lines we used RNA expression and metabolomics data from the DepMap portal. Betaine, a standard readout metabolite for CHDH function, was significantly elevated in H/I low cell lines, consistent with our previous observations. We also observed that 1-methylnicotinamide, produced by Nicotinamide N-methyltransferase (NNMT), was identified as the metabolite most upregulated in H/I high cell lines. CHDH and NNMT both contribute to one-carbon metabolism in the SAM cycle, with opposing influences. Previous studies have demonstrated that dormancy and late recurrence in the context of HR+ breast cancer is driven by epithelial-mesenchymal plasticity (EMP). To test the association between SAM flux and differing epithelial and mesenchymal phenotypes, we created a CHDH:NNMT score and correlated this against epithelial-mesenchymal phenotypes in patient tumors from the TCGA Firehouse Legacy dataset. A significant association was found in all tumor types, with a conglomerate p-value across tumor types of <10-300. We also observed high SAM levels in tumors associated with markers of an epithelial-like state. We then demonstrated that shRNA knockdown of NNMT is sufficient to increase expression of epithelial proteins in cell lines displaying a mesenchymal phenotype. We will next test the ability of CHDH and NNMT to alter EMP in breast cancer cells and identify EMP associated metabolic pathways. In total, we have demonstrated that metabolic enzymes regulating SAM flux are highly associated with late-recurrence in HR+ breast tumors. Ongoing experiments will assess how metabolism controls epithelial-mesenchymal plasticity that may mediate the phenotype. Bryce Ordway, Isabella Vianna, Johannes Kreuzer, Wilhelm Haas, Dennis Sgroi, Leif W. Ellisen. Metabolic mechanisms underlying late recurrence in hormone receptor positive breast cancer [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 7472.