Abstract 6038: KDM2B regulates Serine-Glycine-One Carbon (SGOC) metabolism by targeting the SGOC enzyme genes via a combination of direct and indirect epigenetic mechanisms

Abstract

Abstract Our earlier studies had shown that overexpression of the JmjC domain histone demethylase KDM2B renders mouse embryo fibroblasts (MEFs) resistant to oxidative stress due to the role of KDM2B in the regulation of antioxidant mechanisms. Here we present evidence that the knockdown of KDM2B in basal-like breast cancer cell lines results in a decrease of Glutathione (GSH) levels, a secondary increase of intracellular ROS levels and in enhanced sensitivity to deubiquitinase inhibitors. The expression of the Glutamate-Cystine antiporter, the Glutamate-Cysteine Ligase GCLC/GCLM and the Glutathione Peroxidase GPX4, all of which regulate GSH abundance was not affected. To address the mechanism of the GSH regulation we carried out RNA-Seq, quantitative proteomics and metabolomics analyses in shKDM2B- and empty vector-transduced MDA-MB-231 cells. The results showed that the KD of KDM2B causes major shifts in metabolism and that one of the metabolic pathways whose activity depends on KDM2B is the SGOC pathway, which has a major role in GSH biosynthesis. Experiments in cultured cells confirmed the importance of KDM2B in the regulation of this pathway and they also showed that the inhibition of the pathway via the KD of KDM2B is partly responsible for the shKDM2B-induced inhibition of cell proliferation in culture and in xenograft experiments in NSG mice. More important, the transcriptomic signature of the SGOC pathway correlates with the expression of KDM2B in basal like mammary adenocarcinomas in the TCGA database. The genes encoding the majority of the enzymes in the SGOC pathway are known to be regulated by MYC and ATF4 and our data show that both MYC and ATF4 are under the regulatory control of KDM2B. ATAC-Seq and ChIP-Seq experiments in shKDM2B and control MDA-MB-231 cells also showed that KDM2B binds the promoter region of not only MYC and ATF4, but also of the genes encoding the SGOC enzymes and that it regulates chromatin accessibility and the abundance of H3K4me3/H3K27Ac active histone marks in these promoters. Overall, our data indicate that KDM2B regulates the SGOC pathway by targeting MYC and ATF4 and by making the promoters of the genes encoding the SGOC enzymes accessible to these regulators. Overall, our data provide new evidence on SGOC regulation, and identify novel KDM2B-dependent metabolic vulnerabilities in basal like breast cancer. Citation Format: Evangelia Chavdoula, Vollter Anastas, Allesandro La Ferlita, Julian Aldana, Giuseppe Carota, Mariarita Spampinato, Sameer Parashar, Ilaria Cosentini, Burak Soysal, Giovanni Nigita, Michael Freitas, Philip Tsichlis. KDM2B regulates Serine-Glycine-One Carbon (SGOC) metabolism by targeting the SGOC enzyme genes via a combination of direct and indirect epigenetic mechanisms. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6038.