Deciphering the role of EP300 in maintaining the enhancer landscape and lineage-specific epigenetic vulnerability in multiple myeloma

Abstract BackgroundGene expression is regulated by post-translational modification of chromatin structures by a network of epigenetic regulators. EP300 and CREBBP (CBP) are paralogous histone acetyltransferases that regulate enhancer activity and transcription mainly by histone H3 lysine 27 acetylation (H3K27ac). Although these co-transcription factors display overlapping regulatory roles, their functional overlap varies across cancers. Multiple myeloma (MM) is a hematological malignancy reliant on enhancer-driven transcription factors such as the IRF4-MYC axis. However, the specific contribution of EP300 remains to be explored. Here, we investigated the role and selective dependency of EP300 in MM, its functional non-redundancy relative to CBP, and its potential as a therapeutic target.MethodsTo investigate the role of EP300, we used shRNA and PROTAC JQAD1 to selectively degrade EP300 in MM cell lines. We evaluated the functional changes by performing cell viability, apoptosis, migration, and invasion assays. Transcriptomic changes following EP300 loss were assessed via RNA sequencing. Chromatin remodeling and enhancer function were profiled using ATAC-seq and ChIP-seq for EP300, CBP, and H3K27ac. EP300 and CBP-associated protein complexes were identified via immunoprecipitation followed by mass spectrometry (IP–MS). To examine EP300 dependency in MM, CUT&RUN was performed on CD138⁺ plasma cells isolated from newly diagnosed and relapsed/refractory MM patients. Simultaneously, we employed public databases such as DepMap to determine EP300 dependency in MM cell lines and its correlation with high-risk cytogenic factors such as t(4;14), del(17p), 1q gain, and RAS mutations. ResultsWe observed decreased cell viability, increased apoptosis, reduced cell migration, and invasion potential following EP300 degradation across MM cell lines. Reduction of EP300 resulted in a wide array of transcriptomic changes tied to the enhancer network across different cell lines. Epigenomic profiling revealed global enhancer disruption and loss of H3H27ac at key regulatory regions and IRF4-MYC super enhancers. IP-Mass spectroscopy revealed unique interacting partners with EP300, which did not interact with paralogous CBP. Furthermore, CUT&RUN sequencing from patient samples confirmed EP300 binding with the lineage-defining enhancers.DepMap analysis supported a consistent pattern of EP300 dependency across MM lines, especially in the context of IRF4-high expression, regardless of genetic subtype.ConclusionAlthough EP300 and CBP share 90% structural similarity, EP300 uniquely regulates the enhancer activity required for transcriptional identity and survival of MM. Importantly, selective degradation of EP300, as opposed to dual EP300/CBP targeting, leads to decreased thrombocytopenia in pre-clinical models. In addition, combining EP300 inhibition with other treatment modalities exhibit enhanced therapeutic efficacy. Overall, our findings endorse further development of EP300-targeted aproaches for patients with high-risk and relapsed multiple myeloma.