Abstract B016: Targeting the epigenome through combined Facilitates Chromatin Transcription (FACT) and Bromodomain and Extra-Terminal Domain (BET) inhibition in Diffuse Midline Glioma (DMG)
Authors: Holly Holliday, Aaminah Khan, Nisitha Jayatilleke, Chelsea Mayoh, Samuel E. Ross, Yolanda Colino Sanguino, Anjana Gopalakrishnan, Anahid Ehteda, Benjamin Rayner, Maria Tsoli, David S. Ziegler
Journal: Cancer Research (2024)

Abstract Aberrant epigenetic regulation is a hallmark of Diffuse Midline Glioma (DMG), an incurable tumor that primarily arises in the brainstem of young children. The H3K27M driver histone mutation and resulting permissive chromatin indicates epigenetic targeting as a key therapeutic strategy against this aggressive cancer. One such epigenetic target is the Facilitates Chromatin Transcription (FACT) histone chaperone. FACT is targeted by the curaxin compound CBL0137 which is currently in phase I/II clinical trial for pediatric cancer patients (NCT04870944). This study aims to decipher the mechanism of CBL0137 to find effective combination therapies for the next round of clinical implementation. To this end, we applied a multi-omics approach by integrating epigenetic profiling with transcriptomic data sets (CUT&amp;RUN, ATAC-seq and RNA-seq) to interrogate the therapeutic mechanism of CBL0137 in DMG. We then employed in vitro cytotoxicity assays and in vivo orthotopic patient-derived xenograft (PDX) pre-clinical models to test a novel, mechanistic-anchored epigenetic combination therapy. We found FACT to be enriched at the promoters of developmental genes, coinciding with regions of open chromatin and binding motifs of the core DMG regulatory transcription factors TCF12 and OLIG2. Furthermore, FACT interacted and co-localized with the Bromodomain and Extra-Terminal Domain (BET) protein BRD4, suggesting cooperation between FACT and BRD4 in DMG. Given that BRD4 is an established therapeutic target in DMG and other cancers, we investigated the combination of the FACT-inhibitor CBL0137 with the BET-inhibitor JQ1. Combination treatment was cytotoxic against DMG in vitro, with enhanced cytotoxicity observed against H3K27M-mutant cells. We demonstrated a significant survival extension in three independent orthotopic PDX mouse models treated with CBL0137 and JQ1 in combination. Mechanistically, CBL0137 and JQ1 decreased chromatin accessibility and transcription of genes involved in RNA regulatory processes, such as RNA methylation and splicing. Consistently, combination treatment led to increased intron retention, highlighting a possible link between chromatin disruption and the splicing machinery in DMG. Future work will investigate whether treatment-induced intron retention acts as a source of neoantigens, with the potential to enhance DMG immunogenicity. In sum, this study has identified a promising new epigenetic combination therapy – FACT + BET inhibition – while uncovering intriguing new insights into DMG epigenetics and pathobiology. Citation Format: Holly Holliday, Aaminah Khan, Nisitha Jayatilleke, Chelsea Mayoh, Samuel E. Ross, Yolanda Colino Sanguino, Anjana Gopalakrishnan, Anahid Ehteda, Benjamin Rayner, Maria Tsoli, David S. Ziegler. Targeting the epigenome through combined Facilitates Chromatin Transcription (FACT) and Bromodomain and Extra-Terminal Domain (BET) inhibition in Diffuse Midline Glioma (DMG) [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr B016.